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What to Know About Chlamydia

• 1 Division of Infectious Disease, Department of Internal Medicine, Michigan Medicine, Ann Arbor
• US Preventive Services Task Force USPSTF Recommendation: Screening for Chlamydia and Gonorrhea US Preventive Services Task Force; Karina W. Davidson, PhD, MASc; Michael J. Barry, MD; Carol M. Mangione, MD, MSPH; Michael Cabana, MD, MA, MPH; Aaron B. Caughey, MD, PhD; Esa M. Davis, MD, MPH; Katrina E. Donahue, MD, MPH; Chyke A. Doubeni, MD, MPH; Alex H. Krist, MD, MPH; Martha Kubik, PhD, RN; Li Li, MD, PhD, MPH; Gbenga Ogedegbe, MD, MPH; Lori Pbert, PhD; Michael Silverstein, MD, MPH; Melissa A. Simon, MD, MPH; James Stevermer, MD, MSPH; Chien-Wen Tseng, MD, MPH, MSEE; John B. Wong, MD JAMA
• US Preventive Services Task Force USPSTF Review: Screening for Chlamydial and Gonococcal Infections Amy Cantor, MD, MPH; Tracy Dana, MLS; Jessica C. Griffin, MS; Heidi D. Nelson, MD, MPH; Chandler Weeks, MPH; Kevin L. Winthrop, MD, MPH; Roger Chou, MD JAMA
• JAMA Patient Page Patient Information: Screening for Chlamydia and Gonorrhea Jill Jin, MD, MPH JAMA
• JAMA Patient Page Patient Information: What to Know About Gonorrhea Sarah Kurz, MD; Adam Ressler, MD, MPH JAMA

Chlamydia is a sexually transmitted infection caused by the bacterium Chlamydia trachomatis .

Chlamydia is the most common bacterial cause of sexually transmitted infections (STIs) in the US. The Centers for Disease Control and Prevention (CDC) estimates that approximately 4 million people in the US develop new chlamydia infections each year, and nearly two-thirds occur in young people aged 15 to 24 years.

Chlamydia is acquired through genital, anal, or oral sex with someone who has chlamydia. Pregnant individuals can transmit chlamydia to their newborns during passage through the birth canal.

Signs and Symptoms of Chlamydia

Chlamydia infection is usually asymptomatic. When symptoms occur, they may include burning or pain with urination, increased discharge from the vagina or penis, pain in the testicles, and testicular swelling. When chlamydia infects the rectum, it may cause anal discharge, rectal bleeding, and painful bowel movements. Chlamydia infection of the eye can cause conjunctivitis (pink eye). People with chlamydia may also develop painful joints and swollen lymph nodes.

Diagnosis and Testing for Chlamydia

Chlamydia is diagnosed by testing a sample taken from affected body sites, such as a urine sample or a swab of the vagina or rectum.

Individuals with signs or symptoms of chlamydia should avoid sex and seek testing from a clinician, an STI clinic, or a health department. Because infection with chlamydia is usually asymptomatic, it is important to screen people who are at high risk of infection but have no symptoms. The CDC recommends at least annual screening for all sexually active women younger than 25 years and for those 25 years or older with risk factors such as a new sex partner, multiple sex partners, or known exposure to an STI. Screening for chlamydia should also be performed for all pregnant people younger than 25 years and for pregnant people who are 25 years or older and at increased risk of infection (those who have a new or more than 1 sex partner). People with HIV and men who have sex with men should be routinely screened for chlamydia. Other sexually active young men may be screened if there are high rates of chlamydia infection in their community.

Why Is It Important to Treat Chlamydia?

Chlamydia infection increases the risk of HIV infection and transmission. Additionally, untreated chlamydia infection can lead to infection of the uterus and fallopian tubes (pelvic inflammatory disease), which may increase the risk of infertility, chronic pelvic pain, and ectopic pregnancy. Individuals with chlamydia infection during pregnancy have an increased risk of premature delivery. Newborns who acquire chlamydia infection during delivery can develop conjunctivitis and pneumonia.

How Is Chlamydia Treated?

Chlamydia infection is treated with antibiotics. Depending on the antibiotic, treatment may be given as a single dose or prescribed for 7 days. Patients should not have sex for at least 1 week after starting treatment and until all their sex partners have also been tested and treated for chlamydia. Because repeat infections are common, individuals diagnosed with chlamydia should be retested about 3 months after completing treatment of their initial infection.

How to Reduce the Spread of Chlamydia

Sexually active individuals can decrease their risk of acquiring and transmitting chlamydia by using latex condoms with all sexual activity (including oral, anal, and vaginal sex), limiting the number of sexual partners, and avoiding anonymous sex.

For More Information

Centers for Disease Control and Prevention

Published Online: September 22, 2023. doi:10.1001/jama.2023.15460

Conflict of Interest Disclosures: Dr Ressler reported stock ownership in Cisco Systems, Johnson & Johnson, and Harvard Bioscience. No other disclosures were reported.

Sources: Dombrowski JC. Chlamydia and gonorrhea. Ann Intern Med . 2021;174(10):ITC145-ITC160. doi:10.7326/AITC202110190

Centers for Disease Control and Prevention. https://www.cdc.gov/std/chlamydia/stdfact-chlamydia-detailed.htm

See More About

Ressler A , Kurz S. What to Know About Chlamydia. JAMA. 2023;330(14):1398. doi:10.1001/jama.2023.15460

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• Review Article
• Published: 25 April 2016

Chlamydia cell biology and pathogenesis

• Cherilyn Elwell 1 ,
• Kathleen Mirrashidi 1 &
• Joanne Engel 1  

Nature Reviews Microbiology volume  14 ,  pages 385–400 ( 2016 ) Cite this article

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• Bacterial host response
• Bacterial infection
• Bacterial pathogenesis
• Bacterial secretion

Chlamydia spp. are obligate intracellular pathogens that are important causes of human and animal diseases. Chlamydiae share a common developmental cycle in which they alternate between the extracellular, infectious elementary body and the intracellular, non-infectious reticulate body.

Chlamydiae use several redundant mechanisms to enter host cells and to establish their intracellular membrane bound niche — the inclusion.

Chlamydiae deliver effector proteins into the inclusion membrane and into host cells to promote replication and survival.

Chlamydiae encode a unique set of T3SS effectors, the inclusion membrane proteins (Incs), which are inserted into the inclusion membrane where they may function as structural determinants of the membrane or as scaffolds to interface with various cell pathways in the host.

Recent studies have solved the 'chlamydial anomaly' and reveal that Chlamydia spp. do synthesize peptidoglycan and use an atypical mechanism of cell division.

The recent major advances in chlamydial genetics open the door for the development of tools and avenues of research that were not previously accessible to this historically intractable pathogen.

Chlamydia spp. are important causes of human disease for which no effective vaccine exists. These obligate intracellular pathogens replicate in a specialized membrane compartment and use a large arsenal of secreted effectors to survive in the hostile intracellular environment of the host. In this Review, we summarize the progress in decoding the interactions between Chlamydia spp. and their hosts that has been made possible by recent technological advances in chlamydial proteomics and genetics. The field is now poised to decipher the molecular mechanisms that underlie the intimate interactions between Chlamydia spp. and their hosts, which will open up many exciting avenues of research for these medically important pathogens.

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Stefan Pan, Imran T. Malik, … Peter Sass

Bachmann, N. L., Polkinghorne, A. & Timms, P. Chlamydia genomics: providing novel insights into chlamydial biology. Trends Microbiol. 22 , 464–472 (2014).

Article   CAS   PubMed   Google Scholar  

Mandell, G. L., Bennett, J. E. & Dolin, R. (eds) Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases 7th edn Vol. 2 (Churchill Livingstone/Elsevier, 2010).

Google Scholar  

Rank, R. G. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 285–310 (ASM Press, 2012).

Malhotra, M., Sood, S., Mukherjee, A., Muralidhar, S. & Bala, M. Genital Chlamydia trachomatis : an update. Indian J. Med. Res. 138 , 303–316 (2013).

PubMed   PubMed Central   Google Scholar  

de Vrieze, N. H. & de Vries, H. J. Lymphogranuloma venereum among men who have sex with men. An epidemiological and clinical review. Expert Rev. Anti Infect. Ther. 12 , 697–704 (2014).

Murthy, A. K., Arulanandam, B. P. & Zhong, G. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 311–333 (ASM Press, 2012).

Bastidas, R. J., Elwell, C. A., Engel, J. N. & Valdivia, R. H. Chlamydial intracellular survival strategies. Cold Spring Harb. Perspect. Med. 3 , a010256 (2013).

Article   CAS   PubMed   PubMed Central   Google Scholar  

Stephens, R. S. et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis . Science 282 , 754–759 (1998).

Myers, G. S. A., Crabtree, J. & Creasy, H. H. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 27–50 (ASM press, 2012).

Betts-Hampikian, H. J. & Fields, K. A. The chlamydial type III secretion mechanism: revealing cracks in a tough nut. Front. Microbiol. 1 , 114 (2010).

Article   PubMed   PubMed Central   Google Scholar  

Fields, K. A. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 192–216 (ASM press, 2012).

Lei, L. et al. Reduced live organism recovery and lack of hydrosalpinx in mice infected with plasmid-free Chlamydia muridarum . Infect. Immun. 82 , 983–992 (2014).

Nelson, D. E. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 74–96 (ASM Press, 2012).

Omsland, A., Sixt, B. S., Horn, M. & Hackstadt, T. Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities. FEMS Microbiol. Rev. 38 , 779–801 (2014).

Saka, H. A. et al. Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms. Mol. Microbiol. 82 , 1185–1203 (2011).

Hackstadt, T. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 126–148 (ASM press, 2012).

Hegemann, J. H. & Moelleken, K. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 97–125 (ASM press, 2012).

Mehlitz, A. & Rudel, T. Modulation of host signaling and cellular responses by Chlamydia . Cell Commun. Signal. 11 , 90 (2013).

Tan, M. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 149–169 (ASM press, 2012).

Moore, E. R. & Ouellette, S. P. Reconceptualizing the chlamydial inclusion as a pathogen-specified parasitic organelle: an expanded role for Inc proteins. Front. Cell. Infect. Microbiol. 4 , 157 (2014).

Elwell, C. A. & Engel, J. N. Lipid acquisition by intracellular Chlamydiae . Cell. Microbiol. 14 , 1010–1018 (2012).

Barta, M. L. et al. Atypical response regulator ChxR from Chlamydia trachomatis is structurally poised for DNA binding. PLoS ONE 9 , e91760 (2014).

Rosario, C. J., Hanson, B. R. & Tan, M. The transcriptional repressor EUO regulates both subsets of Chlamydia late genes. Mol. Microbiol. 94 , 888–897 (2014).

Barta, M. L., Battaile, K. P., Lovell, S. & Hefty, P. S. Hypothetical protein CT398 (CdsZ) interacts with σ 54 (RpoN)-holoenzyme and the type III secretion export apparatus in Chlamydia trachomatis . Protein Sci. 24 , 1617–1632 (2015).

Hanson, B. R., Slepenkin, A., Peterson, E. M. & Tan, M. Chlamydia trachomatis type III secretion proteins regulate transcription. J. Bacteriol. 197 , 3238–3244 (2015).

Shen, L. et al. Multipart chaperone–effector recognition in the type III secretion system of Chlamydia trachomatis . J. Biol. Chem. 290 , 28141–28155 (2015).

Byrne, G. I. & Beatty, W. L. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 265–284 (ASM press, 2012).

Kim, J. H. et al. Endosulfatases SULF1 and SULF2 limit Chlamydia muridarum infection. Cell. Microbiol. 15 , 1560–1571 (2013).

Rosmarin, D. M. et al. Attachment of Chlamydia trachomatis L2 to host cells requires sulfation. Proc. Natl Acad. Sci. USA 109 , 10059–10064 (2012).

Article   PubMed   Google Scholar  

Ajonuma, L. C. et al. CFTR is required for cellular entry and internalization of Chlamydia trachomatis . Cell Biol. Int. 34 , 593–600 (2010).

Stallmann, S. & Hegemann, J. H. The Chlamydia trachomatis Ctad1 invasin exploits the human integrin β1 receptor for host cell entry. Cell. Microbiol. http://dx.doi.org/10.1111/cmi.12549 (2015).

Becker, E. & Hegemann, J. H. All subtypes of the Pmp adhesin family are implicated in chlamydial virulence and show species-specific function. Microbiologyopen 3 , 544–556 (2014).

Molleken, K., Becker, E. & Hegemann, J. H. The Chlamydia pneumoniae invasin protein Pmp21 recruits the EGF receptor for host cell entry. PLoS Pathog. 9 , e1003325 (2013).

Elwell, C. A., Ceesay, A., Kim, J. H., Kalman, D. & Engel, J. N. RNA interference screen identifies Abl kinase and PDGFR signaling in Chlamydia trachomatis entry. PLoS Pathog. 4 , e1000021 (2008).

Kim, J. H., Jiang, S., Elwell, C. A. & Engel, J. N. Chlamydia trachomatis co-opts the FGF2 signaling pathway to enhance infection. PLoS Pathog. 7 , e1002285 (2011).

Subbarayal, P. et al. EphrinA2 receptor (EphA2) is an invasion and intracellular signaling receptor for Chlamydia trachomatis . PLoS Pathog. 11 , e1004846 (2015).

Gerard, H. C., Fomicheva, E., Whittum-Hudson, J. A. & Hudson, A. P. Apolipoprotein E4 enhances attachment of Chlamydophila ( Chlamydia ) pneumoniae elementary bodies to host cells. Microb. Pathog. 44 , 279–285 (2008).

Ferrell, J. C. & Fields, K. A. A working model for the type III secretion mechanism in Chlamydia . Microbes Infect. 18 , 84–92 (2015).

Nans, A., Saibil, H. R. & Hayward, R. D. Pathogen–host reorganization during Chlamydia invasion revealed by cryo-electron tomography. Cell. Microbiol. 16 , 1457–1472 (2014).

Dumoux, M., Nans, A., Saibil, H. R. & Hayward, R. D. Making connections: snapshots of chlamydial type III secretion systems in contact with host membranes. Curr. Opin. Microbiol. 23 , 1–7 (2015).

Korhonen, J. T. et al. Chlamydia pneumoniae entry into epithelial cells by clathrin-independent endocytosis. Microb. Pathog. 52 , 157–164 (2012).

Dai, W. & Li, Z. Conserved type III secretion system exerts important roles in Chlamydia trachomatis . Int. J. Clin. Exp. Pathol. 7 , 5404–5414 (2014).

CAS   PubMed   PubMed Central   Google Scholar  

Jiwani, S. et al. Chlamydia trachomatis TarP harbors distinct G and F actin binding domains that bundle actin filaments. J. Bacteriol. 195 , 708–716 (2013).

Thwaites, T. et al. The Chlamydia effector TarP mimics the mammalian leucine–aspartic acid motif of paxillin to subvert the focal adhesion kinase during invasion. J. Biol. Chem. 289 , 30426–30442 (2014).

Chen, Y. S. et al. The Chlamydia trachomatis type III secretion chaperone Slc1 engages multiple early effectors, including TepP, a tyrosine-phosphorylated protein required for the recruitment of CrkI-II to nascent inclusions and innate immune signaling. PLoS Pathog. 10 , e1003954 (2014). This study provides the first genetic validation of the role of a C. trachomatis T3SS effector and reveals a hierarchical order in bacterial effector translocation into host cells by differential binding to shared chaperones.

Pais, S. V., Milho, C., Almeida, F. & Mota, L. J. Identification of novel type III secretion chaperone–substrate complexes of Chlamydia trachomatis . PLoS ONE 8 , e56292 (2013).

Bullock, H. D., Hower, S. & Fields, K. A. Domain analyses reveal that Chlamydia trachomatis CT694 protein belongs to the membrane-localized family of type III effector proteins. J. Biol. Chem. 287 , 28078–28086 (2012).

Mojica, S. A. et al. SINC, a type III secreted protein of Chlamydia psittaci , targets the inner nuclear membrane of infected cells and uninfected neighbors. Mol. Biol. Cell 26 , 1918–1934 (2015).

Kokes, M. & Valdivia, R. H. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 170–191 (ASM press, 2012).

Richards, T. S., Knowlton, A. E. & Grieshaber, S. S. Chlamydia trachomatis homotypic inclusion fusion is promoted by host microtubule trafficking. BMC Microbiol. 13 , 185 (2013).

Mital, J., Lutter, E. I., Barger, A. C., Dooley, C. A. & Hackstadt, T. Chlamydia trachomatis inclusion membrane protein CT850 interacts with the dynein light chain DYNLT1 (Tctex1). Biochem. Biophys. Res. Commun. 462 , 165–170 (2015).

Bocker, S. et al. Chlamydia psittaci inclusion membrane protein IncB associates with host protein Snapin. Int. J. Med. Microbiol. 304 , 542–553 (2014).

Damiani, M. T., Gambarte Tudela, J. & Capmany, A. Targeting eukaryotic Rab proteins: a smart strategy for chlamydial survival and replication. Cell. Microbiol. 16 , 1329–1338 (2014).

Gambarte Tudela, J. et al. The late endocytic Rab39a GTPase regulates multivesicular bodies–chlamydial inclusion interaction and bacterial growth. J. Cell Sci. 128 , 3068–3081 (2015).

Leiva, N., Capmany, A. & Damiani, M. T. Rab11-family of interacting protein 2 associates with chlamydial inclusions through its Rab-binding domain and promotes bacterial multiplication. Cell. Microbiol. 15 , 114–129 (2013).

Schlager, M. A. et al. Bicaudal D family adaptor proteins control the velocity of Dynein-based movements. Cell Rep. 8 , 1248–1256 (2014).

Moorhead, A. M., Jung, J. Y., Smirnov, A., Kaufer, S. & Scidmore, M. A. Multiple host proteins that function in phosphatidylinositol-4-phosphate metabolism are recruited to the chlamydial inclusion. Infect. Immun. 78 , 1990–2007 (2010).

Moore, E. R., Mead, D. J., Dooley, C. A., Sager, J. & Hackstadt, T. The trans -Golgi SNARE syntaxin 6 is recruited to the chlamydial inclusion membrane. Microbiology 157 , 830–838 (2011).

Kabeiseman, E. J., Cichos, K. H. & Moore, E. R. The eukaryotic signal sequence, YGRL, targets the chlamydial inclusion. Front. Cell. Infect. Microbiol. 4 , 129 (2014).

Lucas, A. L., Ouellette, S. P., Kabeiseman, E. J., Cichos, K. H. & Rucks, E. A. The trans -Golgi SNARE syntaxin 10 is required for optimal development of Chlamydia trachomatis . Front. Cell. Infect. Microbiol. 5 , 68 (2015).

Kabeiseman, E. J., Cichos, K., Hackstadt, T., Lucas, A. & Moore, E. R. Vesicle-associated membrane protein 4 and syntaxin 6 interactions at the chlamydial inclusion. Infect. Immun. 81 , 3326–3337 (2013).

Pokrovskaya, I. D. et al. Chlamydia trachomatis hijacks intra-Golgi COG complex-dependent vesicle trafficking pathway. Cell. Microbiol. 14 , 656–668 (2012).

Ronzone, E. & Paumet, F. Two coiled-coil domains of Chlamydia trachomatis IncA affect membrane fusion events during infection. PLoS ONE 8 , e69769 (2013).

Ronzone, E. et al. An α-helical core encodes the dual functions of the chlamydial protein IncA. J. Biol. Chem. 289 , 33469–33480 (2014).

Gauliard, E., Ouellette, S. P., Rueden, K. J. & Ladant, D. Characterization of interactions between inclusion membrane proteins from Chlamydia trachomatis . Front. Cell. Infect. Microbiol. 5 , 13 (2015).

Geisler, W. M., Suchland, R. J., Rockey, D. D. & Stamm, W. E. Epidemiology and clinical manifestations of unique Chlamydia trachomatis isolates that occupy nonfusogenic inclusions. J. Infect. Dis. 184 , 879–884 (2001).

Mirrashidi, K. M. et al. Global mapping of the Inc–human interactome reveals that retromer restricts Chlamydia infection. Cell Host Microbe 18 , 109–121 (2015). This study reports the first large-scale chlamydial Inc–host interactome and suggests that by sequestering retromer components Chlamydia spp. can overcome host mechanisms that typically restrict the growth of pathogens.

Aeberhard, L. et al. The proteome of the isolated Chlamydia trachomatis containing vacuole reveals a complex trafficking platform enriched for retromer components. PLoS Pathog. 11 , e1004883 (2015). This study describes the quantitative analysis of the host-cell-derived proteome of inclusions isolated from C. trachomatis and demonstrates that retromer-associated sorting nexins and other components of host cell trafficking are enriched at the inclusion.

Seaman, M. N. The retromer complex — endosomal protein recycling and beyond. J. Cell Sci. 125 , 4693–4702 (2012).

Fisher, D. J., Fernandez, R. E. & Maurelli, A. T. Chlamydia trachomatis transports NAD via the Npt1 ATP/ADP translocase. J. Bacteriol. 195 , 3381–3386 (2013).

Gurumurthy, R. K. et al. Dynamin-mediated lipid acquisition is essential for Chlamydia trachomatis development. Mol. Microbiol. 94 , 186–201 (2014).

Reiling, J. H. et al. A CREB3–ARF4 signalling pathway mediates the response to Golgi stress and susceptibility to pathogens. Nat. Cell Biol. 15 , 1473–1485 (2013).

Elwell, C. A. et al. Chlamydia trachomatis co-opts GBF1 and CERT to acquire host sphingomyelin for distinct roles during intracellular development. PLoS Pathog. 7 , e1002198 (2011).

Derre, I., Swiss, R. & Agaisse, H. The lipid transfer protein CERT interacts with the Chlamydia inclusion protein IncD and participates to ER– Chlamydia inclusion membrane contact sites. PLoS Pathog. 7 , e1002092 (2011).

Agaisse, H. & Derre, I. Expression of the effector protein IncD in Chlamydia trachomatis mediates recruitment of the lipid transfer protein CERT and the endoplasmic reticulum-resident protein VAPB to the inclusion membrane. Infect. Immun. 82 , 2037–2047 (2014).

Cox, J. V., Naher, N., Abdelrahman, Y. M. & Belland, R. J. Host HDL biogenesis machinery is recruited to the inclusion of Chlamydia trachomatis -infected cells and regulates chlamydial growth. Cell. Microbiol. 14 , 1497–1512 (2012).

Yao, J., Dodson, V. J., Frank, M. W. & Rock, C. O. Chlamydia trachomatis scavenges host fatty acids for phospholipid synthesis via an acyl-acyl carrier protein synthetase. J. Biol. Chem. 290 , 22163–22173 (2015).

Yao, J., Cherian, P. T., Frank, M. W. & Rock, C. O. Chlamydia trachomatis relies on autonomous phospholipid synthesis for membrane biogenesis. J. Biol. Chem. 290 , 18874–18888 (2015).

Yao, J. et al. Type II fatty acid synthesis is essential for the replication of Chlamydia trachomatis . J. Biol. Chem. 289 , 22365–22376 (2014).

Heuer, D. et al. Chlamydia causes fragmentation of the Golgi compartment to ensure reproduction. Nature 457 , 731–735 (2009). This study reveals that C. trachomatis induces the fragmentation of the Golgi apparatus during infection to acquire lipids and replicate.

Kokes, M. et al. Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia . Cell Host Microbe 17 , 716–725 (2015). This study describes a defined library of chemically mutagenized and sequenced chlamydial strains and its use for genetic screens.

Al-Zeer, M. A. et al. Chlamydia trachomatis remodels stable microtubules to coordinate Golgi stack recruitment to the chlamydial inclusion surface. Mol. Microbiol. 94 , 1285–1297 (2014).

Kokes, M. & Valdivia, R. H. Differential translocation of host cellular materials into the Chlamydia trachomatis inclusion lumen during chemical fixation. PLoS ONE 10 , e0139153 (2015).

Boncompain, G. et al. The intracellular bacteria Chlamydia hijack peroxisomes and utilize their enzymatic capacity to produce bacteria-specific phospholipids. PLoS ONE 9 , e86196 (2014).

Saka, H. A. et al. Chlamydia trachomatis infection leads to defined alterations to the lipid droplet proteome in epithelial cells. PLoS ONE 10 , e0124630 (2015).

Soupene, E., Rothschild, J., Kuypers, F. A. & Dean, D. Eukaryotic protein recruitment into the Chlamydia inclusion: implications for survival and growth. PLoS ONE 7 , e36843 (2012).

Soupene, E., Wang, D. & Kuypers, F. A. Remodeling of host phosphatidylcholine by Chlamydia acyltransferase is regulated by acyl-CoA binding protein ACBD6 associated with lipid droplets. Microbiologyopen 4 , 235–251 (2015).

Derre, I. Chlamydiae interaction with the endoplasmic reticulum: contact, function and consequences. Cell. Microbiol. 17 , 959–966 (2015).

Agaisse, H. & Derre, I. STIM1 is a novel component of ER– Chlamydia trachomatis inclusion membrane contact sites. PLoS ONE 10 , e0125671 (2015).

Barker, J. R. et al. STING-dependent recognition of cyclic di-AMP mediates type I interferon responses during Chlamydia trachomatis infection. mBio 4 , e00018-13 (2013). This study provides the first example of a Gram-negative bacterium that synthesizes its own cyclic di-AMP to activate STING and induce the production of type I interferons.

Shima, K. et al. The role of endoplasmic reticulum-related BiP/GRP78 in interferon-γ-induced persistent Chlamydia pneumoniae infection. Cell. Microbiol. 17 , 923–934 (2015).

Mehlitz, A. et al. The chlamydial organism Simkania negevensis forms ER vacuole contact sites and inhibits ER-stress. Cell. Microbiol. 16 , 1224–1243 (2014).

Dumoux, M., Clare, D. K., Saibil, H. R. & Hayward, R. D. Chlamydiae assemble a pathogen synapse to hijack the host endoplasmic reticulum. Traffic 13 , 1612–1627 (2012).

Volceanov, L. et al. Septins arrange F-actin-containing fibers on the Chlamydia trachomatis inclusion and are required for normal release of the inclusion by extrusion. mBio 5 , e01802-14 (2014).

Patel, A. L. et al. Activation of epidermal growth factor receptor is required for Chlamydia trachomatis development. BMC Microbiol. 14 , 277 (2014).

Dumoux, M., Menny, A., Delacour, D. & Hayward, R. D. A Chlamydia effector recruits CEP170 to reprogram host microtubule organization. J. Cell Sci. 128 , 3420–3434 (2015).

Hybiske, K. & Stephens, R. S. Mechanisms of host cell exit by the intracellular bacterium Chlamydia . Proc. Natl Acad. Sci. USA 104 , 11430–11435 (2007). This paper describes two distinct strategies that Chlamydia spp. use to exit the host cell at the end of the developmental cycle.

Snavely, E. A. et al. Reassessing the role of the secreted protease CPAF in Chlamydia trachomatis infection through genetic approaches. Pathog. Dis. 71 , 336–351 (2014). This study, together with reference 145, provides genetic evidence that CPAF is dispensable for several phenotypes that were previously attributed to CPAF activity and also reveals that CPAF may have a role in dismantling the host cell prior to bacterial exit.

Yang, Z., Tang, L., Sun, X., Chai, J. & Zhong, G. Characterization of CPAF critical residues and secretion during Chlamydia trachomatis infection. Infect. Immun. 83 , 2234–2241 (2015).

Lutter, E. I., Barger, A. C., Nair, V. & Hackstadt, T. Chlamydia trachomatis inclusion membrane protein CT228 recruits elements of the myosin phosphatase pathway to regulate release mechanisms. Cell Rep. 3 , 1921–1931 (2013).

Chin, E., Kirker, K., Zuck, M., James, G. & Hybiske, K. Actin recruitment to the Chlamydia inclusion is spatiotemporally regulated by a mechanism that requires host and bacterial factors. PLoS ONE 7 , e46949 (2012).

Karunakaran, K., Subbarayal, P., Vollmuth, N. & Rudel, T. Chlamydia -infected cells shed Gp96 to prevent chlamydial re-infection. Mol. Microbiol. 98 , 694–711 (2015).

Flores, R. & Zhong, G. The Chlamydia pneumoniae inclusion membrane protein Cpn1027 interacts with host cell Wnt signaling pathway regulator cytoplasmic activation/proliferation-associated protein 2 (Caprin2). PLoS ONE 10 , e0127909 (2015).

Sharma, M. & Rudel, T. Apoptosis resistance in Chlamydia -infected cells: a fate worse than death? FEMS Immunol. Med. Microbiol. 55 , 154–161 (2009).

Gonzalez, E. et al. Chlamydia infection depends on a functional MDM2–p53 axis. Nat. Commun. 5 , 5201 (2014).

Siegl, C., Prusty, B. K., Karunakaran, K., Wischhusen, J. & Rudel, T. Tumor suppressor p53 alters host cell metabolism to limit Chlamydia trachomatis infection. Cell Rep. 9 , 918–929 (2014).

Kun, D., Xiang-Lin, C., Ming, Z. & Qi, L. Chlamydia inhibit host cell apoptosis by inducing Bag-1 via the MAPK/ERK survival pathway. Apoptosis 18 , 1083–1092 (2013).

Bohme, L., Albrecht, M., Riede, O. & Rudel, T. Chlamydia trachomatis -infected host cells resist dsRNA-induced apoptosis. Cell. Microbiol. 12 , 1340–1351 (2010).

Chen, A. L., Johnson, K. A., Lee, J. K., Sutterlin, C. & Tan, M. CPAF: a chlamydial protease in search of an authentic substrate. PLoS Pathog. 8 , e1002842 (2012). This study reports that the proteolysis of many of the previously reported CPAF substrates occurs during the preparation of lysates from cells that are infected with Chlamydia spp. rather than in intact cells.

Bothe, M., Dutow, P., Pich, A., Genth, H. & Klos, A. DXD motif-dependent and -independent effects of the Chlamydia trachomatis cytotoxin CT166. Toxins (Basel) 7 , 621–637 (2015).

Article   CAS   Google Scholar  

Brown, H. M. et al. Multinucleation during C. trachomatis infections is caused by the contribution of two effector pathways. PLoS ONE 9 , e100763 (2014).

Huang, J., Lesser, C. F. & Lory, S. The essential role of the CopN protein in Chlamydia pneumoniae intracellular growth. Nature 456 , 112–115 (2008).

Nawrotek, A. et al. Biochemical and structural insights into microtubule perturbation by CopN from Chlamydia pneumoniae . J. Biol. Chem. 289 , 25199–25210 (2014).

Sun, H. S., Sin, A. T., Poirier, M. & Harrison, R. E. Chlamydia trachomatis inclusion disrupts host cell cytokinesis to enhance its growth in multinuclear cells. J. Cell Biochem. 117 , 132–143 (2015).

Knowlton, A. E. et al. Chlamydia trachomatis infection causes mitotic spindle pole defects independently from its effects on centrosome amplification. Traffic 12 , 854–866 (2011).

Mital, J., Miller, N. J., Fischer, E. R. & Hackstadt, T. Specific chlamydial inclusion membrane proteins associate with active Src family kinases in microdomains that interact with the host microtubule network. Cell. Microbiol. 12 , 1235–1249 (2010).

Chumduri, C., Gurumurthy, R. K., Zadora, P. K., Mi, Y. & Meyer, T. F. Chlamydia infection promotes host DNA damage and proliferation but impairs the DNA damage response. Cell Host Microbe 13 , 746–758 (2013).

Fukasawa, K., Choi, T., Kuriyama, R., Rulong, S. & Vande Woude, G. F. Abnormal centrosome amplification in the absence of p53. Science 271 , 1744–1747 (1996).

Knowlton, A. E., Fowler, L. J., Patel, R. K., Wallet, S. M. & Grieshaber, S. S. Chlamydia induces anchorage independence in 3T3 cells and detrimental cytological defects in an infection model. PLoS ONE 8 , e54022 (2013).

Padberg, I., Janssen, S. & Meyer, T. F. Chlamydia trachomatis inhibits telomeric DNA damage signaling via transient hTERT upregulation. Int. J. Med. Microbiol. 303 , 463–474 (2013).

Nagarajan, U. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 217–239 (ASM press, 2012).

Darville, T. & O'Connell, C. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 240–264 (ASM press, 2012).

Shimada, K., Crother, T. R. & Arditi, M. Innate immune responses to Chlamydia pneumoniae infection: role of TLRs, NLRs, and the inflammasome. Microbes Infect. 14 , 1301–1307 (2012).

Najarajan, U. in Bacterial Activation of Type I Interferons (ed. Parker, D.) 101–102 (Springer, 2014).

Zhang, Y. et al. The DNA sensor, cyclic GMP–AMP synthase, is essential for induction of IFN-β during Chlamydia trachomatis infection. J. Immunol. 193 , 2394–2404 (2014). This study demonstrates that DNA from C. trachomatis binds to cGAS to activate STING and induce type I IFN responses during infection.

Abdul-Sater, A. A. et al. Enhancement of reactive oxygen species production and chlamydial infection by the mitochondrial Nod-like family member NLRX1. J. Biol. Chem. 285 , 41637–41645 (2010).

Itoh, R. et al. Chlamydia pneumoniae harness host NLRP3 inflammasome-mediated caspase-1 activation for optimal intracellular growth in murine macrophages. Biochem. Biophys. Res. Commun. 452 , 689–694 (2014).

Wolf, K. & Fields, K. A. Chlamydia pneumoniae impairs the innate immune response in infected epithelial cells by targeting TRAF3. J. Immunol. 190 , 1695–1701 (2013).

Abu-Lubad, M., Meyer, T. F. & Al-Zeer, M. A. Chlamydia trachomatis inhibits inducible NO synthase in human mesenchymal stem cells by stimulating polyamine synthesis. J. Immunol. 193 , 2941–2951 (2014).

Al-Zeer, M. A., Al-Younes, H. M., Lauster, D., Abu Lubad, M. & Meyer, T. F. Autophagy restricts Chlamydia trachomatis growth in human macrophages via IFNγ-inducible guanylate binding proteins. Autophagy 9 , 50–62 (2013).

Haldar, A. K. et al. Ubiquitin systems mark pathogen-containing vacuoles as targets for host defense by guanylate binding proteins. Proc. Natl Acad. Sci. USA 112 , E5628–E5637 (2015).

Haldar, A. K., Piro, A. S., Pilla, D. M., Yamamoto, M. & Coers, J. The E2-like conjugation enzyme Atg3 promotes binding of IRG and Gbp proteins to Chlamydia - and Toxoplasma -containing vacuoles and host resistance. PLoS ONE 9 , e86684 (2014).

Finethy, R. et al. Guanylate binding proteins enable rapid activation of canonical and noncanonical inflammasomes in Chlamydia -infected macrophages. Infect. Immun. 83 , 4740–4749 (2015).

Haldar, A. K. et al. IRG and GBP host resistance factors target aberrant, “non-self” vacuoles characterized by the missing of “self” IRGM proteins. PLoS Pathog. 9 , e1003414 (2013). This study reveals that the intracellular immune recognition of pathogen-containing vacuoles is partly dictated by the lack of 'self' IRGM proteins from these structures.

Wolf, K., Plano, G. V. & Fields, K. A. A protein secreted by the respiratory pathogen Chlamydia pneumoniae impairs IL-17 signalling via interaction with human Act1. Cell. Microbiol. 11 , 769–779 (2009).

Kessler, M. et al. Chlamydia trachomatis disturbs epithelial tissue homeostasis in fallopian tubes via paracrine Wnt signaling. Am. J. Pathol. 180 , 186–198 (2012).

Pennini, M. E., Perrinet, S., Dautry-Varsat, A. & Subtil, A. Histone methylation by NUE, a novel nuclear effector of the intracellular pathogen Chlamydia trachomatis . PLoS Pathog. 6 , e1000995 (2010).

Olive, A. J. et al. Chlamydia trachomatis -induced alterations in the host cell proteome are required for intracellular growth. Cell Host Microbe 15 , 113–124 (2014). This study uses a global protein stability platform (GPS) to survey changes in host protein stability in response to infection with Chlamydia spp.

Furtado, A. R. et al. The chlamydial OTU domain-containing protein Chla OTU is an early type III secretion effector targeting ubiquitin and NDP52. Cell. Microbiol. 15 , 2064–2079 (2013).

Misaghi, S. et al. Chlamydia trachomatis -derived deubiquitinating enzymes in mammalian cells during infection. Mol. Microbiol. 61 , 142–150 (2006).

Claessen, J. H. et al. Catch-and-release probes applied to semi-intact cells reveal ubiquitin-specific protease expression in Chlamydia trachomatis infection. Chembiochem 14 , 343–352 (2013).

Conrad, T., Yang, Z., Ojcius, D. & Zhong, G. A path forward for the chlamydial virulence factor CPAF. Microbes Infect. 15 , 1026–1032 (2013).

Article   CAS   PubMed Central   Google Scholar  

Johnson, K. A., Lee, J. K., Chen, A. L., Tan, M. & Sutterlin, C. Induction and inhibition of CPAF activity during analysis of Chlamydia -infected cells. Pathog. Dis. 73 , 1–8 (2015).

Tan, M. & Sutterlin, C. The Chlamydia protease CPAF: caution, precautions and function. Pathog. Dis. 72 , 7–9 (2014).

Dille, S. et al. Golgi fragmentation and sphingomyelin transport to Chlamydia trachomatis during penicillin-induced persistence do not depend on the cytosolic presence of the chlamydial protease CPAF. PLoS ONE 9 , e103220 (2014).

Hooppaw, A. J. & Fisher, D. J. A coming of age story: Chlamydia in the post-genetic era. Infect. Immun. 84 , 612–621 (2015).

Buckner, L. R. et al. Innate immune mediator profiles and their regulation in a novel polarized immortalized epithelial cell model derived from human endocervix. J. Reprod. Immunol. 92 , 8–20 (2011).

Hall, J. V. et al. The multifaceted role of oestrogen in enhancing Chlamydia trachomatis infection in polarized human endometrial epithelial cells. Cell. Microbiol. 13 , 1183–1199 (2011).

Kintner, J., Schoborg, R. V., Wyrick, P. B. & Hall, J. V. Progesterone antagonizes the positive influence of estrogen on Chlamydia trachomatis serovar E in an Ishikawa/SHT-290 co-culture model. Pathog. Dis. 73 , ftv015 (2015).

Mueller, K. E., Plano, G. V. & Fields, K. A. New frontiers in type III secretion biology: the Chlamydia perspective. Infect. Immun. 82 , 2–9 (2014).

Dehoux, P., Flores, R., Dauga, C., Zhong, G. & Subtil, A. Multi-genome identification and characterization of Chlamydiae -specific type III secretion substrates: the Inc proteins. BMC Genomics 12 , 109 (2011).

Lutter, E. I., Martens, C. & Hackstadt, T. Evolution and conservation of predicted inclusion membrane proteins in Chlamydiae . Comp. Funct. Genomics 2012 , 362104 (2012).

Mital, J., Miller, N. J., Dorward, D. W., Dooley, C. A. & Hackstadt, T. Role for chlamydial inclusion membrane proteins in inclusion membrane structure and biogenesis. PLoS ONE 8 , e63426 (2013).

Jeffrey, B. M., Maurelli, A. T. & Rockey, D. D. in Intracellular Pathogens 1: Chlamydiales Vol. 1 (eds Tan, M. & Bavoil, P. M.) 334–351 (Washington, 2012).

Tam, J. E., Davis, C. H. & Wyrick, P. B. Expression of recombinant DNA introduced into Chlamydia trachomatis by electroporation. Can. J. Microbiol. 40 , 583–591 (1994).

Binet, R. & Maurelli, A. T. Transformation and isolation of allelic exchange mutants of Chlamydia psittaci using recombinant DNA introduced by electroporation. Proc. Natl Acad. Sci. USA 106 , 292–297 (2009). This study reports the first generation of stable transformants of Chlamydia spp. by allelic exchange and, together with the studies in references 157, 163 and 166, has helped to open the door towards easier genetic manipulation of chlamydial species.

Wang, Y. et al. Development of a transformation system for Chlamydia trachomatis : restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector. PLoS Pathog. 7 , e1002258 (2011). In this study the authors develop a new shuttle vector based on the Chlamydia cryptic plasmid and modify transformation and selection protocols to achieve stable transformants of Chlamydia spp.

Wickstrum, J., Sammons, L. R., Restivo, K. N. & Hefty, P. S. Conditional gene expression in Chlamydia trachomatis using the tet system. PLoS ONE 8 , e76743 (2013).

Agaisse, H. & Derre, I. A. C. trachomatis cloning vector and the generation of C. trachomatis strains expressing fluorescent proteins under the control of a C. trachomatis promoter. PLoS ONE 8 , e57090 (2013).

Bauler, L. D. & Hackstadt, T. Expression and targeting of secreted proteins from Chlamydia trachomatis . J. Bacteriol. 196 , 1325–1334 (2014).

Weber, M. M., Bauler, L. D., Lam, J. & Hackstadt, T. Expression and localization of predicted inclusion membrane proteins in Chlamydia trachomatis . Infect. Immun. 83 , 4710–4718 (2015).

Mueller, K. E. & Fields, K. A. Application of β-lactamase reporter fusions as an indicator of effector protein secretion during infections with the obligate intracellular pathogen Chlamydia trachomatis . PLoS ONE 10 , e0135295 (2015).

Nguyen, B. D. & Valdivia, R. H. Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches. Proc. Natl Acad. Sci. USA 109 , 1263–1268 (2012). In this study the authors use chemical mutagenesis, coupled with whole-genome sequencing and a system for DNA exchange in infected cells, to generate mutants of C. trachomatis that can be used to correlate phenotype with genotype.

Demars, R., Weinfurter, J., Guex, E., Lin, J. & Potucek, Y. Lateral gene transfer in vitro in the intracellular pathogen Chlamydia trachomatis . J. Bacteriol. 189 , 991–1003 (2007).

Rajaram, K. et al. Mutational analysis of the Chlamydia muridarum plasticity zone. Infect. Immun. 83 , 2870–2881 (2015).

Johnson, C. M. & Fisher, D. J. Site-specific, insertional inactivation of incA in Chlamydia trachomatis using a group II intron. PLoS ONE 8 , e83989 (2013). This study reports the first application-specific intron targeting to insertionally inactivate a gene in the chromosome of C. trachomatis .

Kari, L. et al. Generation of targeted Chlamydia trachomatis null mutants. Proc. Natl Acad. Sci. USA 108 , 7189–7193 (2011).

Jacquier, N., Viollier, P. H. & Greub, G. The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly. FEMS Microbiol. Rev. 39 , 262–275 (2015).

Pilhofer, M. et al. Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ. Nat. Commun. 4 , 2856 (2013).

Liechti, G. W. et al. A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis . Nature 506 , 507–510 (2014). In this study the authors use a novel click-chemistry-based approach to demonstrate for the first time that C. trachomatis has peptidoglycan and functional peptidoglycan-modifying enzymes.

Ouellette, S. P. et al. Analysis of MreB interactors in Chlamydia reveals a RodZ homolog but fails to detect an interaction with MraY. Front. Microbiol. 5 , 279 (2014).

Kemege, K. E. et al. Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB. Mol. Microbiol. 95 , 365–382 (2015).

Jacquier, N., Frandi, A., Pillonel, T., Viollier, P. H. & Greub, G. Cell wall precursors are required to organize the chlamydial division septum. Nat. Commun. 5 , 3578 (2014).

Packiam, M., Weinrick, B., Jacobs, W. R. & Maurelli, A. T. Structural characterization of muropeptides from Chlamydia trachomatis peptidoglycan by mass spectrometry resolves “chlamydial anomaly”. Proc. Nat. Acad. Sci. USA 112 , 11660–11665 (2015). This study provides the first structural confirmation of peptidoglycan in pathogenic chlamydiae and the evidence from this study is consistent with the study in reference 170.

Klockner, A. et al. AmiA is a penicillin target enzyme with dual activity in the intracellular pathogen Chlamydia pneumoniae . Nat. Commun. 5 , 4201 (2014).

Frandi, A., Jacquier, N., Theraulaz, L., Greub, G. & Viollier, P. H. FtsZ-independent septal recruitment and function of cell wall remodelling enzymes in chlamydial pathogens. Nat. Commun. 5 , 4200 (2014).

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Acknowledgements

The authors apologize to those colleagues in the field whose work could not be included owing to space constraints. The authors gratefully acknowledge financial support from the US National Institutes of Health (R01 AI073770, AI105561 and AI122747) to J.E., and from the University of California, San Francisco (UCSF)-Gladstone Institute for Virology and Immunology, and the Center for AIDS Research to C.E.

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Cherilyn Elwell, Kathleen Mirrashidi & Joanne Engel

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Variants that differ physiologically and/or biochemically from other strains of a particular species.

A subdivision of a species or subspecies that is distinguished by a characteristic set of antigens.

(T5SS). A system that exports autotransporters that are composed of a carboxy-terminal β-barrel translocator domain and an amino-terminal passenger domain that passes through the interior of the barrel to face the external environment.

(T2SS). A system that exports proteins across the bacterial inner membrane through the general secretory (Sec) pathway and across the outer membrane through secretin. In chlamydiae, T2SS effectors are secreted into the inclusion lumen, but can access the host cytosol through outer membrane vesicles.

(T3SS). A needle-like apparatus found in Gram-negative bacteria that delivers proteins, called effectors, across the inner and outer bacterial membranes and across eukaryotic membranes to the host membrane or the cytosol.

The fusion between cells or vesicles of the same type. For cells that are infected with some Chlamydia spp., several inclusions undergo fusion with each other to form one, or a few, larger inclusions.

Bacterial proteins that direct the binding of RNA polymerase to promoters, which enables the initiation of transcription.

Subunits of bacterial two-component signal transduction pathways that regulate output in response to an environmental stimulus.

(PMP). A member of a diverse group of surface-localized, immunodominant proteins that are secreted by the type V secretion system (T5SS) of Chlamydia spp.

(ARF6). A member of the GTPase family of small GTPases that regulates vesicular transport, in which they function to recruit coat proteins that are necessary for the formation of vesicles.

A multisubunit complex found in eukaryotic cells that binds to the motor protein dynein and aids in the microtubule-based transport of vesicles.

(Soluble N -ethylmaleimide-sensitive factor (NSF) attachment protein receptor proteins). Soluble NSF attachment proteins are a large superfamily of proteins that mediate vesicle fusion by pairing with each other on adjacent membranes through SNARE domains.

Small GTPases that localize to the cytosolic face of specific intracellular membranes, where they regulate intracellular trafficking and membrane fusion. Different RABs are specific for distinct subcellular compartments.

A family of enzymes that generates phosphorylated variants of phosphatidylinositols (secondary messengers), which are important for signalling and membrane remodelling. Organelles are, in part, identified by the specific lipid species that they contain.

(MVBs). A specialized set of late endosomes that contains internal vesicles formed by the inward budding of the outer endosomal membrane. MVBs are involved in protein sorting and are rich in lipids, including sphingolipids and cholesterol.

A large GTPase that is involved in the scission of newly formed vesicles from the cell surface, endosomes and the Golgi apparatus.

(CERT). A cytosolic protein that mediates the non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi apparatus where it is converted to sphingomyelin.

A type of fatty acid synthesis in which the enzymes that catalyse each step in the synthesis pathway exist as distinct, individual proteins rather than as a multi-enzyme complex as in type I fatty acid synthesis.

A family of cysteine proteases that has essential roles in apoptosis, necrosis and inflammation.

A family of conserved regulatory molecules that usually binds to a phosphoserine or phosphothreonine residue found in functionally diverse signalling proteins in eukaryotic cells.

(STING). A signalling molecule that recognizes cytosolic cyclic dinucleotides and activates the production of type I interferons.

A stress pathway that is activated by perturbations in protein folding, lipid and steroid biosynthesis, and intracellular calcium stores.

A family of GTP-binding proteins that assembles into oligomeric complexes to form large filaments and rings that act as scaffolds and diffusion barriers

(CPAF). A type II secreted broad-spectrum protease produced by Chlamydia spp. that may have a role in cleaving host proteins on release into the host cell cytosol late in infection or extracellularly following the lysis of the host cell.

Members of the B cell lymphoma 2 (BCL-2) protein family, which are essential initiators of programmed cell death and are required for apoptosis that is induced by cytotoxic stimuli.

A eukaryotic signal transduction pathway that signals through the binding of the WNT protein ligand to a frizzled family cell surface receptor, which results in changes to gene transcription, cell polarity or intracellular calcium levels.

A programmed form of cell death that involves the degradation of cellular constituents by caspases that are activated through either the intrinsic (mitochondria-mediated) or extrinsic (death receptor-mediated) apoptotic pathways.

A eukaryotic tumour suppressor that maintains genome integrity by activating DNA repair, arresting the cell cycle or initiating apoptosis.

The physical process of cell division, which divides the cytoplasm of a parental cell into two daughter cells.

(TLRs). Transmembrane proteins that have a key role in the innate immune system by recognizing pathogen-associated molecular patterns (PAMPs), which are structurally conserved molecules derived from microorganisms.

(Type I IFNs). A subgroup of interferon proteins produced as part of the innate immune response against intracellular pathogens.

(NOD1). A cytosolic pattern-recognition receptor that recognizes bacterial peptidoglycan.

A multiprotein complex, consisting of caspase1, NOD-, LRR- and PYD domain-containing protein 3 (NLRP3) and apoptosis-associated speck-like protein containing a CARD (ASC), that processes the pro-inflammatory cytokines interleukin-1β (IL-1β) and IL-18 into their mature forms.

The ability of a host cell to eliminate an invasive infectious agent, which relies on microbial proteins, specialized degradative compartments and programmed host cell death.

(NF-κB) A protein complex that is translocated from the cytosol to the nucleus and regulates DNA transcription, cytokine production and cell survival in response to harmful cellular stimuli.

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Elwell, C., Mirrashidi, K. & Engel, J. Chlamydia cell biology and pathogenesis. Nat Rev Microbiol 14 , 385–400 (2016). https://doi.org/10.1038/nrmicro.2016.30

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A Collection on the prevention, diagnosis, and treatment of sexually transmitted infections: Call for research papers

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Citation: Low N, Broutet N, Turner R (2017) A Collection on the prevention, diagnosis, and treatment of sexually transmitted infections: Call for research papers. PLoS Med 14(6): e1002333. https://doi.org/10.1371/journal.pmed.1002333

Copyright: © 2017 Low et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Competing interests: We have read the journal's policy and have the following conflicts: NL receives a stipend as a specialty consulting editor for PLOS Medicine and serves on the journal's editorial board. RT’s individual competing interests are at http://journals.plos.org/plosmedicine/s/staff-editors . PLOS is funded partly through manuscript publication charges, but the PLOS Medicine Editors are paid a fixed salary (their salaries are not linked to the number of papers published in the journal).

Abbreviations: HPV, human papillomavirus; STI, sexually transmitted infection

Provenance: Commissioned; not externally peer-reviewed.

Sexually transmitted infections (STIs) are common, diverse, and dangerous to health—extending from bacterial diseases that may be readily treatable once diagnosed to viral infections such as HIV that can be life-threatening and, as yet, have no cure. A wide range of sexually transmissible pathogens have adverse effects on sexual and reproductive health, including infertility in women and several different types of cancer, with the global burden of cervical cancer a particular concern. Having an STI can also lead to low self-esteem, stigma, and sexual dysfunction. Moreover, some STIs are transmitted from mother to child and thereby lead to poor pregnancy, neonatal, and child health outcomes, including stillbirth. Emerging pathogens that prove to be sexually transmissible, recently exemplified by Ebola and Zika viruses, can be expected to evoke substantial and widespread concern where the risks and possible consequences of a disease outbreak are sketchily understood.

According to WHO [ 1 ], more than 30 different bacteria, viruses, and parasites lead to greater than 1 million sexually transmitted infections each day. Chlamydia (with an estimated 131 million new infections annually), gonorrhea (78 million infections), syphilis (5.6 million infections), and trichomoniasis (143 million infections) are 4 of the most common infections worldwide that can, at present, be treated with existing antibiotic regimens. However, antimicrobial resistance is a growing threat, particularly for gonorrhea and Mycoplasma genitalium . The most prevalent viral STIs are genital herpes simplex virus infection (affecting an estimated 500 million people worldwide) and human papillomavirus (HPV) infection (affecting 290 million women and leading to some 500,000 cases of cervical cancer annually). While antiviral treatment may control recurring herpes in some people, disease prevention and, where possible, vaccine development and deployment are priorities in the absence of curative interventions. Enmeshed as they are in human biology, behavior, and culture, STIs provide great challenges to those responsible for disease surveillance, planning services, and provision of treatment in all countries.

Because of the enormous burden of STIs and their wide-ranging adverse health effects, decisive action will be an essential part of efforts to meet the health component of the Sustainable Development Goals, and the targets of the global health sector strategy on sexually transmitted infections 2016–2021 [ 2 ], which were adopted by the 69th World Health Assembly in May 2016. Accompanying this Editorial are several articles forming part of a WHO-sponsored Collection addressing global policy and practice aimed at achieving control of STIs. Andrew Seale and colleagues discuss the development process for the global strategy to counter STIs [ 3 ]. Global targets for STI control specify, by 2030, achievement of a 90% reduction in syphilis incidence; a 90% reduction in gonorrhea incidence; and occurrence of 50 or fewer cases of congenital syphilis per 100,000 live births in 80% of countries, and Melanie Taylor and colleagues discuss systems for STI surveillance and monitoring of treatment resistance towards these targets [ 4 ]. Taylor and colleagues also discuss programs and criteria aimed at elimination of mother-to-child transmission of syphilis and HIV [ 5 ]. Finally, Paul Bloem and colleagues discuss HPV vaccination for control of cervical cancer and other HPV-related diseases [ 6 ] in different settings, illustrating the prospects of new interventions for STI control. Further discussion articles will appear in future issues of PLOS Medicine , and, as part of the cross-journal Collection, research papers are being published in PLOS Medicine and in other PLOS journals [ 7 ].

To accompany this Collection, we are inviting submission of reports of high-quality research studies with the potential to inform clinical practice or thinking relevant to STIs, focused on the following:

• Epidemiological studies on the incidence, prevalence, and disease burden of STIs, including emerging and re-emerging infections, mother-to-child transmission of STIs, and STIs in the context of new HIV prevention approaches;
• Molecular and genomic studies relevant to clinical advances in STI research, including antimicrobial resistance and microbiome analysis;
• Studies investigating treatment, partner notification, vaccination, behavioral, and combination interventions for STIs, with reports of randomized controlled trials particularly welcome;
• Implementation research, especially focused on interventions for STI prevention and point-of-care approaches to disease diagnosis in low- and middle-income countries, including qualitative research on issues such as stigma;
• Modelling and cost-effectiveness studies relevant to STIs, addressing prevention and treatment interventions.

Please submit your manuscript at http://journals.plos.org/plosmedicine/s/submit-now . We (NL and NB) will be the guest editors for the Collection, and successful submissions will be published, following peer review, from December 2017 onwards. Papers to be published in December should be submitted by August 11, 2017 but submissions will still be considered, and can be included in the Collection, after that date. Presubmission inquiries are not required, but we ask that you indicate your interest in this call for papers in your cover letter.

Author Contributions

• Conceptualization: NL NB RT.
• Writing – original draft: RT.
• Writing – review & editing: NL NB RT.
• 1. World Health Organization. Sexually transmitted infections factsheet. [Cited 2017 May 18]. Available from: http://www.who.int/mediacentre/factsheets/fs110/en/
• 2. World Health Organization. Global health sector strategy on sexually transmitted infections, 2016–2021. [Cited 2017 May 18]. Available from: http://www.who.int/reproductivehealth/publications/rtis/ghss-stis/en/
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Article Contents

Introduction, historical overview of clo research, biological diversity of clos, clos as emerging pathogens, clo diagnostics, clo research—where to from here.

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Twenty years of research into Chlamydia -like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae

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Alyce Taylor-Brown, Lloyd Vaughan, Gilbert Greub, Peter Timms, Adam Polkinghorne, Twenty years of research into Chlamydia -like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae , Pathogens and Disease , Volume 73, Issue 1, February 2015, Pages 1–15, https://doi.org/10.1093/femspd/ftu009

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Chlamydiae are obligate intracellular bacteria that share a unique but remarkably conserved biphasic developmental cycle that relies on a eukaryotic host cell for survival. Although the phylum was originally thought to only contain one family, the Chlamydiaceae , a total of nine families are now recognized. These so-called Chlamydia -like organisms (CLOs) are also referred to as ‘environmental chlamydiae’, as many were initially isolated from environmental sources. However, these organisms are also emerging pathogens, as many, such as Parachlamydia sp., Simkania sp. and Waddlia sp., have been associated with human disease, and others, such as Piscichlamydia sp. and Parilichlamydia sp., have been documented in association with diseases in animals. Their strict intracellular nature and the requirement for cell culture have been a confounding factor in characterizing the biology and pathogenicity of CLOs. Nevertheless, the genomes of seven CLO species have now been sequenced, providing new information on their potential ability to adapt to a wide range of hosts. As new isolation and diagnostic methods advance, we are able to further explore the richness of this phylum with further research likely to help define the true pathogenic potential of the CLOs while also providing insight into the origins of the ‘traditional’ chlamydiae.

The Chlamydiae are an assemblage of bacteria that are united by their unique developmental cycle and obligate intracellular lifestyle. Chlamydiae depend on a eukaryotic host cell for their replication, which takes place in an inclusion inside the host cell, and for their dispersal, occurring following cell lysis. The genus Chlamydia remains the most widely studied of the Chlamydiae , as until the 1990s it was thought to be the only family of the order Chlamydiales (Kahane et al. ,  1993 ; Everett, Bush and Andersen 1999 ), and is comprised of 11 species that are well-recognized pathogens of humans and animals. Chlamydia trachomatis is the leading cause of trachoma, which can lead to blindness if left untreated (Taylor et al. ,  2014 ). The same organism is also the most prevalent cause of sexually transmitted diseases worldwide (Bebear and de Barbeyrac 2009 ). Another human pathogen, C. pneumonia e, causes respiratory infections in humans, but can also cause disease in a range of animals including horse and frogs (Roulis, Polkinghorne and Timms 2013 ). Blindness and infertility caused by C. pecorum have contributed to the decline in koala populations (Polkinghorne, Hanger and Timms 2013 ) and this same pathogen can cause arthritis in cows and sheep (Fukushi and Hirai 1992 ). While some chlamydial species are specific to their hosts, others, such as C. abortus and C. psittaci , pose a zoonotic threat (Beeckman and Vanrompay 2009 ).

While our knowledge of the diversity and significance of members of the family Chlamydiaceae has been well established thanks to more than 50 years of intensive biological and medical research, studies over the last 20 years have also revealed that this family only represents the ‘tip of the iceberg’ in terms of diversity within the phylum Chlamydiae . In this, we are referring to the recent explosion of the description of eight additional families of genetically related obligate intracellular bacteria including (i) the most well documented, the Parachlamydiaceae , consisting of five genera [ Parachlamydia (Amann et al. ,  1997 ; Everett et al. ,  1999 ), Neochlamydia (Horn et al. ,  2000 ) , Protochlamydia (Collingro et al. ,  2005b ), Mesochlamydia (Corsaro et al. ,  2013 ) and Metachlamydia ( Corsaro et al. ,  2010 )] that have been detected in a wide range of hosts; (ii) Waddliaceae , a monophyletic family, containing two species, Waddlia chondrophila (Rurangirwa et al. ,  1999 ) and W. malaysiensis (Chua et al. ,  2005 ); (iii) the Simkaniaceae , containing four reported species ( Simkania negevensi s (Kahane et al. ,  1993 ), Fritschea bemisiae, F. eriococci (Thao et al. ,  2003 ; Everett et al. ,  2005 ) and the recently proposed Syngnamydia venezia (Fehr et al. ,  2013 ); (iv) the Rhabdochlamydiaceae , containing two species in the genus Rhabdochlamydia (Kostanjsek et al. ,  2004 ; Corsaro et al. ,  2007 ), as well as an additional species Renichlamydia lutjani (Corsaro and Work 2012 ) among a number of uncultured isolates; (v) the Criblamydiaceae contains two genera, Estrella and Criblamydia , both recovered from river water (Thomas, Casson and Greub 2006 ; Lienard et al. ,  2011b ); and (vi) the Piscichlamydiaceae (Draghi et al. ,  2004 ), Clavichlamydiaceae (Karlsen et al. ,  2008 ) (originally denoted as Clavochlamydiaceae ) and Parilichlamydiaceae (Stride et al. ,  2013b ), three families whose members have been isolated solely from fish.

Formally and informally, these new families are often collectively referred to as ‘ Chlamydia -like organisms’ (CLOs), ‘ Chlamydia -related bacteria’ or ‘environmental chlamydiae’. These names have historical precedence but also significant shortcomings. For example, the use of the term ‘ Chlamydia -like’ is due to the fact that the chlamydial developmental cycle is remarkably conserved across the phylum Chlamydiae and indeed similar to the Chlamydia genus. However, there are some significant biological differences between the different members of the phylum. Equally, the term ‘environmental chlamydiae’ does not do them justice, as although most of the founding isolates from each new CLO species have come from environmental samples (Kahane et al. ,  1993 ; Amann et al. ,  1997 ; Collingro et al. ,  2005b ; Thomas et al. ,  2006 ; Lienard et al. ,  2011b ), as will be discussed in this review, several species clearly do cause disease in both humans and animals. For the purpose of this review, we will nevertheless collectively refer to these organisms as CLOs.

Research efforts by an initially small but growing number of research groups around the world have revealed a previously unprecedented range of terrestrial and aquatic hosts that can be infected by CLOs, ranging from humans and warm-blooded terrestrial vertebrates to fish, reptiles, amphibians and down to eukaryotic microorganisms such as amoeba. The diverse host range of CLOs has had an unfortunate consequence for their study, as their apparently strict intracellular nature has prevented culturing for most of the species that infect ‘non-model’ organisms. As a result, many taxa still retain their candidatus status.

It has been estimated that the members of the genus Chlamydia ( Chlamydiaceae family) and the CLOs ( Parachlamydiaceae family) diverged more than 700 million years ago, from a last common ancestor that also resided within a host cell (Greub and Raoult 2003 ). This realization has meant that molecular and cell biology studies of CLOs should be viewed as an opportunity to ‘look into the window of the past’ for members of the Chlamydiaceae . Indeed, cell biology studies and a growing number of genome sequence efforts have revealed amazing new insights into the adaptations that chlamydiae have evolved to survive and subvert their diverse host cell environments.

Given the significant advances in our understanding of the diversity of CLOs since their first description nearly 20 years ago, this review will provide an opportunity to reflect on the discovery of each new CLO and examine current knowledge on their biology, phylogeny and genetics. This review will also discuss the potential role of CLOs in human and animal disease and highlight potential avenues for further exploration of these unique, ubiquitous and enigmatic organisms.

Given the relatively recent (20 years) description of CLOs, we have elected to describe the most significant events in the description and classification of the CLOs chronologically (Fig. 1 ).

Significant events in the detection, isolation and identification of CLOs over the last 20 years. Genome sequencing events are also included. Boxes and lines are coloured based on families: red, Waddliaceae ; blue, Simkaniaceae ; green, Parachlamydiaceae ; dark orange, Rhabdochlamydiaceae ; pale orange, Piscichlamydiaceae ; yellow, Parilichlamydiaceae ; pale green, Clavichlamydiaceae ; pale blue, Criblamydiaceae . Dashed lines represent events regarding the type strains of these families, while dotted lines represent events regarding other species in these families. Arrowed lines join events corresponding to the same family. Some years are included for context. PFGE, Pulsed-field gel electrophoresis; NGS, Next-generation sequencing.

Initial isolation and identification of CLOs

The first CLO to appear in the literature was a previously undescribed obligate intracellular bacterium (WSU-86-1044 T ) isolated from an aborted bovine foetus (Dilbeck et al. ,  1990 ). The organism exhibited a development cycle and two distinct morphological forms that resembled that of Chlamydiae (Kocan et al. ,  1990 ), but did not share antigenic determinants with Chlamydiae . As such, it was suggested to belong to the Rickettsiae , until further taxonomic assignment could be given.

Three years later, a cell-culture contaminant able to grow in a range of cultured cells and possessing a 5–7 day developmental cycle with morphological characteristics similar to that of Chlamydia was described as microorganism ‘Z’ (Kahane et al. ,  1993 ). In 1995, the 16S rRNA encoding gene of ‘Z’ was shown to be 83% identical to members of the Chlamydiaceae , and thus ‘Z’ was postulated to belong to a novel genus, Simkania (Kahane, Metzer and Friedman 1995 ). Human exposure to this organism was subsequently shown to be widespread (Kahane et al. ,  1998 ; Friedman et al. ,  1999 ).

Shortly following the description of ‘Z’, clinical and environmental Acanthamoeba specimens were found to be infected with organisms physiologically resembling Chlamydiae (Fritsche et al. ,  1993 ; Amann et al. ,  1997 ). Using the approach taken by Kahane et al. for ‘Z’, the authors demonstrated 86–87% 16S rDNA nucleotide similarities with other chlamydiae, and this organism was proposed as ‘Candidatus Parachlamydia acanthamoebae ’ (Everett et al. ,  1999 ). The discovery of this bacterium suggested for the first time that amoebae could potentially act as environmental reservoirs for pathogens belonging to the Chlamydiae phylum.

Amended taxonomic classification of Chlamydiae

The identification and description of multiple strains related to but distinct from members of the Chlamydiaceae prompted an amendment to the taxonomic classification system for the Chlamydiae , and this system separated ‘Z’, WSU-86 and P. acanthamoebae from the Chlamydiaceae at the family level. As such, these strains became the type species for three new families: S. negevensis as the type species for the genus Simkania and family Simkaniaceae (Everett et al. ,  1999 ; Kahane et al. ,  1999 ), W. chondrophila as the type species for the family Waddliaceae (Rurangirwa et al. ,  1999 ) and P. acanthamoebae as the type species for Parachlamydiaceae (Everett et al. ,  1999 ) (Figs 1 and 2 ).

Order Chlamydiales phylogenetic tree based on near-full-length 16S rRNA gene sequences. Sequences for the 16S rRNA gene were obtained from Genbank, NCBI. Sequences longer than 1100 bp were included for analysis. Unclassified isolates with sequences >1100 bp were also included to capture the entire chlamydial diversity. Consensus sequences of related isolates were generated prior to alignment in Geneious, and the number of sequences used for each consensus sequence is represented in square brackets. Phylogenetic tree was generated in Geneious; MrBayes tree using a HKY85 substitution model. Chlamydial families were coloured using iTOL (see the legend). Coloured squares or rectangles represent chlamydial hosts or sources which these organisms have been isolated from (see the legend). Uncoloured clades represent the diversity of the as yet uncharacterized sequences, which are mostly comprised of environmental isolates.

The year 1999 marked a watershed, with an explosion of publications describing CLOs in more depth than seen previously. The initial genetic characterization of the first CLO, S. negevenis strain ZT (Kahane et al. ,  1999 ) followed culture in Vero cells, which coincided with the culturing of W. chondrophila (WSU-86) and the description of its 16S rRNA gene sequence (Rurangirwa et al. ,  1999 ). Given the diversity of hosts and ecological niches CLOs had been isolated from, researchers were prompted to further investigate the presence of these bacteria in other amoebae and subsequently, other potential reservoirs. Additional amoebal endosymbionts were thus described and classified into the Parachlamydiaceae ( Neochlamydia sp. , Protochlamydia sp.), and, soon after their initial description, they were shown to be able to survive and replicate in both amoebal cells and human macrophages (Greub, Mege and Raoult 2003 ). Concomitantly, new species were identified from an arthropod: Ca. Rhabdochlamydia porcellionis (Kostanjsek et al. ,  2004 ), originally thought to be a Rickettsia (Radek 2000 ) and a fish, Ca. Piscichlamydia salmonicola (Draghi et al. ,  2004 ) and these formed new, distinct lineages in the Chlamydiales , with P. salmonis representing the deepest branch (Fig. 2 ). In 2005, two novel strains that were identified in cattle-associated insects were described as a new genus ( Ca. Fritschea) in the Simkaniaceae (Everett et al. , 2005 ).

Water sources have proven to be a rich source of CLO diversity, with an additional two species described in 2006, Criblamydia sequanensis (Thomas et al. ,  2006 ), and 2011, Estrella lausannensis (Lienard et al. ,  2011b ), both part of a novel family, the Criblamydiaceae . Moreover, two new members of the Parachlamydiaceae family were also retrieved from water samples (Corsaro et al. ,  2010 , 2013 ). Fish have also been found to play host to a number of CLOs, and these have been characterized over the last 10 years (genera Piscichlamydia, Clavichlamydia, Renichlamydia, Parilichlamydia, Similichlamdyia and Syngnamydia) (Draghi et al. ,  2004 ; Karlsen et al. ,  2008 ; Corsaro and Work 2012 ; Fehr et al. ,  2013 ; Stride et al. ,  2013a , b , c ).

CLOs in the genomics era

In the absence of genome sequencing data, a direct result of the non-cultivable status of most of these CLOs, 16S rRNA gene sequencing was the most widely used tool for phylogenetic analyses (Fig. 2 ), with nearly all genetic information on CLOs limited to sequencing of near full-length fragments of this ribosomal RNA gene. This changed in 2004 with the sequencing of the genome of P. amoebophila (Horn et al. ,  2004 ) which, as will be discussed later, presented the first opportunity for researchers to pry open the genetic secrets of CLOs. The genomes of the type species of Parachlamydiaceae , Waddliaceae and Simkaniaceae were subsequently characterized and analysed in 2009, 2010 and 2011 (Fig. 1 ), respectively (Greub et al. ,  2009 ; Bertelli et al. ,  2010 ; Collingro et al. ,  2011 ), and bioinformatics methods have allowed the ‘Pan-genome’ of the Chlamydiae to be investigated (Collingro et al. ,  2011 ). Mostly recently, the draft genome of Neochlamydia hartmanellae was made available (Ishida et al. ,  2014 ), making the Parachlamydiaceae the best described CLO family to date.

Growth, morphology and developmental cycle

The existence of a unique biphasic developmental cycle is common among all chlamydiae. The simplified developmental cycle begins with endocytosis of the infectious elementary bodies (EBs) into the host cell. Here, they reside within a cytoplasmic inclusion, which facilitates condensation of the DNA and conversion from the EB to the reticulate body (RB). The RBs replicate and de-differentiate back to EBs, lysing the inclusion and host cell, perpetuating the infectious cycle.

Members of the Parachlamydiaceae have a particular preference for intracellular growth in free-living amoebal hosts from environmental origins. The developmental cycle and growth of several species in the family Parachlamydiaceae have been well studied revealing that (i) developmental stages of P. acanthamoebae appear to be similar to that of other chlamydiae, (Greub and Raoult 2002 ), (ii) they can be endosymbiotic or lytic to free-living amoeba, depending on temperature (Greub, La Scola and Raoult 2003 ) and (iii) they are capable of growing in a range of cells from amoebae to human macrophages and pneumocytes (Greub et al. ,  2003 ; Casson et al. ,  2006 ) (Fig. 3 ). Additionally, a third developmental body has been described for these CLOs; the crescent bodies are reported to be an infectious stage akin to EBs and are associated with prolonged incubation time (Greub and Raoult 2002 ). The different morphology is thought to reflect a different composition of the parachlamydial cell wall compared to that of the Chlamydiaceae (Greub and Raoult 2002 ). Unique to this family, P. acanthamoebae, P. amoebophila and N. hartmanellae have also been observed outside the inclusion, residing in the cytoplasm of their amoebal hosts (Greub and Raoult 2002 ).

Electron micrographs of selected CLOs, demonstrating differences in cell morphology of EBs and RBs. Parachlamydia acanthamoeba (a) in A. polyphaga (15 000 × magnification), W. chondrophila (b) within a macrophage at 16 h post-infection (4500 × magnification), Ca. Clavichlamydia salmonicola (c) and Ca. Piscichlamydia salmonicola (d) in gill epithelial cells of Brown trout, E. lausannensis (e) within Acanthamoeba commandonii at 48 h post-infection (4500 × magnification) and Ca. Syngnamydia venezia (f) in gill epithelial cells of broad-nosed pipefish. Scale bars are shown in individual images. Note the diversity in EB and RB morphologies among different CLOs and the number of chlamydial cells in each inclusion.

Cell biology studies have revealed that (i) W. chondrophila can proliferate within human macrophages and induce cell lysis (Goy and Greub 2009 ) (Fig. 3 ), rapidly evading host cell endocytic pathways (Croxatto and Greub 2010 ), and (ii) host cell mitochondria are recruited to the Waddlia -containing vacuoles along with the endoplasmic reticulum (ER), suggestive of a requirement of these organelles in Waddlia intracellular replication (Croxatto and Greub 2010 ). Interestingly, no cytopathic effect was observed in endometrial cells, but this appears to be replaced by the development of aberrant bodies (Kebbi-Beghdadi, Cisse and Greub 2011 ), a biological phenomenon that was also observed when Waddlia bacteria were treated with penicillin derivatives, suggesting that chlamydial peptidoglycan is important for bacterial division (Jacquier et al. ,  2014 ). Besides amoebal cells, W. chondrophila replicates well in fish epithelial and gonad cell lines exhibiting a 2–6 day lifecycle (Kebbi-Beghdadi, Batista and Greub 2011 ), and is also capable of replicating in ovine trophoblast cells, where it elicits an inflammatory immune response (Wheelhouse et al. ,  2014 ), as well as Vero cells and pneumocytes (Kebbi-Beghdadi et al. ,  2011 ). Studies such as these provide strong evidence for a pathogenic role of these bacteria in animals and humans.

Similar to W. chondrophila , S. negevensis interacts with the infected host cell ER forming a single vacuolar system between the bacteria-containing vacuole and this organelle (Mehlitz et al. ,  2014 ). This process appears to be directly regulated by the bacteria's interference of stress signalling pathways of the ER. Simkania negevensis has been successfully cultured in a range of epithelial and endothelial cell lines (Kahane et al. ,  1999 , 2007 ), and demonstrates a significantly longer developmental cycle time than the Chlamydiaceae and other CLOs, reaching a growth plateau at 2–3 days, while the cytopathic effect lasts for 12 or more days (Kahane et al. ,  1999 ). Kahane, Dvoskin and Friedman ( 2008 ) have also shown transmission from Simkania -infected Acanthamoeba to a macrophage cell line, which resulted in death of the amoebae, highlighting a potential route of transmission for these CLOs. In contrast to P. amoebophila , S. negevensis survives encystment (Kahane et al. ,  2001 ), a mechanism likely to assist survival and later dissemination. Another member of the Simkaniaceae , S. venezia has an ovular EB shape and shares a rippled outer membrane with other Simkaniaceae species (Fehr et al. ,  2013 ) (Fig. 3 ).

Estrella lausannensis and C. sequanensis have been studied using amoebal co-culture (Thomas et al. ,  2006 ; Lienard et al. ,  2011b ). Estrella lausannensis , the first member of the Chlamydiales to be cultured in Dictyostelium discoideum , a genetically tractable soil amoebae (Lienard et al. ,  2011b ), potentially provides a novel model system for studying CLO biology, given the huge numbers of mutants available. Both species exhibit star-like EBs (Fig. 3 ), but this has been since shown to be an artefact of fixative methods used (Rusconi et al. ,  2013 ). Neither species has been successfully cultured in a mammalian cell line, but E. lausennensis is capable of replicating in fish cell lines, albeit poorly (Kebbi-Beghdadi et al. ,  2011 ).

While most CLOs exhibit reasonably spherical EBs, members of the Rhabdochlamydiaceae possess distinct rod-shaped EBs that are contained by a five-layer cell wall and include translucent oblong structures in their cytoplasm (Kostanjsek et al. ,  2004 ; Corsaro et al. ,  2007 ). Similar to other CLOs, these species exhibit an additional intermediate body.

Host range and phylogeny

Following the initial isolation of Simkania sp. from cell culture contaminants, this species has been isolated from hosts as diverse as humans (Kahane et al. ,  1998 ; Friedman et al. ,  1999 ; Jelocnik et al. ,  2013 ), amoebae (Kahane et al. ,  2001 ) and reptiles (Soldati et al. ,  2004 ). Two strains of an additional candidatus genera, Ca. Fritschea spp. have been isolated from insects (Thao et al. , 2003 ; Everett et al. ,  2005 ), while water sources, including drinking water, have also been described as reservoirs for Simkania spp. (Kahane et al. ,  2004 , 2007 ). Expanding the host range of this family even further, an endosymbiont of a deuterosome has been described (Israelsson 2007 ), as has a novel agent of epitheliocystis in a broad-nosed pipefish (Fehr et al. ,  2013 ) (Fig. 2 ). The varied host range of this family offers a myriad of avenues for further exploration of this family as pathogens of a range of hosts.

Members of the Parachlamydiaceae appear to be ubiquitous among amoebae, with amoebal hosts including Acanthamoeba castellanii and A. polyphaga (Greub and Raoult 2002 ). In the environment, Parachlamydiaceae -containing amoebae have been retrieved from activated sludge (Collingro et al. ,  2005a ), hot springs (Sampo et al. ,  2014 ) and soil (Fritsche et al. ,  1993 ), while clinical specimens such as corneal and nasal samples have been found to harbour Parachlamydia spp. (Fritsche et al. ,  1993 ; Corsaro, Valassina and Venditti 2003 ). Two members of the Parachlamydiaceae , Ca. Metachlamydia lacustris (Corsaro et al. ,  2010 ) and Ca. Mesochlamydia elodeae (Corsaro et al. ,  2013 ) were initially isolated from aquatic amoebae and demonstrate high host specificity in contrast to other Parachlamydiaceae , which can grow in Acanthamoeba species. Interestingly, these species co-inhabit the amoebae with members of either alpha-proteobacteria or beta-proteobacteria (Corsaro et al. ,  2010 ), and such close association could offer opportunities for genetic exchange.

Conversely, the taxonomic diversity of Chlamydiae that infect fish is a reflection of the taxonomic diversity in the hosts. Two candidatus families, Piscichlamydiaceae and Parilichlamydiaceae , represent the most distantly related members of the Chlamydiae phylum (Fig. 2 ). Interestingly, Ca. Clavichlamydia sp., another fish pathogen, is more closely related to the Chlamydiaceae than the above-mentioned families. The diversity of chlamydiae isolated from fish has also extended to the Simkaniaceae and Rhabdochlamydiaceae (Corsaro and Work 2012 ; Fehr et al. ,  2013 ). The initial proposal that each fish species may harbour a unique lineage is likely to reflect undersampling, as Piscichlamydia and Clavichlamydia were found together in the same brown trout (Schmidt-Posthaus et al. ,  2012 ). The ongoing identification of novel CLOs in fish suggests that we are only just beginning to appreciate the full host range of aquatic CLOs (Stride, Polkinghome and Nowak 2014 ), and, with an estimated 26 000 fish species worldwide, the potential for novel CLOs is indeed vast.

Finally, a large biodiversity of CLOs has been detected in ticks from Switzerland and Algeria (Croxatto et al. ,  2014 ). A possible transmission of these bacteria by ticks however remains to be confirmed.

DNA sequencing and bioinformatics to illustrate the diversity of CLOs

Beyond the use of 16S rRNA sequencing as the first tool for the characterization, classification and phylogenetic analysis of the recently described CLOs, researchers are beginning to make use of the ever-expanding metagenomic and amplicon datasets that are available in diverse databases to discover new CLOs. Recently, Lagkouvardos et al. ( 2014 ) used advanced, high stringency bioinformatic analyses to interrogate over 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences found in diverse databases. Using near-full-length sequences and a conservative clustering approach, 17 family-level lineages supported by two or more isolates were identified, and this number increased to 28 when considering families represented by only one isolate. Similar analysis of the V4–V6 region of the 16S rRNA gene in over 12 000 amplicons resulted in 181 putative families each supported by at least two isolates. At the species level, a potential 1161–2276 OTUs were represented, depending on the bioinformatic method used (Lagkouvardos et al. ,  2014 ).

Ecological analyses revealed the majority of OTUs belonging to marine and freshwater environments and only a small proportion arising from terrestrial environments (2%) (Lagkouvardos et al. ,  2014 ). As exciting as the prospect of potentially 200 or so chlamydial families is, real progress will only ensue when we utilize this information to answer biological, genetic, ecological and evolutionary questions wherever possible. Considerations to be made when novel sequences are isolated include (i) what are the health implications for humans or animals?, (ii) is there a zoonotic risk associated with this isolation? and (iii) could this isolation represent a potential reservoir or vector? Given the isolation of a vast number of CLOs from environmental sources (water, soil) and traditional vectors (protozoa, insects, bats), there is no doubt that these sources have the capacity to act as reservoirs and/or vectors of potentially ‘environmental-pathogenic’ chlamydiae.

While researchers are largely restricted by the uncultivable status of most CLOs, in its absence, the advent of next-generation sequencing (NGS) technologies has not only revolutionized our understanding of the biology of both member species in the Chlamydiaceae but also CLOs (Bachmann et al. ,  2014 ). Members of the Chlamydiaceae are notable for their high degree of genomic synteny (Stephens et al. ,  1998 ; Read et al. ,  2000 ). On the contrary, little to no synteny is observed within the Parachlamydiaceae , for which the genomes of four species are available, and between the Simkaniaceae , Parachlamydiaceae and Waddliaceae when compared with the Chlamydiaceae (Collingro et al. ,  2011 ). This lack of synteny probably reflects the evolutionary distance between these families and their different evolutionary trajectories as symbionts of protozoa and pathogens of animals (Horn et al. ,  2004 ; Nunes and Gomes 2014 ).

CLOs possess uncharacteristically large genomes for intracellular bacteria (Table 1 ). Yet, despite the increase in genome size, the lengths of the coding regions and proportion of coding regions are rather conserved, with the notable exception of P. amoebophila which encodes more than 50 large leucine-rich proteins, which evolved by serial duplication and include some proteins exhibiting significant similarity with mammalian Nod (nucleotide-binding oligomerization domain) proteins (Eugster, Roten and Greub 2007 ). These large genomes likely reflect the different ecology of CLOs, which may use amoebae as a melting pot for genetic transfer (Greub 2009 ). Like their Chlamydiaceae brethren, over half of the CDSs in the CLO genomes have an as yet unknown function. Collingro et al. ( 2011 ) identified 560 ‘core genes’ common across the Chlamydiaceae and the CLOs with genomes available. More recently, similar analysis identified members of 304 protein families to belong to the ‘core’ gene set of the Chlamydiae (Psomopoulos et al. ,  2012 ), while larger genomes correlated with a higher number of unique genes (Table 1 ). Among the conserved genes, many are housekeeping genes that are presumably involved in the highly conserved intracellular lifestyle and unique developmental cycle (Collingro et al. ,  2011 ), as well as basic genetic processing roles such as transcription and translation (Psomopoulos et al. ,  2012 ). Importantly, the core gene set also contains members of all 100 clusters of orthologues, which are conserved among all intracellular bacteria. Additional species-specific proteins are predicted to be involved in transport and metabolism, and this likely correlates to a less strict or more recent obligate association with the host, and/or a vital requirement to adapt to changing conditions (Nunes and Gomes 2014 ).

Features of sequenced genomes of CLOs compared to representatives of the Chlamydiaceae . Note the significant difference in genome size of the CLOs, coupled with the increased number of unique genes.

∧ Present in some other strains of C. pneumoniae

Np, Not present; Nr, Not reported

The type three secretion system (T3SS) is a gene cassette common to several Gram-negative bacteria that confers the ability to sense eukaryotic cells and secretes effector proteins in order to fuse with the host cell membrane, and thus infect the cell via a needle-like injection mechanism. A high number of structural and chaperone components of the T3SS are conserved between the CLOs and the Chlamydiaceae , including inner membrane proteins and needle formation proteins (Bertelli et al. ,  2010 ; Collingro et al. ,  2011 ). However, the Chlamydiaceae genomes also encode some flagellar proteins that are missing from the CLO genomes which could have implications for intracellular survival (Collingro et al. ,  2011 ). Despite many structural components of the T3SS being encoded by the CLOs, many effectors recognized in the Chlamydiaceae are not. Of particular interest are the Inc proteins (inclusion membrane proteins), which have virtually no homologues in other microorganisms. Just three Inc proteins are conserved throughout the Chlamydiae (Collingro et al. ,  2011 ) and the differences in sequence homology could indicate differing degrees of virulence and/or success at infecting a range of cell types. Additionally, TARP, a translocated actin-recruiting protein, which is translocated by the T3SS and thus implicated in chlamydial invasion in the Chlamydiaceae (Lane et al. ,  2008 ), is absent from the CLO genomes, suggesting a host cell entry mechanism distinct from that of the Chlamydiaceae . Taken together, the conservation of T3SS structural proteins coupled with the lack of homologous effector proteins indicates that all chlamydiae share some mechanisms for host cell entry but differ greatly in their host survival mechanisms, perhaps reflecting the varying pressures placed on these organisms by their diverse range of host cells.

The chlamydial outer membrane is crucial for host cell adhesion and invasion. The Chlamydiaceae possess a unique outer membrane complex, the main component of which is the major outer membrane protein (MOMP). Simkania encodes 35 MOMP-like proteins, while Waddlia encodes 11 (Bertelli et al. ,  2010 ; Collingro et al. ,  2011 ). Parachlamydia and Neochlamydia are almost devoid of MOMP-like proteins, while Protochlamydia appears to have replaced them with structurally similar porin proteins (Heinz et al. ,  2009 , 2010 ). Similarly, a lower number of Pmps are encoded in all CLO genomes (Bertelli et al. ,  2010 ; Collingro et al. ,  2011 ; Ishida et al. ,  2014 ). Despite low-sequence homologies, structural similarities show that although the outer membrane proteins are a highly diverse group of proteins, they are nonetheless conserved throughout the Chlamydiae . This again reflects the previously acknowledged versatility of the environmental chlamydiae and their hosts compared to the Chlamydiaceae , and can probably account for some of the differences seen in the EB and RB morphology.

Homologous of a number of Chlamydiaceae virulence factors are encoded by Simkaniaceae , Parachlamydiaceae and Waddliaceae (Collingro et al. ,  2011 ). The Chlamydia protease-like activity factor, CPAF, previously thought to be common to all Chlamydiae , is missing from only the Simkania genome. As it is thought to interfere with major histocompatibility complex expression and has roles in intracellular vacuole formation (Bednar et al. ,  2011 ), its absence could signify a reduced pathogenicity of Simkania . However, two proteases homologous to proteins present in CPAF are encoded by Simkania ; whether these proteins could compensate for CPAF remains unknown but this evidence would support Simkania as a pathogen.

A sizeable number of proteins containing eukaryotic domains are seen in the Simkaniaceae , Parachlamydiaceae and Waddliaceae genomes. In other intracellular bacteria, the presence of eukaryotic domains has been associated with intracellular proliferation in protozoan and mammalian hosts (Habyarimana et al. ,  2008 ), offering more clues to pathogenesis mechanisms of these organisms.

The expanding number of available chlamydial sequences has allowed researchers to explore the evolutionary history of the Chlamydiae by tracing the acquisition of particular genes. Some authors suggest that the altered gene order seen in CLOs reflects a gene reorganization following divergence of environmental and pathogenic chlamydiae. Distribution of the CDSs in the P. amoebophila UWE25 genome suggests gene acquisition over a number of lateral gene transfer events, most of which occurred prior to the divergence from pathogenic chlamydiae (Horn et al. , 2004 ). Gene exchanges may have been facilitated by the presence of a DNA conjugative system encoded in a genomic island (Pam100G) on the chromosome of P. amoebophila (Greub et al. , 2004 ). Similar analysis also suggests that the last common ancestor was intracellular but less dependent on host metabolism (Horn et al. , 2004 ). Indeed, some CLOs such as W. chondrophila encode as many as 12 different amino acids (Bertelli et al. , 2010 ).

A major driver of research interest in CLOs has been the repeated association between these bacteria and a range of different diseases in humans and animals, highlighting their potential as emerging bacterial pathogens but also illustrating that direct evidence for the majority of CLOs as pathogens is lacking (Table 2 ).

CLOs are emerging pathogens of a range of terrestrial and aquatic hosts. CLO diseases most commonly involve epithelial cells. Different diagnostic methods are available for different CLOs. Diagnostic methods: PCR, Polymerase chain reaction (followed by amplicon sequencing), ELISA, Enzyme linked immunosorbent assay; TEM, Transmission electron microscopy, ISH, In situ hybridization; IHC, Immunohistochemistry; MIF, Microimmunoflourescence; HE, Histopathological examination; WB, Western blot; IEM, Immunoelectron microscopy.

S. negevensis : an agent of respiratory illness

Following the initial isolation of Simkania ‘Z’ from cell culture contaminants, this CLO has been associated with respiratory disease in humans by both serological and molecular methods. Detection of IgG antibodies to S. negevensis indicated a previous infection in 37–62% of pneumonia patients in two separate cohorts, with a small proportion of those indicating a current acute infection (Lieberman et al. ,  1997 ; Friedman et al. ,  2006 ). Kahane et al. ( 1998 ) observed a 25% prevalence rate in bronchiolitis patients by culture and/or PCR. Further, the drinking water was postulated to be the source of infection in a cohort of children with pneumonia, based on immunoassay and culture, as well as S. negevensis 16S rRNA sequence amplification from 76% of nasopharyngeal swabs and corresponding drinking water (Kahane et al. ,  2007 ). Drinking water supplies and wastewater in Israel also tested positive for S. negevensis antigens, often in association with amoebic antigens (Kahane et al. ,  2004 ). Other studies have found a range of prevalence rates in healthy populations (Friedman et al. ,  1999 ; Husain et al. ,  2007 ), suggesting the potential opportunistic nature of this organism. In vitro studies have also demonstrated successful Simkania growth in several epithelial cell types in which an inflammatory response was also observed (Kahane et al. ,  2007 ). More recently, S. negevensis antibodies were also detected in association with gastrointestinal symptoms (Donati et al. ,  2013 ).

Parachlamydia spp: mucosal pathogens in humans and animals

The pathogenicity of P. acanthamoebae was first suspected when the bacteria was isolated from an amoeba recovered from the water of a humidifier implied in an outbreak of fever (Birtles et al. ,  1997 ). Since then, a growing body of evidence has suggested that these CLOs may be pathogenic to humans and a variety of animal hosts. Like S. negevensis , in humans, molecular and serological studies have linked infections of Parachlamydia spp. to respiratory disease (Greub 2009 ). Additional reports of this bacterium in respiratory samples have backed up speculation of this bacterium as a respiratory pathogen (Greub et al. ,  2003 ; Lamoth et al. ,  2011 ) (Table 2 ).

The permissivity of pneumocytes, lung fibroblasts and macrophages to P. acanthamoebae (Greub et al. ,  2003 ; Casson et al. ,  2006 ) has also been demonstrated, adding support for the pathogenic potential of these bacteria and also indicating a potential route of dissemination through the body. Further strengthening the argument for Parachlamydia as a respiratory pathogen, both a murine and bovine model of parachlamydial respiratory disease (Casson et al. ,  2008 ; Lohr et al. ,  2014 ) have been established, fulfilling the third and fourth of Koch's postulates.

There is a growing body of evidence to suggest that Parachlamydia spp. may also be linked to adverse pregnancy outcomes in ruminants (Borel et al. ,  2007 ; Barkallah et al. ,  2014 ) (Table 2 ) and, moreover, in humans (Baud et al. ,  2007 ). The prevalence of Parachlamydia spp. associated with abortion in cattle has been studied extensively in Europe, with initial Swiss studies showing prevalence of over 60% in placental lesions by immunohistochemistry (Borel et al. ,  2007 ), while further studies have demonstrated slightly lower prevalence rates (Ruhl et al. ,  2008 , 2009 ). In Scotland, prevalence has been reported at around 20%, with a higher prevalence by PCR detection (Wheelhouse et al. ,  2012 ). Blumer et al. ( 2011 ) also found the presence of CLOs as mixed infections with Chlamydiaceae or other CLOs in ruminants.

Considering Parachlamydia has been isolated from both ruminant foetal tissue and human respiratory samples, this bacterium potentially poses a zoonotic threat, particularly in individuals who have contact with livestock. Interestingly, in a study of healthy individuals, detection of Parachlamydia sp. was associated with interaction with farm animals (Baud et al. ,  2009 ), supporting a potential role of this bacteria as a zoonotic agent. Further, Parachlamydia and other CLOs have been isolated from cattle drinking water (Wheelhouse et al. ,  2011 ), suggesting a possible source of infection and mode of transmission for this pathogen to cattle and potentially humans. Maternal-foetal transmission of Parachlamydia has also been demonstrated in a case study and was postulated to be a result of zoonotic transmission (Baud et al. ,  2009 ).

W . chondrophila : an abortifacient

As previously mentioned, W. chondrophila was originally isolated from an aborted bovine foetus (Dilbeck et al. ,  1990 ) and has since been described as an abortigenic agent in a number of studies on adverse pregnancy outcomes in cattle throughout Europe, using both molecular and serological methods (Dilbeck-Robertson et al. ,  2003 ; Borel et al. ,  2007 ) (Table 2 ). The disparity between reports from different authors highlights the prospect of an unknown determinant of susceptibility to infection and/or progression to disease.

In humans, W. chondrophila has been reported in association with miscarriage and other adverse pregnancy outcomes in up to 30% of cohorts studied (Baud et al. ,  2007 , 2014 ). Waddlia chondrophilawas also recently shown to multiply inside endometrial cells (Kebbi-Beghdadi et al. ,  2011 ). At 96 h post-infection, the bacteria transform into persistent enlarged aberrant bodies that could be linked to recurrent episodes of miscarriage. Studies that show some evidence of acute or previous Waddlia infection in women who have miscarried suggests a possible reactivation of a latent asymptomatic infection, further strengthening this argument (Baud et al. ,  2014 ). While initial studies focused on cervicovaginal swabs, a recent study detected W. chondrophila in a placenta from miscarriage by both PCR and IHC (Baud et al. ,  2011 ), providing convincing evidence of a pathogenic role of Waddlia in abortion. What does remain to be established is the route of entry and transmission of this pathogen, as well as the underlying mechanism of pathogenesis. Studies of well water suggest that this could be one potential reservoir (Codony et al. ,  2012 ), while other authors hypothesize that routes of entry could be sexual transmission or via the bloodstream following a respiratory infection (Baud et al. ,  2014 ), or acquired following contact with animals (Baud et al. ,  2007 ).

Piscichlamydia, Parilichlamydia, Similichlamydia, Clavichlamydia, Actinochlamydia : epitheliocystis agents in wild and cultured fish

The term epitheliocystis was coined after cyst-like inclusions were observed in gill epithelial cells of the Bluegill (Hoffman et al. ,  1969 ), though this phenomenon was originally reported as ‘Mucophilosis’ (Plehn 1920 ). To date, epitheliocystis has been reported from over 90 species of fish globally (Stride et al. ,  2014 ) (Table 2 ), including both wild and cultured fish from marine and freshwater environments. Initially, it was believed that the same aetiological agent caused epitheliocystis in all fish species, but as early as 1977 it was recognized that these agents demonstrated a high degree of host specificity (Zachary and Paperna 1977 ). Fredericks and Relman's postulates (Bebear and de Barbeyrac 2009 ) have been fulfilled (as opposed to Koch's, as no in vitro culture system is available for these organisms) for a number of CLOs. Candidatus Piscichlamydia salmonis was the first to be comprehensively described as the epitheliocystis agent in farmed Atlantic salmon (Draghi et al. ,  2004 ). Candidatus Clavichlamydia salmonicola has been detected in Atlantic salmon and Brown trout species, both species belonging to the same genus Salmo (Karlsen et al. ,  2008 ; Mitchell et al. ,  2010 ; Schmidt-Posthaus et al. ,  2012 ), while Ca. Parilichlamydia carangidicola and Ca. Actinochlamydia clariae were independently proposed as founding species of a novel family causing disease in Yellowtail kingfish and African catfish, respectively (Steigen et al. ,  2013 ; Stride et al. ,  2013b ). An additional CLO, Renichlamydia lutjani , was identified in a blue-striped snapper from Hawaii (Corsaro and Work 2012 ) and its role as a purely epitheliocystis agent is questionable due to its detection in inner organs as opposed to the gills or skin. On the other hand, few epitheliocystis studies have included internal organs in the analysis, an aspect needing closer attention in future as this would have implications for disease progression and dissemination. In addition to these characterized organisms, short Chlamydiales 16S rRNA sequences have also been detected in association with cases of epitheliocystis in a diverse range of fish species, including Leopard shark (Polkinghorne et al. ,  2010 ), Eagle ray (Camus et al. ,  2013 ), Leafy sea dragon and Silver perch (Meijer et al. ,  2006 ). For all of these agents but also for the species proposed in these novel CLO families, virtually nothing is known about their transmission and acquisition, and whether the utilization of a reservoir such as amoebae could explain the diverse, widespread nature of these agents and disease.

There have been two major challenges in demonstrating that members of the CLO group can cause disease in humans and animals. Firstly, they are very difficult to grow in vitro and secondly, species-specific reagents are generally lacking for most CLOs, raising questions over the interpretation of diagnostic results in screening surveys. Practically, cell culture is not routinely available in diagnostic laboratories. It may, however, prove useful to isolate new species, particularly if they involve the use of a variety of cell lines including different types of free-living amoeba. Indeed, free-living amoebae represent an ideal tool for culturing strict intracellular microbes when applicable (Kebbi-Beghdadi and Greub 2014 ), and this method has been used successfully to not only isolate a number of these organisms but also to study their biology and interactions with their hosts (Horn et al. ,  2000 ; Thomas et al. ,  2006 ; Lienard et al. ,  2011b ).

PCR is now the main approach used in most clinical diagnostic laboratories for the diagnosis of infections due to viruses and/or strict intracellular bacteria. 16S rRNA PCR assays were widely used during the first years of CLO research (Kahane et al. ,  1993 ; Corsaro, Venditti and Valassina 2002 ). Pan- Chlamydiales primer sets based on the 16S rRNA gene have proven successful for detecting chlamydial DNA in both clinical and environmental samples (Everett, Hornung and Andersen 1999 ; Ossewaarde and Meijer 1999 ). These PCRs were often not very specific or sensitive, the latter due to a requirement to amplify > 500 bp gene fragments and the need to assess amplification by agarose gel electrophoresis (Corsaro and Greub 2006 ). Nested PCR strategies have been utilized to increase the specificity of these PCRs. Recently, these first generation PCRs have been replaced by several real-time PCRs targeting 16S or 23S rRNA, which have proven to be more specific and more sensitive, detecting fewer than five genome copies (Corsaro and Greub 2006 ). To increase species specificity, additional targets have also been used including the gene encoding the ATP-ADP translocase, which is present only in Rickettsiales and Chlamydiales (Greub and Raoult 2003 ) and the secY gene (Lienard et al. ,  2011b ). Other authors have opted for PCR assays targeting characteristic indel signatures in essential genes (Griffiths, Petrich and Gupta 2005 ), which could have diagnostic applications. Nevertheless, since the diversity of Chlamydiales is still largely unknown, the development of a pan- Chlamydiales quantitative PCR (Lienard et al. ,  2011a ) represents an important tool for screening clinical and environmental samples for CLOs.

Apart from molecular diagnosis, serology still remains useful not only for epidemiological purposes but also to assess the pathogenic potential of these novel CLOs. Immunofluorescence is generally considered as the gold standard for the Chlamydiaceae (Dowell et al. ,  2001 ) with cutoff for positivity of 1/64 for IgG and 1/32 for IgM (Corsaro and Greub 2006 ). Western-blotting, also not amenable for large-scale testing, has been used to confirm positive immunofluorescence (Greub et al. ,  2003 ; Baud et al. ,  2007 ), and this should ideally be performed to confirm specificity. However, there is a clear need for species-specific ELISA tests for CLOs. Early studies on Simkania prevalence applied an ELISA to a cohort of pneumonia patients and successfully showed seropositivity (Friedman et al. ,  1999 ). Such a test is not yet available for all the CLOs, although for both Parachlamydia and Waddlia , immunogenic proteins have been identified through genome sequencing that might be used to develop a specific and sensitive ELISA (Greub et al. ,  2009 ; Kebbi-Beghdadi et al. ,  2012 ). Perhaps not surprisingly, there is remarkably little cross-reactivity between members of different family level lineages when immunofluorescence is performed (Casson, Entenza and Greub 2007 ). The same is true for immunohistochemistry, with antibodies raised against CLOs appearing to be highly specific (Borel et al. ,  2007 ; Casson et al. ,  2007 ). Immunofluorescence alongside in situ hybridization of short CLO-specific sequences is of crucial importance for demonstrating the presence of suspected CLO pathogens in lesions and thus confirming their suspected pathogenic role.

As we rapidly approach the 20th anniversary of the identification of the first CLO, Simkania , it is staggering to think how research into CLOs has changed our understanding of the genetic diversity, host range and biology of this unique phylum of obligate intracellular parasites.

In terms of where CLO research should be headed, a review of the CLO literature quickly reveals that there is a sampling bias toward environmental sources. Primary targets for expanded screening for CLOs should potentially focus on the estimated 26 000 species of marine and fresh water vertebrates, the immediate precursors to land animals. This area is clearly under-represented, and could be key in understanding the evolutionary history of these enigmatic organisms. This largest group of vertebrate hosts has well developed innate and humoral immune systems and, as such, likely provided the immediate training ground for the evolution of many Chlamydiaceae and their specialization for air-breathing land animals.

The sequencing of the full genomes of several members of the current families has added significant credibility to this group of organisms. A next step would be to characterize a selection of CLOs at the strain level, as has been done for numerous species in the Chlamydiaceae (Bachmann et al. ,  2014 ). Applying a comparative genomics approach to CLO strains isolated from diverse environments, hosts and reservoirs would provide further clues to the acquisition and loss of genes in response to adaptation to a diverse range of environments, with the common thread being the restrictive intracellular environment. While our ability to sequence the genomes of non-cultivable CLOs makes this prospect challenging, recent breakthroughs in culture-independent genome analysis of human C. trachomatis strains may hold promise to overcome these limitations (Seth-Smith et al. ,  2013a , b ). In doing so, genome analysis could also inform novel approaches to cultivate these bacteria with their enhanced metabolic capabilities potentially giving researchers opportunities to establish the first host-free culture methods for chlamydiae. In addition, some CLOs may prove to be interesting model organisms for studying chlamydial biology. In this regard, Waddlia are particularly promising since they replicate faster and exhibit slightly larger bacterial cells than Chlamydiaceae and grow in amoebae such as D. discoideum , a genetically tractable eukaryote (Tosetti, Croxatto and Greub 2014 ).

As already mentioned, there is a clear need to develop better species-specific detection and diagnostic methods, especially for serology. One significant step forward would be the development of novel PCR targets for each group. There is a challenge here though, as first it will be necessary to uncover their true biodiversity (and hence sequence diversity), before it will be possible to develop accurate diagnostic tools that may be used in large-scale epidemiological studies. However, the recent availability of a pan- Chlamydiales broad-range PCR targeting the 16 rRNA encoding gene (Lienard et al. ,  2011a ) has at least the advantage to more easily tackle the whole diversity present in a given sample, even if at a low copy number.

While research efforts begin to better characterize the farthest reaches of this phylum, it is inevitable that much of the field's attention will remain on the CLOs’ namesakes, the members of the Chlamydiaceae . With the advent of genome sequencing and genetic manipulation technologies (Wang et al. ,  2011 ; Humphrys et al. ,  2013 ), researchers are beginning to unravel how members of the Chlamydiaceae interact with and manipulate their intracellular niche. Nevertheless, major questions still remain over what are the exact determinants of tissue tropism or host specificity for many of these chlamydial species. While some question marks remain over the pathogenic potential of CLOs, the fact that they are the closest relatives of the ‘traditional’ chlamydiae and that the host range of these organisms is significantly expanded makes them a tantalizing target for such studies. In doing so, research into CLOs will undoubtedly continue to revolutionize our understanding of all members of this biologically fascinating bacterial phylum.

Conflict of interest statement. None declared.

Amann R Springer N Schonhuber W et al.  Obligate intracellular bacterial parasites of acanthamoebae related to Chlamydia spp Appl Environ Microb 1997 63 115 21

Google Scholar

Bachmann NL Fraser TA Bertelli C et al.  Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum BMC Genomics 2014 15 667

Barkallah M Gharbi Y Hassena AB et al.  Survey of infectious etiologies of bovine abortion during mid- to late gestation in dairy herds PLoS One 2014 9 e91549

Baud D Goy G Gerber S et al.  Evidence of maternal-fetal transmission of Parachlamydia acanthamoebae Emerg Infect Dis 2009 15 120 1

Baud D Goy G Osterheld MC et al.  Waddlia chondrophila : from bovine abortion to human miscarriage Clin Infect Dis 2011 52 1469 71

Baud D Goy G Osterheld MC et al.  Role of Waddlia chondrophila placental infection in miscarriage Emerg Infect Dis 2014 20 460 4

Baud D Kebbi C Kulling JP et al.  Seroprevalence of different Chlamydia -like organisms in an asymptomatic population Clin Microbiol Infect 2009 15 Suppl 2 213 5

Baud D Thomas V Arafa A et al.  Waddlia chondrophila , a potential agent of human fetal death Emerg Infect Dis 2007 13 1239 43

Bebear C de Barbeyrac B Genital Chlamydia trachomatis infections Clin Microbiol Infect 2009 15 4 10

Bednar MM Jorgensen I Valdivia RH et al.  Chlamydia protease-like activity factor (CPAF): characterization of proteolysis activity in vitro and development of a nanomolar affinity CPAF zymogen-derived inhibitor Biochemistry 2011 50 7441 3

Beeckman DS Vanrompay DC Zoonotic Chlamydophila psittaci infections from a clinical perspective Clin Microbiol Infect 2009 15 11 7

Bertelli C Collyn F Croxatto A et al.  The Waddlia genome: a window into chlamydial biology PLoS One 2010 5 e10890

Birtles RJ Rowbotham TJ Storey C et al.  Chlamydia -like obligate parasite of free-living amoebae Lancet 1997 349 925 6

Blumer S Greub G Waldvogel A et al.  Waddlia, Parachlamydia and Chlamydiaceae in bovine abortion Vet Microbiol 2011 152 385 93

Borel N Ruhl S Casson N et al.  Parachlamydia spp . and related Chlamydia -like organisms and bovine abortion Emerg Infect Dis 2007 13 1904 7

Camus A Soto E Berliner A et al.  Epitheliocystis hyperinfection in captive spotted eagle rays Aetobatus narinari associated with a novel Chlamydiales 16S rDNA signature sequence Dis Aquat Organ 2013 104 13 21

Casson N Entenza JM Borel N et al.  Murine model of pneumonia caused by Parachlamydia acanthamoebae Microb Pathogenesis 2008 45 92 7

Casson N Entenza JM Greub G Serological cross-reactivity between different Chlamydia -like organisms J Clin Microbiol 2007 45 234 6

Casson N Medico N Bille J et al.  Parachlamydia acanthamoebae enters and multiplies within pneumocytes and lung fibroblasts Microbes Infect 2006 8 1294 300

Chua PK Corkill JE Hooi PS et al.  Isolation of Waddlia malaysiensis , a novel intracellular bacterium, from fruit bat ( Eonycteris spelaea ) Emerg Infect Dis 2005 11 271 7

Codony F Fittipaldi M Lopez E et al.  Well water as a possible source of Waddlia chondrophila infections Microbes Environ 2012 27 529 32

Collingro A Poppert S Heinz E et al.  Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp Microbiology 2005a 151 301 9

Collingro A Tischler P Weinmaier T et al.  Unity in variety–the pan-genome of the Chlamydiae Mol Biol Evol 2011 28 3253 70

Collingro A Toenshoff ER Taylor MW et al.  ‘ Candidatus Protochlamydia amoebophila’, an endosymbiont of Acanthamoeba spp Int J Syst Evol Micr 2005b 55 1863 6

Corsaro D Greub G Pathogenic potential of novel Chlamydiae and diagnostic approaches to infections due to these obligate intracellular bacteria Clin Microbiol Rev 2006 19 283 97

Corsaro D Michel R Walochnik J et al.  Saccamoeba lacustris , sp. nov. (Amoebozoa: Lobosea: Hartmannellidae), a new lobose amoeba, parasitized by the novel chlamydia ‘ Candidatus Metachlamydia lacustris’ ( Chlamydiae: Parachlamydiaceae ) Eur J Protistol 2010 46 86 95

Corsaro D Muller KD Wingender J et al.  ‘ Candidatus Mesochlamydia elodeae’ ( Chlamydiae: Parachlamydiaceae ), a novel chlamydia parasite of free-living amoebae Parasitol Res 2013 112 829 38

Corsaro D Thomas V Goy G et al.  ‘ Candidatus Rhabdochlamydia crassificans’, an intracellular bacterial pathogen of the cockroach Blatta orientalis ( Insecta: Blattodea ) Syst Appl Microbiol 2007 30 221 8

Corsaro D Valassina M Venditti D Increasing diversity within Chlamydiae Crit Rev Microbiol 2003 29 37 78

Corsaro D Venditti D Valassina M New parachlamydial 16S rDNA phylotypes detected in human clinical samples Res Microbiol 2002 153 563 7

Corsaro D Work TM Candidatus Renichlamydia lutjani, a Gram-negative bacterium in internal organs of blue-striped snapper Lutjanus kasmira from Hawaii Dis Aquat Organ 2012 98 249 54

Croxatto A Greub G Early intracellular trafficking of Waddlia chondrophila in human macrophages Microbiology 2010 156 340 55

Croxatto A Rieille N Kernif T et al.  Presence of Chlamydiales DNA in ticks and fleas suggests that ticks are carriers of Chlamydiae Ticks Tick Borne Dis 2014 5 359 65

Dilbeck PM Evermann JF Crawford TB et al.  Isolation of a previously undescribed rickettsia from an aborted bovine fetus J Clin Microbiol 1990 28 814 6

Dilbeck-Robertson P McAllister MM Bradway D et al.  Results of a new serologic test suggest an association of Waddlia chondrophila with bovine abortion J Vet Diagn Invest 2003 15 568 9

Donati M Fiani N Di Francesco A et al.  IgG and IgA response to Simkania negevensis in sera of patients with respiratory and gastrointestinal symptoms New Microbiol 2013 36 303 6

Dowell SF Peeling RW Boman J et al.  Standardizing Chlamydia pneumoniae assays: recommendations from the Centers for Disease Control and Prevention (USA) and the Laboratory Centre for Disease Control (Canada) Clin Infect Dis 2001 33 492 503

Draghi A 2nd Bebak J Daniels S et al.  Identification of ‘ Candidatus Piscichlamydia salmonis’ in Arctic charr Salvelinus alpinus during a survey of charr production facilities in North America Dis Aquat Organ 2010 89 39 49

Draghi A 2nd Bebak J Popov VL et al.  Characterization of a Neochlamydia -like bacterium associated with epitheliocystis in cultured Arctic charr Salvelinus alpinus Dis Aquat Organ 2007 76 27 38

Draghi A 2nd Popov VL Kahl MM et al.  Characterization of ‘ Candidatus piscichlamydia salmonis’ (order Chlamydiales ), a chlamydia-like bacterium associated with epitheliocystis in farmed Atlantic salmon ( Salmo salar ) J Clin Microbiol 2004 42 5286 97

Eugster M Roten CA Greub G Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats BMC Evol Biol 2007 7 231

Everett KD Bush RM Andersen AA Emended description of the order Chlamydiales , proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae , including a new genus and five new species, and standards for the identification of organisms Int J Syst Bacteriol 1999 49 Pt 2 415 40

Everett KD Hornung LJ Andersen AA Rapid detection of the Chlamydiaceae and other families in the order Chlamydiales: three PCR tests J Clin Microbiol 1999 37 575 80

Everett KD Thao M Horn M et al.  Novel chlamydiae in whiteflies and scale insects: endosymbionts ‘ Candidatus Fritschea bemisiae’ strain Falk and ‘ Candidatus Fritschea eriococci’ strain Elm Int J Syst Evol Microbiol 2005 55 1581 7

Fehr A Walther E Schmidt-Posthaus H et al.  Candidatus Syngnamydia venezia, a novel member of the phylum Chlamydiae from the broad nosed pipefish, Syngnathus typhle PLoS One 2013 8 e70853

Friedman MG Galil A Greenberg S et al.  Seroprevalence of IgG antibodies to the chlamydia-like microorganism ‘ Simkania Z ’ by ELISA Epidemiol Infect 1999 122 117 23

Friedman MG Kahane S Dvoskin B et al.  Detection of Simkania negevensis by culture, PCR, and serology in respiratory tract infection in Cornwall, UK J Clin Pathol 2006 59 331 3

Fritsche TR Gautom RK Seyedirashti S et al.  Occurrence of bacterial endosymbionts in Acanthamoeba spp . isolated from corneal and environmental specimens and contact lenses J Clin Microbiol 1993 31 1122 6

Fukushi H Hirai K Proposal of Chlamydia pecorum sp. nov. for Chlamydia strains derived from ruminants Int J Syst Bacteriol 1992 42 306 8

Goy G Greub G Antibiotic susceptibility of Waddlia chondrophila in Acanthamoeba castellanii amoebae Antimicrob Agents Ch 2009 53 2663 6

Greub G Parachlamydia acanthamoebae , an emerging agent of pneumonia Clin Microbiol Infect 2009 15 18 28

Greub G Boyadjiev I La Scola B et al.  Serological hint suggesting that Parachlamydiaceae are agents of pneumonia in polytraumatized intensive care patients Ann NY Acad Sci 2003 990 311 9

Greub G Collyn F Guy L et al.  A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system BMC Microbiol 2004 4 48

Greub G Kebbi-Beghdadi C Bertelli C et al.  High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach PLoS One 2009 4 e8423

Greub G La Scola B Raoult D Parachlamydia acanthamoeba is endosymbiotic or lytic for Acanthamoeba polyphaga depending on the incubation temperature Ann NY Acad Sci 2003 990 628 34

Greub G Mege JL Raoult D Parachlamydia acanthamoebae enters and multiplies within human macrophages and induces their apoptosis [corrected] Infect Immun 2003 71 5979 85

Greub G Raoult D Crescent bodies of Parachlamydia acanthamoeba and its life cycle within Acanthamoeba polyphaga : an electron micrograph study Appl Environ Microb 2002 68 3076 84

Greub G Raoult D History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago Appl Environ Microb 2003 69 5530 5

Griffiths E Petrich AK Gupta RS Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification Microbiology 2005 151 2647 57

Habyarimana F Al-Khodor S Kalia A et al.  Role for the Ankyrin eukaryotic-like genes of Legionella pneumophila in parasitism of protozoan hosts and human macrophages Environ Microbiol 2008 10 1460 74

Haider S Collingro A Walochnik J et al.  Chlamydia -like bacteria in respiratory samples of community-acquired pneumonia patients FEMS Microbiol Lett 2008 281 198 202

Heinz E Pichler P Heinz C et al.  Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies Proteomics 2010 10 4363 76

Heinz E Tischler P Rattei T et al.  Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae BMC Genomics 2009 10 634

Hoffman GL Dunbar CE Wolf K et al.  Epitheliocystis, a new infectious disease of the bluegill ( Lepomis macrochirus ) A Van Leeuw 1969 35 146 58

Horn M Collingro A Schmitz-Esser S et al.  Illuminating the evolutionary history of chlamydiae Science 2004 304 728 30

Horn M Wagner M Muller KD et al.  Neochlamydia hartmannellae gen. nov., sp. nov. ( Parachlamydiaceae ), an endoparasite of the amoeba Hartmannella vermiformis Microbiology 2000 146 Pt 5 1231 9

Humphrys MS Creasy T Sun Y et al.  Simultaneous transcriptional profiling of bacteria and their host cells PLoS One 2013 8 e80597

Husain S Kahane S Friedman MG et al.  Simkania negevensis in bronchoalveolar lavage of lung transplant recipients: a possible association with acute rejection Transplantation 2007 83 138 43

Ishida K Sekizuka T Hayashida K et al.  Amoebal endosymbiont Neochlamydia genome sequence illuminates the bacterial role in the defense of the host amoebae against Legionella pneumophila PLoS One 2014 9 e95166

Israelsson O Chlamydial symbionts in the enigmatic Xenoturbella ( Deuterostomia ) J Invertebr Pathol 2007 96 213 20

Jacquier N Frandi A Pillonel T et al.  Cell wall precursors are required to organize the chlamydial division septum Nat Commun 2014 5 3578

Jelocnik M Frentiu FD Timms P et al.  Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle, and koalas J Clin Microbiol 2013 51 2625 32

Kahane S Dvoskin B Friedman MG The role of monocyte/macrophages as vehicles of dissemination of Simkania negevensis : an in vitro simulation model FEMS Immunol Med Mic 2008 52 219 27

Kahane S Dvoskin B Mathias M et al.  Infection of Acanthamoeba polyphaga with Simkania negevensis and S. negevensis survival within amoebal cysts Appl Environ Microb 2001 67 4789 95

Kahane S Everett KD Kimmel N et al.  Simkania negevensis strain ZT: growth, antigenic and genome characteristics Int J Syst Bacteriol 1999 49 Pt 2 815 20

Kahane S Fruchter D Dvoskin B et al.  Versatility of Simkania negevensis infection in vitro and induction of host cell inflammatory cytokine response J Infect 2007 55 e13 21

Kahane S Gonen R Sayada C et al.  Description and partial characterization of a new Chlamydia -like microorganism FEMS Microbiol Lett 1993 109 329 33

Kahane S Greenberg D Friedman MG et al.  High prevalence of ‘ Simkania Z ,’ a novel Chlamydia -like bacterium, in infants with acute bronchiolitis J Infect Dis 1998 177 1425 9

Kahane S Greenberg D Newman N et al.  Domestic water supplies as a possible source of infection with Simkania J Infect 2007 54 75 81

Kahane S Metzer E Friedman MG Evidence that the novel microorganism ‘Z’ may belong to a new genus in the family Chlamydiaceae FEMS Microbiol Lett 1995 126 203 7

Kahane S Platzner N Dvoskin B et al.  Evidence for the presence of Simkania negevensis in drinking water and in reclaimed wastewater in Israel Appl Environ Microb 2004 70 3346 51

Kalman S Mitchell W Marathe R et al.  Comparative genomes of Chlamydia pneumoniae and C. trachomatis Nat Genet 1999 21 385 9

Karlsen M Nylund A Watanabe K et al.  Characterization of ‘ Candidatus Clavochlamydia salmonicola’: an intracellular bacterium infecting salmonid fish Environ Microbiol 2008 10 208 18

Kebbi-Beghdadi C Batista C Greub G Permissivity of fish cell lines to three Chlamydia -related bacteria: Waddlia chondrophila , Estrella lausannensis and Parachlamydia acanthamoebae FEMS Immunol Med Mic 2011 63 339 45

Kebbi-Beghdadi C Cisse O Greub G Permissivity of vero cells, human pneumocytes and human endometrial cells to Waddlia chondrophila Microbes Infect 2011 13 566 74

Kebbi-Beghdadi C Greub G Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm Environ Microbiol Rep 2014 6 309 24

Kebbi-Beghdadi C Lienard J Uyttebroeck F et al.  Identification of immunogenic proteins of Waddlia chondrophila PLoS One 2012 7 e28605

Kocan KM Crawford TB Dilbeck PM et al.  Development of a rickettsia isolated from an aborted bovine fetus J Bacteriol 1990 172 5949 55

Kostanjsek R Strus J Drobne D et al.  ‘ Candidatus Rhabdochlamydia porcellionis’, an intracellular bacterium from the hepatopancreas of the terrestrial isopod Porcellio scaber ( Crustacea: Isopoda ) Int J Syst Evol Microbiol 2004 54 543 9

Lagkouvardos I Weinmaier T Lauro FM et al.  Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae ISME J 2014 8 115 25

Lamoth F Aeby S Schneider A et al.  Parachlamydia and Rhabdochlamydia in premature neonates Emerg Infect Dis 2009 15 2072 5

Lamoth F Jaton K Vaudaux B et al.  Parachlamydia and Rhabdochlamydia : emerging agents of community-acquired respiratory infections in children Clin Infect Dis 2011 53 500 1

Lane BJ Mutchler C Al Khodor S et al.  Chlamydial entry involves TARP binding of guanine nucleotide exchange factors PLoS Pathog 2008 4 e1000014

Lieberman D Kahane S Lieberman D et al.  Pneumonia with serological evidence of acute infection with the Chlamydia -like microorganism ‘Z’ Am J Resp Crit Care 1997 156 578 82

Lienard J Croxatto A Aeby S et al.  Development of a new Chlamydiales -specific real-time PCR and its application to respiratory clinical samples J Clin Microbiol 2011a 49 2637 42

Lienard J Croxatto A Prod'hom G et al.  Estrella lausannensis , a new star in the Chlamydiales order Microbes Infect 2011b 13 1232 41

Lohr M Prohl A Ostermann C et al.  A bovine model of a respiratory Parachlamydia acanthamoebae infection Pathog Dis 2014 doi:10.1016/j.micpath.2014.07.009

Mehlitz A Karunakaran K Herweg JA et al.  The chlamydial organism Simkania negevensis forms ER vacuole contact sites and inhibits ER-stress Cell Microbiol 2014 16 1224 43

Meijer A Roholl PJ Ossewaarde JM et al.  Molecular evidence for association of Chlamydiales bacteria with epitheliocystis in leafy seadragon ( Phycodurus eques ), silver perch ( Bidyanus bidyanus ), and barramundi ( Lates calcarifer ) Appl Environ Microb 2006 72 284 90

Mitchell SO Steinum T Rodger H et al.  Epitheliocystis in Atlantic salmon, Salmo salar L., farmed in fresh water in Ireland is associated with ‘ Candidatus Clavochlamydia salmonicola’ infection J Fish Dis 2010 33 665 73

Niemi S Greub G Puolakkainen M Chlamydia -related bacteria in respiratory samples in Finland Microbes Infect 2011 13 824 7

Nunes A Gomes JP Evolution, phylogeny, and molecular epidemiology of Chlamydia Infect Genet Evol 2014 23 49 64

Ossewaarde JM Meijer A Molecular evidence for the existence of additional members of the order Chlamydiales Microbiology 1999 145 Pt 2 411 7

Plehn M Praktikum der Fischkrankheiten Handbuch der Binnenfischerei Mitteleuropas 1920 Schweizerbart, Stuttgart

Polkinghorne A Hanger J Timms P Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas Vet Microbiol 2013 165 214 23

Polkinghorne A Schmidt-Posthaus H Meijer A et al.  Novel Chlamydiales associated with epitheliocystis in a leopard shark Triakis semifasciata Dis Aquat Organ 2010 91 75 81

Psomopoulos FE Siarkou VI Papanikolaou N et al.  The chlamydiales pangenome revisited: structural stability and functional coherence Genes (Basel) 2012 3 291 319

Radek R Light and electron microscopic study of a Rickettsiella species from the cockroach Blatta orientalis J Invertebr Pathol 2000 76 249 56

Read TD Brunham RC Shen C et al.  Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 Nucleic Acids Res 2000 28 1397 406

Roulis E Polkinghorne A Timms P Chlamydia pneumoniae : modern insights into an ancient pathogen Trends Microbiol 2013 21 120 8

Ruhl S Casson N Kaiser C et al.  Evidence for Parachlamydia in bovine abortion Vet Microbiol 2009 135 169 74

Ruhl S Goy G Casson N et al.  Parachlamydia acanthamoebae infection and abortion in small ruminants Emerg Infect Dis 2008 14 1966 8

Rurangirwa FR Dilbeck PM Crawford TB et al.  Analysis of the 16S rRNA gene of micro-organism WSU 86–1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales : proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov Int J Syst Bacteriol 1999 49 Pt 2 577 81

Rusconi B Lienard J Aeby S et al.  Crescent and star shapes of members of the Chlamydiales order: impact of fixative methods A Van Leeuw 2013 104 521 32

Sampo A Matsuo J Yamane C et al.  High-temperature adapted primitive Protochlamydia found in Acanthamoeba isolated from a hot spring can grow in immortalized human epithelial HEp-2 cells Environ Microbiol 2014 16 486 97

Schmidt-Posthaus H Polkinghorne A Nufer L et al.  A natural freshwater origin for two chlamydial species, Candidatus Piscichlamydia salmonis and Candidatus Clavochlamydia salmonicola, causing mixed infections in wild brown trout ( Salmo trutta ) Environ Microbiol 2012 14 2048 57

Seth-Smith HM Harris SR Scott P et al.  Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA Nat Protoc 2013a 8 2404 12

Seth-Smith HM Harris SR Skilton RJ et al.  Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture Genome Res 2013b 23 855 66

Soldati G Lu ZH Vaughan L et al.  Detection of mycobacteria and chlamydiae in granulomatous inflammation of reptiles: a retrospective study Vet Pathol 2004 41 388 97

Steigen A Nylund A Karlsbakk E et al.  ‘ Cand . Actinochlamydia clariae’ gen. nov., sp. nov., a unique intracellular bacterium causing epitheliocystis in catfish ( Clarias gariepinus ) in Uganda PLoS One 2013 8 e66840

Stephens RS Kalman S Lammel C et al.  Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis Science 1998 282 754 9

Stride MC Polkinghorne A Miller TL et al.  Molecular characterization of ‘ Candidatus Similichlamydia latridicola’ gen. nov., sp. nov. ( Chlamydiales : ‘ Candidatus Parilichlamydiaceae’), a novel Chlamydia -like epitheliocystis agent in the striped trumpeter, Latris lineata (Forster) Appl Environ Microb 2013a 79 4914 20

Stride MC Polkinghorne A Miller TL et al.  Molecular characterization of ‘ Candidatus Parilichlamydia carangidicola’, a novel Chlamydia -like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, ‘ Candidatus Parilichlamydiaceae’ fam. nov. (order Chlamydiales ) Appl Environ Microb 2013b 79 1590 7

Stride MC Polkinghome A Nowak BF Chlamydial infections of fish: diverse pathogens and emerging causes of disease in aquaculture species Vet Microbiol 2014 171 258 66

Stride MC Polkinghorne A Powell MD et al.  ‘ Candidatus Similichlamydia laticola’, a novel Chlamydia -like agent of epitheliocystis in seven consecutive cohorts of farmed Australian barramundi, Lates calcarifer (Bloch) PLoS One 2013c 8 e82889

Taylor HR Burton MJ Haddad D et al.  Trachoma Lancet 2014 doi:10.1016/S0140-6736(13)62182-0

Thao ML Baumann L Hess JM et al.  Phylogenetic evidence for two new insect-associated Chlamydia of the family Simkaniaceae Curr Microbiol 2003 47 46 50

Thomas V Casson N Greub G Criblamydia sequanensis , a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture Environ Microbiol 2006 8 2125 35

Tosetti N Croxatto A Greub G Amoebae as a tool to isolate new bacterial species, to discover new virulence factors and to study the host-pathogen interactions Microb Pathog 2014 Bio:1m0.1h0a1r6d/j.mWic,paPtohl.2k0in14g.0h7o.0r0n9e

von Bomhard W Polkinghorne A Lu ZH et al.  Detection of novel chlamydiae in cats with ocular disease Am J Vet Res 2003 64 1421 8

Wang Y Kahane S Cutcliffe LT et al.  Development of a transformation system for Chlamydia trachomatis : restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector PLoS Pathog 2011 7 e1002258

Wheelhouse N Coyle C Barlow PG et al.  Waddlia chondrophila infects and multiplies in ovine trophoblast cells stimulating an inflammatory immune response PLoS One 2014 9 e102386

Wheelhouse N Howie F Gidlow J et al.  Involvement of Parachlamydia in bovine abortions in Scotland Vet J 2012 193 586 8

Wheelhouse N Longbottom D Willoughby K Chlamydia in cases of cattle pneumonia in Scotland Vet Rec 2013 172 110

Wheelhouse N Sait M Gidlow J et al.  Molecular detection of Chlamydia -like organisms in cattle drinking water Vet Microbiol 2011 152 196 9

Zachary A Paperna I Epitheliocystis disease in the striped bass Morone saxatilis from the Chesapeake Bay Can J Microbiol 1977 23 1404 14

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Chlamydia and Chlamydophila

• First Online: 17 March 2023

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• Subhash Chandra Parija 2  

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The taxonomy of Chlamydia has undergone extensive revision recently based on genomic studies of this microorganism. They are included in the family Chlamydiaceae, which includes two genera: Chlamydia and Chlamydophila . The species Chlamydia trachomatis is included in the genus Chlamydia , whereas Chlamydophila psittaci and Chlamydophila pneumoniae are included in the new genus Chlamydophila . A fourth species, Chlamydophila pecorum , is normally present in the intestine, and vagina of ruminants is responsible for various pathological conditions in ruminants, swine and koalas.

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Chlamydia vaccine shows promise in early trial

An early-stage clinical trial yielded promising results for a chlamydia vaccine, researchers reported Thursday in The Lancet Infectious Diseases. 

There is currently no vaccine to protect against the sexually transmitted infection , which is the most common bacterial STI in the United States, according to the Centers for Disease Control and Prevention . In 2022, there were more than 1.6 million cases .

Chlamydia remains one of the most common causes of infertility in women, said Dr. Jay Varma, professor of population health sciences at Weill Cornell Medicine in New York City. Untreated, the infection — which usually doesn’t cause symptoms in women — can cause  pelvic inflammatory disease, which can lead to scar tissue that makes it harder to get pregnant.  

“This is desperately needed,” said David Harvey, executive director of the National Coalition of STD Directors. “We have the highest STI rates in America since the 1950s and possibly beyond.”

The bacteria can also cause an eye infection that’s responsible for vision loss in 1.9 million people worldwide. 

The phase 1 clinical trial, led by researchers in the United Kingdom and Denmark, found that the experimental vaccine was safe and induced an immune response. The study took place from 2020 through 2022 and participants were equally split between healthy men and women with an average age of 26. None had chlamydia. The researchers tested several different dosages for the vaccine, and participants got either the vaccine or a placebo on three separate days over a period of almost four months. 

Since the research on the vaccine is in the early stages, many questions remain.

“Does it confer the ability to hold off infection with chlamydia?” said Dr. Hilary Reno, a professor of medicine at Washington University School of Medicine in St. Louis and medical director of the St. Louis County Sexual Health Clinic. “If you do have an infection, does it mean you’re more likely to have an asymptomatic infection?” 

“We don’t know that and that’s what the next phase of studies would be,” she said. 

The researchers are now planning to launch a larger, phase 2 trial that would look at the vaccine’s effectiveness.

The hope is that one day the vaccine would be able to prevent both infection in the reproductive system, as well as in the eyes, said Jes Dietrich, a senior scientist at Statens Serum Institut in Denmark and a lead author of the study. 

In addition to a shot in the arm, people in the study also got a vaccine in the form of an eye drop. 

“I was very pleasantly surprised because it’s really difficult to induce immunity in the eye,” Dietrich said. 

Varma, who was not involved with the clinical trial, said that “it’s exciting to see research on potentially effective vaccines for sexually transmitted infections.”

There are already a handful of vaccines available to prevent certain sexually transmitted infections: the HPV vaccine , the hepatitis B vaccine and the mpox vaccine .

Akshay Syal, M.D., is a medical fellow with the NBC News Health and Medical Unit. 

Paper-based molecular diagnostic for Chlamydia trachomatis

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• 1 Biomedical Engineering, Boston University, Boston, MA, 02215.
• 2 BioHelix Corporation, Beverly, MA, 01915.
• PMID: 25309740
• PMCID: PMC4188396
• DOI: 10.1039/C4RA07911F

Herein we show the development of a minimally instrumented paper-based molecular diagnostic for point of care detection of sexually transmitted infections caused by Chlamydia trachomatis . This new diagnostic platform incorporates cell lysis, isothermal nucleic acid amplification, and lateral flow visual detection using only a pressure source and heat block, eliminating the need for expensive laboratory equipment. This paper-based test can be performed in less than one hour and has a clinically relevant limit of detection that is 100x more sensitive than current rapid immunoassays used for chlamydia diagnosis.

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• U01 AI082522/AI/NIAID NIH HHS/United States

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• v.318(7186); 1999 Mar 20

Evidence based case report

Chlamydia infection in general practice.

a Directorate of Public Health and Health Policy, Oxfordshire Health Authority, Oxford OX3 7LG, b Hollow Way Medical Centre, Oxford OX4 2NJ

M Fleminger

How common is chlamydia infection, and who should be investigated and treated for it? Is the net benefit of investigation worth the cost? At a recent discussion in our general practice it soon became apparent that our views and practices varied widely. Was there any evidence to help us reach a consensus? We resolved to try and find out.

Summary points

• Chlamydia infection is the commonest treatable sexually transmitted disease in the United Kingdom; it is most common in sexually active women aged under 20
• Serological studies suggest that chlamydial infection may account for a large proportion of cases of tubal infertility and ectopic pregnancy
• 60-80% of genital chlamydia infections in women may be asymptomatic
• In one randomised trial, screening high risk women and treating those found to be infected reduced the incidence of pelvic inflammatory disease by about half in 12 months
• Access to the internet allows valid, relevant information to be identified and retrieved quickly—but appraising the evidence and deciding how best to reflect it in practice takes considerably longer

Case report

Ms A, a 20 year old secretary, was worried because she had had vaginal discharge and irritation for three days. The discharge was slight, clear, watery, and non-offensive, and she had no abnormal vaginal bleeding. Ms A had changed her sexual partner two months previously. Soon after this she had contracted genital thrush, which responded to topical clotrimazole. She uses a combined contraceptive pill and does not use condoms. Ms A has no other sexual partners, and thinks it unlikely her partner has. However, she has little knowledge of his previous sexual history.

The only noteworthy finding at vaginal examination was that Ms A’s cervix bled easily when swabbed. A high vaginal swab was taken from the posterior fornix, and two swabs were taken from the endocervix and the urethra—a standard cotton swab and a plastic shafted chlamydia swab respectively. Ms A was prescribed doxycycline (200 mg for seven days) and metronidazole (400 mg three times daily for seven days).

A few days later the laboratory reported that chlamydia had been detected. Ms A was invited back to the surgery and was upset to be told that she might have had a sexually transmitted disease. She and her partner were referred to the local sexually transmitted diseases clinic for further investigation and follow up.

Our uncertainty

The case of Ms A prompted discussion in the practice about who we should investigate and treat for chlamydia. Of course, we all wanted to prevent our patients suffering avoidable morbidity—for example, pelvic inflammatory disease, infertility, and ectopic pregnancy—and we also wanted to use the NHS’s scarce resources as wisely as possible. But some of us thought there was no place for chlamydia investigation in primary care, arguing that as chlamydia tests were expensive and insensitive, patients should be treated for chlamydia whenever this organism was suspected clinically. Others felt it important to obtain a microbiological diagnosis wherever possible, and, as chlamydial infection can be asymptomatic, thought we should be searching for asymptomatic cases—for example, among sexually active women attending for cervical smears or for contraceptive advice. However, none of us knew how common chlamydia was in our practice, nor were we certain that treating an asymptomatic infection reduced subsequent morbidity. We did not know the magnitude of any benefits and harms associated with proactive case finding or whether any net benefit would be worth the resources consumed.

Search for evidence

It is frequently written that the first step in evidence based practice is to turn the clinical problem into an answerable question. 1 This proved more difficult than we first thought, as we wanted answers to several questions:

• Is genital chlamydia an important cause of clinically important morbidity?
• Does antibiotic treatment reduce subsequent morbidity in asymptomatic, sexually active women infected with chlamydia?
• If so, is case finding in our population likely to be a cost effective way of reducing clinically important morbidity?

Easy access

In the past, we might first have looked to standard textbooks for our answers. However, textbooks held in libraries are now more difficult to access from general practitioners’ homes and surgeries than are online electronic databases. In addition, traditional textbooks are rarely written in a way that is sufficiently transparent to enable readers to determine how the authors reached their conclusions. More worryingly, the opinions expressed in textbooks may either be out of date even before publication or inconsistent with valid and relevant evidence. 2 We therefore decided to look for answers to our questions using the information we could access from home or the surgery.

Categories of evidence

We thought our questions were unlikely to be original. Similar questions ought to have been addressed by anyone drafting evidence based guidelines. We also thought that a great many original research papers would have been published about chlamydia, and that it would be an inappropriate use of our time to attempt to obtain, read, and appraise every relevant article. We therefore decided to search for recent systematic reviews about chlamydia; evidence based guidelines about the detection and treatment of chlamydia; and randomised controlled trials of treatment or case finding, or both, and treatment of asymptomatic chlamydia published after the most recent systematic review or evidence based guideline that we retrieved. NRH offered to spend up to one hour searching at home for relevant material using a computer connected to the internet.

Where to search?

Before searching, NRH checked the one relevant textbook he had at home. 3 It did not answer our questions. The next stops were Best Evidence 4 and the Cochrane Library, 5 searching with the single word “chlamydia.” The search of Best Evidence identified five articles, none of which had promising titles. The Cochrane Library search produced two completed Cochrane reviews, both about chlamydia in pregnancy, and three reviews listed on the Database of Abstracts of Reviews of Effectiveness. None of these looked relevant, so the next step was the internet.

Controlled trials

The first stop was Bandolier’s home page ( www.jr2.ox.ac.uk/bandolier/ ). A search using “chlamydia” rapidly led to the full text of an article on treatment of chlamydia. 6 This article noted that the Centers for Communicable Disease in the United States had recently changed its recommended treatment for chlamydial infection from oral doxycycline (100 mg twice daily for 7 days) to a single dose (1 g) of azithromycin. 7 Bandolier had searched Medline for trials comparing doxycycline with azithromycin in the treatment of symptomatic and asymptomatic genital chlamydia and confirmed that both were effective treatments.

Bandolier had also looked at cost effectiveness, and it concluded that although azithromycin was more expensive, if compliance were better the higher drug costs would probably be “offset by lower costs associated with pelvic inflammatory disease, chronic pelvic pain, ectopic pregnancy, and tubal infertility.” Perhaps the most startling information in this article, however, was the epidemiological data: chlamydia is the commonest curable bacterial sexually transmitted disease in the United Kingdom and the organism is most likely to be isolated in sexually active women under the age of 20 years, with rates in excess of 350 per 100 000 population (0.35%).

Recent guidelines and systematic reviews

The next step was to search for recent guidelines and systematic reviews. Medline Express for 1996, 1997, and January-March 1998 was searched with WinSpirs. A search for the medical subject heading (MeSH) term “chlamydia” in all subheadings produced 813 articles. This search was then limited by publication type to “meta-analysis” (1 article), “guideline” (2), “review academic” (5), “review” (83), and “randomised controlled trial” (10). Browsing the titles showed that one of the guidelines had been prepared by the Canadian Task Force on the Periodic Health Examination, 8 which has a reputation for using a rigorous approach based on systematic evidence to developing guidelines. The full text of the guideline is available free on the world wide web ( www.cma.ca/cmaj/vol-154/1631.htm ).

Canadian task force review

This text cited 201 references. In using a systematic approach to reviewing published reports and developing its recommendations it had considered many of the questions to which we sought answers. The text reported that in North America, as in Britain, chlamydia is the commonest sexually transmitted disease, and is two to three times as common as gonorrhoea. As in Britain, infection is most prevalent among sexually active women aged 15 to 19 years. In six Canadian studies, 1-25% of women tested were infected. Other risk factors and indicative signs were multiple sexual partners, a new partner in the previous year, no barrier method of contraception, low socioeconomic status, intermenstrual bleeding, cervical friability, and purulent cervical discharge. However, 60-80% of infections in women are asymptomatic. But what startled us most was the statement supported by 18 references that “serologic studies suggest that at least 64% of cases of tubal infertility, and 42% of ectopic pregnancies are attributable to chlamydial infection.” Unfortunately, the guideline authors did not comment on the strength of inference that could be drawn from these 18 papers.

Does case finding reduce morbidity?

But was there any evidence that case finding and treating asymptomatic infection reduced morbidity? The guideline authors could identify only one controlled study in a non-pregnant population. The reference cited a paper presented to the International Symposium on Human Chlamydial Infections, which was unlikely to be retrievable quickly and cheaply. However, scanning the 10 randomised trials that had been identified from Medline indicated that the same study had been published later in the New England Journal of Medicine . 9 This article was readily retrieved the next day from the hospital library. (It could have been retrieved that night from online access to the BMA Library.)

The article reported a randomised controlled trial conducted in Seattle, in which 2607 asymptomatic women were randomised to an invitation to investigation for chlamydial infection (cervical swabs sent for enzyme linked immunosorbent assay and culture) and treatment if positive or to a control group given the “usual care.” Women were followed for 12 months.The chlamydial infection rate in control women was 7%. The rate of clinically defined pelvic inflammatory disease in the 12 months after randomisation was reduced by 56% (relative risk 0.44, 95% confidence interval 0.20 to 0.90) in the intervention group compared with the control women. The absolute risk reduction was 1.1%; 2% of the control group developed pelvic inflammatory disease during follow up compared with 0.9% of the women in the intervention group. In other words, in Seattle, 91 sexually active women aged 18-34 years had to be invited for investigation for chlamydia to prevent one case of pelvic inflammatory disease. The study did not provide information about the impact of case finding on tubal damage, ectopic pregnancy, or infertility. Nor did it comment on any harm that may have resulted—for example, from treating women whose results were falsely positive, from mistaken reassurance of women given false negative results, or from the social implications of being told that one has an asymptomatic sexually transmitted disease. Nevertheless, we thought that this was an important study.

Studies in British general practice

But was the prevalence of chlamydia likely to be as high as 7% among any readily identifiable groups of our patients? We wanted some prevalence data from British general practice. Among the reviews identified on Medline was an article with a promising title. 10 This article cited nine prevalence studies of chlamydial infection undertaken in British general practices. The prevalence of infection ranged from 2% among asymptomatic women aged 15-40 attending for a cervical smear in Fife, Scotland, to 12% among women aged 16-44 requesting termination of pregnancy in inner city east London. The prevalence was also 12% among the mainly social class 3 women aged 19-58 attending for a cervical smear in an inner city Glasgow practice, and it was 11% in premenopausal women undergoing a speculum examination for any reason in a central London general practice.

What we learned and decided

Chlamydia is a much more important public health issue than any of us had suspected. We were all surprised at just how common it can be among young, sexually active women. We were also surprised that serological studies suggest that chlamydia may account for at least two thirds of tubal infertility and nearly half of ectopic pregnancies. Furthermore, we were impressed with the randomised controlled trial from Seattle which showed that in women in whom the prevalence of chlamydial infection was 7%, inviting them for investigation and treatment where necessary reduced the rate of pelvic inflammatory disease by half in 12 months. This suggested to us that much of the morbidity caused by chlamydia may be preventable.

The evidence that we have seen did not allow us to identify unequivocally a single best practice for deciding in whom and how to investigate and treat chlamydia. Given that there is substantial geographical variation in chlamydia prevalence, we think that it is unlikely that a case finding policy can be devised that is equally cost effective for all practices in the United Kingdom. However, the data do suggest that systematic case finding and treatment of chlamydia could reduce potentially life-ruining morbidity for appreciable numbers of British women. Thus, we have decided that in the absence of national guidance we want to discuss and agree a way forward with other local practices, genitourinary physicians, microbiologists, gynaecologists, family planning clinics, and the health authority. One important next step might be to measure the prevalence of chlamydia infection in selected groups of our practice populations.

What about Ms A? We now know that she had several risk factors for chlamydia—she was young, sexually active, had a new sexual partner, and had a friable cervix. We should therefore have suspected chlamydia infection. Until there is a local guideline, we have agreed that whenever we suspect chlamydia we will offer to take chlamydia swabs and treat with doxycycline—unless compliance may be a problem, in which case we will use azithromycin. We will also refer patients and their partners to the genitourinary medicine clinic.

Although the evidence we found did not answer our questions completely it was the best evidence that we could find. We could not escape making a decision about what to do for our patients, as to do nothing would be a decision in itself. Our search took less than an hour plus a 10 minute trip to the library. Reading and discussing the material we retrieved took rather longer, perhaps three hours. We learned a lot and made a decision about patient management that is based on the best evidence we could find. We think that our time was well spent.

Chlamydia trachomatis : the cause of the commonest treatable sexually transmitted disease in the United Kingdom

Competing interests: NRH has received lecture fees for speaking at postgraduate education meetings for general practitioners sponsored by the manufacturers of azithromycin.