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Smelov V, Vrbanac A, van Ess EF, Noz MP, Wan R, Eklund C, Morgan T, Shrier LA, Sanders B, Dillner J, de Vries HJC, Morre SA, Dean D. Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides. Front Microbiol 2017; 8:2195. [PMID: 29180986 PMCID: PMC5693916 DOI: 10.3389/fmicb.2017.02195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/25/2017] [Indexed: 11/17/2022] Open
Abstract
Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted diseases worldwide. The Ct Multi Locus Sequence Typing (MLST) scheme is effective in differentiating strain types (ST), deciphering transmission patterns and treatment failure, and identifying recombinant strains. Here, we analyzed 323 reference and clinical samples, including 58 samples from Russia, an area that has not previously been represented in Ct typing schemes, to expand our knowledge of the global diversification of Ct STs. The 323 samples resolved into 84 unique STs, a 3.23 higher typing resolution compared to the gold standard single locus ompA genotyping. Our MLST scheme showed a high discriminatory index, D, of 0.98 (95% CI 0.97-0.99) confirming the validity of this method for typing. Phylogenetic analyses revealed distinct branches for the phenotypic diseases of lymphogranuloma venereum, urethritis and cervicitis, and a sub-branch for ocular trachoma. Consistent with these findings, single nucleotide polymorphisms were identified that significantly correlated with each phenotype. While the overall number of unique STs per region was comparable across geographies, the number of STs was greater for Russia with a significantly higher ST/sample ratio of 0.45 (95% CI: 0.35-0.53) compared to Europe or the Americas (p < 0.009), which may reflect a higher level of sexual mixing with the introduction of STs from other regions and/or reassortment of alleles. Four STs were found to be significantly associated with a particular geographic region. ST23 [p = 0.032 (95% CI: 1-23)], ST34 [p = 0.019 (95% CI: 1.1-25)]; and ST19 [p = 0.001 (95% CI: 1.7-34.7)] were significantly associated with Netherlands compared to Russia or the Americas, while ST 30 [p = 0.031 (95% CI: 1.1-17.8)] was significantly associated with the Americas. ST19 was significantly associated with Netherlands and Russia compared with the Americans [p = 0.001 (95% CI: 1.7-34.7) and p = 0.006 (95% CI: 1.5-34.6), respectively]. Additionally, recombinant strains were ubiquitous in the data set [106 (32.8%)], although Europe had a significantly higher number than Russia or the Americas (p < 0.04), the majority of which were from Amsterdam [43 (87.8%) of 49)]. The higher number of recombinants in Europe indicates selective pressure and/or adaptive diversification that will require additional studies to elucidate.
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Affiliation(s)
- Vitaly Smelov
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Karolinska Institute, Stockholm, Sweden
- North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Russia
| | - Alison Vrbanac
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | - Eleanne F. van Ess
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
| | - Marlies P. Noz
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
| | - Raymond Wan
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | | | - Tyler Morgan
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | - Lydia A. Shrier
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Blake Sanders
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | | | - Henry J. C. de Vries
- Center for Infection and Immunology Amsterdam, Academic Medical Center, Amsterdam, Netherlands
- Department of Dermatology, Academic Medical Center, Amsterdam, Netherlands
- STI Outpatient Clinic, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, Netherlands
| | - Servaas A. Morre
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
- Institute of Public Health Genomics, Department of Genetics and Cell Biology, Research Institute GROW (School for Oncology and Developmental Biology), Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, Netherlands
| | - Deborah Dean
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Department of Bioengineering, University of California, San Francisco, San Francisco, CA, United States
- Departments of Medicine and Pediatrics, University of California, San Francisco, San Francisco, CA, United States
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