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Patiño LH, Camargo M, Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis. Front Microbiol 2018; 9:1854. [PMID: 30186244 PMCID: PMC6113918 DOI: 10.3389/fmicb.2018.01854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.
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Affiliation(s)
- Luz H. Patiño
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan D. Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Gharsallah H, Frikha-Gargouri O, Bom RJ, Hammami A, Bruisten SM. Comparison of reverse hybridization and ompA sequencing methods applied on Chlamydia trachomatis strains from Tunisia. Microbiologyopen 2017; 7:e00549. [PMID: 29282889 PMCID: PMC5911986 DOI: 10.1002/mbo3.549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022] Open
Abstract
Two techniques based on ompA amplification of Chlamydia trachomatis were compared, being reverse hybridization (RHM) and ompA sequencing (OSA), to investigate the concordance between them and to study the epidemiological relevance of each method. In addition, phylogenetic analysis was performed on the ompA sequences. One hundred and seven C. trachomatis positive samples from Tunisian patients and female sex workers were analyzed using both the RHM and ompA sequencing. The overall genovar distribution obtained with both techniques was very similar. The RHM identified nine genovars, being B, D, E, F, G, H, I, J and K, where B, I, J, and K were only found in mixed infections versus 7 types for the OSA being D, E, F, G, H, I, and K. The agreement between both typing techniques was 87.8%. Both methods showed that genovar E was the most predominant type. In 24.3% of the analyzed samples, mixed infections were detected. In 96.1% of these, the genovar identified by OSA was also detected using the RHM. OmpA sequencing allowed determination of six genovar types that could not be typed using RHM. The analyses of ompA nucleotide variation in the 107 clinical specimens detected ompA genovar variants with distinct ompA mutational patterns for types D2, G1, G2, and H1. In conclusion, RHM and OSA showed a high agreement in C. trachomatis genotyping results with each having their specific benefits.
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Affiliation(s)
- Houda Gharsallah
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba university hospital, Medical School of Sfax, University of Sfax, Sfax, Tunisia
| | - Olfa Frikha-Gargouri
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Reinier J Bom
- Public Health Laboratory, The Netherlands Condomerie, Cluster Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands
| | - Adnene Hammami
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba university hospital, Medical School of Sfax, University of Sfax, Sfax, Tunisia
| | - Sylvia M Bruisten
- Public Health Laboratory, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, the Netherlands
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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] [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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