Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis
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 standardi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-08-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.01854/full |
| _version_ | 1819146059009490944 |
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| author | Luz H. Patiño Luz H. Patiño Milena Camargo Milena Camargo Marina Muñoz Dora I. Ríos-Chaparro Manuel A. Patarroyo Manuel A. Patarroyo Juan D. Ramírez |
| author_facet | Luz H. Patiño Luz H. Patiño Milena Camargo Milena Camargo Marina Muñoz Dora I. Ríos-Chaparro Manuel A. Patarroyo Manuel A. Patarroyo Juan D. Ramírez |
| author_sort | Luz H. Patiño |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T13:07:54Z |
| format | Article |
| id | doaj.art-b44fe24e7d6e4d669109f169348bff27 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-22T13:07:54Z |
| publishDate | 2018-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b44fe24e7d6e4d669109f169348bff272022-12-21T18:24:49ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-08-01910.3389/fmicb.2018.01854343955Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatisLuz H. Patiño0Luz H. Patiño1Milena Camargo2Milena Camargo3Marina Muñoz4Dora I. Ríos-Chaparro5Manuel A. Patarroyo6Manuel A. Patarroyo7Juan D. Ramírez8Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, ColombiaPh.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, ColombiaPh.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, ColombiaMolecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, ColombiaGrupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, ColombiaGrupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, ColombiaMolecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, ColombiaSchool of Medicine and Health Sciences, Universidad del Rosario, Bogotá, ColombiaGrupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, ColombiaMultilocus 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.https://www.frontiersin.org/article/10.3389/fmicb.2018.01854/fullMLSTMLST-genotypingsequence type (ST)schemeschlamydia |
| spellingShingle | Luz H. Patiño Luz H. Patiño Milena Camargo Milena Camargo Marina Muñoz Dora I. Ríos-Chaparro Manuel A. Patarroyo Manuel A. Patarroyo Juan D. Ramírez Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis Frontiers in Microbiology MLST MLST-genotyping sequence type (ST) schemes chlamydia |
| title | Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis |
| title_full | Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis |
| title_fullStr | Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis |
| title_full_unstemmed | Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis |
| title_short | Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis |
| title_sort | unveiling the multilocus sequence typing mlst schemes and core genome phylogenies for genotyping chlamydia trachomatis |
| topic | MLST MLST-genotyping sequence type (ST) schemes chlamydia |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.01854/full |
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