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Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

BACKGROUND: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provid...

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Autores principales: Fookes, Maria C., Hadfield, James, Harris, Simon, Parmar, Surendra, Unemo, Magnus, Jensen, Jørgen S., Thomson, Nicholas R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745988/
https://www.ncbi.nlm.nih.gov/pubmed/29281972
http://dx.doi.org/10.1186/s12864-017-4399-6
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author Fookes, Maria C.
Hadfield, James
Harris, Simon
Parmar, Surendra
Unemo, Magnus
Jensen, Jørgen S.
Thomson, Nicholas R.
author_facet Fookes, Maria C.
Hadfield, James
Harris, Simon
Parmar, Surendra
Unemo, Magnus
Jensen, Jørgen S.
Thomson, Nicholas R.
author_sort Fookes, Maria C.
collection PubMed
description BACKGROUND: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. genitalium relies on molecular tests targeting specific genes or regions of the genome and knowledge is limited by a general under-testing internationally. This is set against a background of drug resistance whereby M. genitalium has developed resistance to mainly all therapeutic antimicrobials. RESULTS: We sequenced 28 genomes of Mycoplasma genitalium from temporally (1980–2010) and geographically (Europe, Japan, Australia) diverse sources. All the strain showed essentially the same genomic content without any accessory regions found. However, we identified extensive recombination across their genomes with a total of 25 regions showing heightened levels of SNP density. These regions include the MgPar loci, associated with host interactions, as well as other genes that could also be involved in this role. Using these data, we generated a robust phylogeny which shows that there are two main clades with differing degrees of genomic variability. SNPs found in region V of 23S rRNA and parC were consistent with azithromycin/erythromycin and fluoroquinolone resistances, respectively, and with their phenotypic MIC data. CONCLUSIONS: The sequence data here generated is essential for designing rational approaches to type and track Mycoplasma genitalium as antibiotic resistance increases. It represents a first approach to its population genetics to better appreciate the role of this organism as a sexually transmitted pathogen. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4399-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-57459882018-01-03 Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure Fookes, Maria C. Hadfield, James Harris, Simon Parmar, Surendra Unemo, Magnus Jensen, Jørgen S. Thomson, Nicholas R. BMC Genomics Research Article BACKGROUND: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. genitalium relies on molecular tests targeting specific genes or regions of the genome and knowledge is limited by a general under-testing internationally. This is set against a background of drug resistance whereby M. genitalium has developed resistance to mainly all therapeutic antimicrobials. RESULTS: We sequenced 28 genomes of Mycoplasma genitalium from temporally (1980–2010) and geographically (Europe, Japan, Australia) diverse sources. All the strain showed essentially the same genomic content without any accessory regions found. However, we identified extensive recombination across their genomes with a total of 25 regions showing heightened levels of SNP density. These regions include the MgPar loci, associated with host interactions, as well as other genes that could also be involved in this role. Using these data, we generated a robust phylogeny which shows that there are two main clades with differing degrees of genomic variability. SNPs found in region V of 23S rRNA and parC were consistent with azithromycin/erythromycin and fluoroquinolone resistances, respectively, and with their phenotypic MIC data. CONCLUSIONS: The sequence data here generated is essential for designing rational approaches to type and track Mycoplasma genitalium as antibiotic resistance increases. It represents a first approach to its population genetics to better appreciate the role of this organism as a sexually transmitted pathogen. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4399-6) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-28 /pmc/articles/PMC5745988/ /pubmed/29281972 http://dx.doi.org/10.1186/s12864-017-4399-6 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Fookes, Maria C.
Hadfield, James
Harris, Simon
Parmar, Surendra
Unemo, Magnus
Jensen, Jørgen S.
Thomson, Nicholas R.
Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title_full Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title_fullStr Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title_full_unstemmed Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title_short Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
title_sort mycoplasma genitalium: whole genome sequence analysis, recombination and population structure
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745988/
https://www.ncbi.nlm.nih.gov/pubmed/29281972
http://dx.doi.org/10.1186/s12864-017-4399-6
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