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Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis.

Jironkin, Aleksey, Brown, Rebecca J., Underwood, Anthony, Chalker, Victoria J. and Spiller, Owen B. 2016. Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis. BMC Genomics 17 , 964. 10.1186/s12864-016-3284-z

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Abstract

Background: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. homins, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms. Results: This study identified pan-genome set of 700 genes found to be present in four published reference genomes. A subset of 417 genes was identified to be core genome for 18 isolates and 1 reference. Leave-one-out analysis of the core genes highlighted set of 48 genes that are required to recapture the original phylogenetic relationships observed using whole genome SNP analysis. Three 7-locus MLST schemas with high diversity index (97%) and low dN/dS ratios (0.1, 0.13, and 0.11) were derived that could be used to confer good discrimination between strains and could be of practical use in future studies direct on clinical specimens. Conclusions: The genes proposed in this study could be utilised to design a costeffective and rapid PCR-based MLST assay that could be applied directly to clinical isolates, without prior isolation. This study includes additional genomic analysis revealing high levels of genetic heterogeneity among this species. This provides a novel and evidence based approach for the development of MLST schema that accurately represent genomic phylogeny for use in epidemiology and transmission studies.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Advanced Research Computing @ Cardiff (ARCCA)
Medicine
Subjects: R Medicine > R Medicine (General)
Uncontrolled Keywords: Mycoplasma hominis – Typing schema – Genomics – Snp analysis
Additional Information: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License
Publisher: BioMed Central
ISSN: 1471-2164
Funders: Public Health England
Date of First Compliant Deposit: 29 November 2016
Date of Acceptance: 9 November 2016
Last Modified: 11 Jun 2020 13:30
URI: http://orca-mwe.cf.ac.uk/id/eprint/95939

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