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

Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis
Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis
Background: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, 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 cost-effective 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.
1471-2164
1-10
Jironkin, Aleksey
507f0980-a52e-4021-a2a6-1f298fd066ab
Brown, Rebecca J.
a4912e7b-0056-4d4d-843d-3baf69f97f58
Underwood, Anthony
1998fc6f-c39e-4742-8c67-118dc058f8fa
Chalker, Victoria
7e7a099b-3b9a-4f62-b8d3-b8e469cb1541
Spiller, Brad
48cd3b49-1415-4680-a9c3-da708890505e
Jironkin, Aleksey
507f0980-a52e-4021-a2a6-1f298fd066ab
Brown, Rebecca J.
a4912e7b-0056-4d4d-843d-3baf69f97f58
Underwood, Anthony
1998fc6f-c39e-4742-8c67-118dc058f8fa
Chalker, Victoria
7e7a099b-3b9a-4f62-b8d3-b8e469cb1541
Spiller, Brad
48cd3b49-1415-4680-a9c3-da708890505e

Jironkin, Aleksey, Brown, Rebecca J., Underwood, Anthony, Chalker, Victoria and Spiller, Brad (2016) Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis. BMC Genomics, 17 (964), 1-10. (doi:10.1186/s12864-016-3284-z).

Record type: Article

Abstract

Background: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, 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 cost-effective 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.

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More information

Accepted/In Press date: 9 November 2016
e-pub ahead of print date: 23 November 2016
Published date: 23 November 2016
Organisations: Clinical & Experimental Sciences

Identifiers

Local EPrints ID: 402940
URI: https://eprints.soton.ac.uk/id/eprint/402940
ISSN: 1471-2164
PURE UUID: 8bd69254-3101-4ba8-a52b-5f3b584d37b6
ORCID for Rebecca J. Brown: ORCID iD orcid.org/0000-0001-5825-6859

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Date deposited: 21 Dec 2016 11:26
Last modified: 03 Dec 2019 01:32

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