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

View Article: PubMed Central - PubMed

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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3284-z) contains supplementary material, which is available to authorized users.

No MeSH data available.


MLST genes stability analysis: Allele mosaic of the 9 genes included from all three schemas shows no variation between alleles for the samples undergone 10 passages (MH2_10 and MH20_10)
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Fig4: MLST genes stability analysis: Allele mosaic of the 9 genes included from all three schemas shows no variation between alleles for the samples undergone 10 passages (MH2_10 and MH20_10)

Mentions: Stability of the genes for all three schemas was assessed in two M. hominis strains. Whole genome sequencing was performed following short-term passage (10 passages) in liquid culture and compared to the original sequence. None of the genes showed allelic variation in the two strains examined (Fig. 4).Fig. 4


Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis
MLST genes stability analysis: Allele mosaic of the 9 genes included from all three schemas shows no variation between alleles for the samples undergone 10 passages (MH2_10 and MH20_10)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5120421&req=5

Fig4: MLST genes stability analysis: Allele mosaic of the 9 genes included from all three schemas shows no variation between alleles for the samples undergone 10 passages (MH2_10 and MH20_10)
Mentions: Stability of the genes for all three schemas was assessed in two M. hominis strains. Whole genome sequencing was performed following short-term passage (10 passages) in liquid culture and compared to the original sequence. None of the genes showed allelic variation in the two strains examined (Fig. 4).Fig. 4

View Article: PubMed Central - PubMed

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.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-016-3284-z) contains supplementary material, which is available to authorized users.

No MeSH data available.