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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.


Core gene mosaic for M. hominis: Allele mosaic of 48 genes found to be necessary and sufficient for reproducing phylogenetic relationships observed in the maximum likelihood tree constructed with whole genome SNP data. Each colour in a column represent an allele, identical colours in the same column correspond to the same allele. However, colours may be repeated between columns
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Fig3: Core gene mosaic for M. hominis: Allele mosaic of 48 genes found to be necessary and sufficient for reproducing phylogenetic relationships observed in the maximum likelihood tree constructed with whole genome SNP data. Each colour in a column represent an allele, identical colours in the same column correspond to the same allele. However, colours may be repeated between columns

Mentions: A subset of genes found across all samples are likely to be highly conserved and carry little phylogenetic signal. Conversely, a small subset of genes could be carrying phylogenetic signal that is similar to the species as a whole, and therefore can be used as a proxy for whole genome evolution. In order to identify genes that carry increased discriminatory potential, leave-one-out analysis was performed. This involved removing one gene at a time from the set of 417 core genes and constructing a phylogenetic tree using the remaining alleles from 416 genes. The resulting phylogenetic tree was compared with the phylogeny derived using whole genome variants (considered the gold standard). Of the 417 genes, 379 genes (88.76%) conferred the same phylogenetic topology as the whole genome tree whilst 48 genes (11.24%) disrupted the phylogenetic relationship of the samples to varying extent. These results suggest that these 48 genes are necessary in reconstructing the correct relationships between the isolates included in this study, Fig. 3(a). To assess the sufficiency of these genes to replicate the topology, a phylogenetic tree was constructed using only these 48 genes (Fig. 3), confirming that these 48 genes were necessary and sufficient for tree reconstruction. These genes are considered the minimum gene set to construct a core-genome MLST scheme for M. hominis as they are present in all reference genomes and the 18 sequenced M. hominis strains, and are each required to reconstruct the whole genome topology.Fig. 3


Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis
Core gene mosaic for M. hominis: Allele mosaic of 48 genes found to be necessary and sufficient for reproducing phylogenetic relationships observed in the maximum likelihood tree constructed with whole genome SNP data. Each colour in a column represent an allele, identical colours in the same column correspond to the same allele. However, colours may be repeated between columns
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Core gene mosaic for M. hominis: Allele mosaic of 48 genes found to be necessary and sufficient for reproducing phylogenetic relationships observed in the maximum likelihood tree constructed with whole genome SNP data. Each colour in a column represent an allele, identical colours in the same column correspond to the same allele. However, colours may be repeated between columns
Mentions: A subset of genes found across all samples are likely to be highly conserved and carry little phylogenetic signal. Conversely, a small subset of genes could be carrying phylogenetic signal that is similar to the species as a whole, and therefore can be used as a proxy for whole genome evolution. In order to identify genes that carry increased discriminatory potential, leave-one-out analysis was performed. This involved removing one gene at a time from the set of 417 core genes and constructing a phylogenetic tree using the remaining alleles from 416 genes. The resulting phylogenetic tree was compared with the phylogeny derived using whole genome variants (considered the gold standard). Of the 417 genes, 379 genes (88.76%) conferred the same phylogenetic topology as the whole genome tree whilst 48 genes (11.24%) disrupted the phylogenetic relationship of the samples to varying extent. These results suggest that these 48 genes are necessary in reconstructing the correct relationships between the isolates included in this study, Fig. 3(a). To assess the sufficiency of these genes to replicate the topology, a phylogenetic tree was constructed using only these 48 genes (Fig. 3), confirming that these 48 genes were necessary and sufficient for tree reconstruction. These genes are considered the minimum gene set to construct a core-genome MLST scheme for M. hominis as they are present in all reference genomes and the 18 sequenced M. hominis strains, and are each required to reconstruct the whole genome topology.Fig. 3

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.