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

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

Tetracycline Resistance Mediated by tet (M) Has Variable Integrative Conjugative Element Composition in Mycoplasma hominis Strains Isolated in the United Kingdom from 2005 to 2015

“…A more intensive examination of ICE (1) strain clustering compared to ICE(-) strains was performed by neighbor-joining tree construction of concatenated multilocus sequence typing loci (Fig. 3) using gene targets that we previously defined (17).…”

“…Variation between strains, sequence veracity, and temporal drift. When developing MLST schemes for M. hominis previously, noted that interstrain diversity was unusually high-to the point where each strain had a unique sequence type (ST) unless it was isolated from the same patient specimen (17). It was based on this observation that the source of failed lung transplants caused by M. hominis infection in a clinical cohort was able to be traced back to the original asymptomatic donor (6) who had right and left lobes transplanted into different recipients, both of which failed due to M. hominis infection.…”

“…Assembled contigs were further analyzed utilizing Geneious sequence analysis software (BioMatters Ltd., New Zealand) and aligned and assessed against reference sequences (Sprott, GenBank accession number NZ_CP011538; PL5, GenBank accession number NZ_JRXA01000009) for the identification of genetic elements and the presence of point mutations and gene rearrangements using Snippy v4.4.5 and Roary v3.12.0 (48,49). Multilocus sequence typing was performed in silico using the targets we previously reported (17). The whole-genome shotgun project for MH15-3 has been deposited at DDBJ/ENA/GenBank under the accession number JACXZU000000000.…”

Phylogenetic variants of Mycoplasma hominis from pregnant women and women presenting with infertility in Nnamdi Azikiwe University Teaching Hospital, Nnewi, Nigeria

“…This finding is in agreement with other studies that made use of molecular typing methods. Using RFLP, Jironkin et al, (15) reported high levels of genetic heterogeneity among M. hominis and Sogaard et al, (16) examined six-house-keeping gene sequences to investigate evidence of genomic recombination in M. hominis to show a high degree of variability between these genes. Ferandon et al, (17) used multiple locus variable number tandem repeat (VNTR) analysis (MLVA) molecular typing system for the discrimination of 210 French M. hominis clinical isolates.…”

Emerging Pathogenic Respiratory Mycoplasma hominis Infections in Lung Transplant Patients: Time to Reassesses it's Role as a Pathogen?

“…Furthermore, in two of their infected transplant patients, who received a lung from a common donor, the M. hominis isolates had identical multi-locus sequence types (MLST). This is particularly significant as constant low level mutation for this organism means that MLST yields an almost unique fingerprint for each organism and usually is only identical when taken from the same patient ( Jironkin et al, 2016 ). This substantiates their conclusion that the source of the infection was the organ donor.…”