A genome-wide investigation of Mycoplasma hominis genes associated with gynecological infections or infertility

Abstract

Background and aim: Mycoplasma hominis is a human pathogenic bacterium that causes a wide range of genital infections and reproductive issues. Previously, based on an extended multilocus sequence typing scheme, we provided evidence for the segregation of M. hominis clinical strains into two distinct pathotypes: gynecological infections or infertility. Here, based on whole genome sequencing (WGS) data, we sought to provide a more refined picture of the phylogenetic relationship between these two M. hominis pathotypes, with the aim to delineate the underlying genetic determinants.

Methods: We carried out WGS of 62 Tunisian M. hominis clinical strains collected over a 17-year period. The majority of these clinical strains are associated with infertility (n = 53) and the remaining nine isolates are from gynecological infections cases. An alignment-free distance-based procedure (Jolytree) was used to infer phylogenetic relationships among M. hominis isolates, while the phylogenetic method treeWAS was used to determine the statistical association between pathotypes of interest and genotypes at all loci.

Results: The total pangenome of M. hominis strains was found to contain 1,590 genes including 966 core genes and 592 accessory genes, representing 60 and 37% of the total genome, respectively. Collectively, phylogenetic analyses based on WGS confirmed the distinction between the two M. hominis pathotypes. Strikingly, genome wide association analyses identified 4 virulence genes associated with gynecological infections, mainly involved in nucleotide salvage pathways and tolerance to oxidative stress, while five genes have been associated with infertility cases, two of which are implicated in biofilm formation.

Conclusion: In sum, this study further established the categorization of M. hominis into two pathotypes, and led to the identification of the associated genetic loci, thus holding out promising prospects for a better understanding of the differential interaction of M. hominis with its host.

Keywords: Mycoplasma hominis; genome-wide association studies; gynecological infections; infertility; pathotype; virulence; whole genome sequencing.

Figure 1

COG classification of genes. (A) Clusters of orthologous genes (COGs) distribution among the 52 M. hominis strains associated with infertility. (B) COGs distribution among the 10 M. hominis strains associated with genital infections. Bars in green, red, and blue, represent the core genome, the accessory genes (shell genes), and unique genes (cloud genes), respectively.

Figure 2

Single nucleotide polymorphism (SNP) distribution among M. hominis strains associated with gynecological infections (red boxplot) and infertility (blue boxplot). Student's t-test was used to assess for statistical significant difference (P < 0.05) between the mean SNPs count values of strains linked to infertility and gynecological infections. ^*Represents the mean SNP count of each boxplot.

Figure 3

TreeWAS-based phylogenetic tree illustrating the relatedness between the 62 Tunisian M. hominis clinical strains based on pathotype association. Strains in red are associated with gynecological infections pathotype and strains in blue are associated with infertility pathotype.

Figure 4

Null distributions of simulated association terminal scores. The red vertical line marks the significance threshold (0.7), above which real associated genes are indicated.