Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

Abstract

Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

“…However, when mapped onto whole-genome phylogenies ( Fig. 2B and SI Materials and Methods), these variants differentiate between significantly diverged "genovars" within the G. vaginalis species (21). The functional classifications of clade-specific genes are largely redundant but transporters, membrane proteins, and toxin-antitoxin systems appear overrepresented in G2 variant genomes (Figs.…”

Cervical and Vaginal Flora Specimens Are Highly Concordant with Respect to Bacterial Vaginosis-Associated Organisms and Commensal Lactobacillus Species in Women of Reproductive Age

“…Studies of G. vaginalis have found that virulent strains are superior to commensal strains in their ability to adhere to both vaginal (15) and cervical (16) epithelium, which may contribute to the correlated concentrations we observed at these sites. In addition, G. vaginalis has a highly diverse population structure (17), and cocolonization with multiple strains is common (18); it is possible that one strain predominates at the cervix and the other in the vagina. BVAB2 and vaginal Megasphaera spp.…”

Targeted and Highly Multiplexed Detection of Microorganisms by Employing an Ensemble of Molecular Probes

“…They found that there were four nonrecombining groups of G. vaginalis genomes and proposed that it "may be appropriate to treat these four groups as separate species." Ahmed et al (27) determined that there are 746 genes in the core G. vaginalis genome and that these core genes make up only ϳ52% of the genome sequences, on average. Therefore, going forward, we would derive Homers for each of the four groups separately based upon sequence differences.…”

“…While the two reverse primers (conventionally called 1492R) had a perfect match, the two forward primers (conventionally called 8F) had no perfect match to any of the three G. vaginalis genome sequences. Ahmed et al (27) compared the genome sequences of 17 G. vaginalis clinical isolates, most of which they sequenced themselves. They found that there were four nonrecombining groups of G. vaginalis genomes and proposed that it "may be appropriate to treat these four groups as separate species."…”