Genome Investigation of Urinary Gardnerella Strains and Their Relationship to Isolates of the Vaginal Microbiota

Abstract

Gardnerella is a frequent member of the urogenital microbiota. Given the association between Gardnerella vaginalis and bacterial vaginosis (BV), significant efforts have been focused on characterizing this species in the vaginal microbiota. However, Gardnerella also is a frequent member of the urinary microbiota. In an effort to characterize the bacterial species of the urinary microbiota, we present here 10 genomes of urinary Gardnerella isolates from women with and without lower urinary tract symptoms. These genomes complement those of 22 urinary Gardnerella strains previously isolated and sequenced by our team. We included these genomes in a comparative genome analysis of all publicly available Gardnerella genomes, which include 33 urinary isolates, 78 vaginal isolates, and 2 other isolates. While once this genus was thought to consist of a single species, recent comparative genome analyses have revealed 3 new species and an additional 9 groups within Gardnerella. Based upon our analysis, we suggest a new group for the species. We also find that distinction between these Gardnerella species/groups is possible only when considering the core or whole-genome sequence, as neither the sialidase nor vaginolysin genes are sufficient for distinguishing between species/groups despite their clinical importance. In contrast to the vaginal microbiota, we found that only five Gardnerella species/groups have been detected within the lower urinary tract. Although we found no association between a particular Gardnerella species/group(s) and urinary symptoms, further sequencing of urinary Gardnerella isolates is needed for both comprehensive taxonomic characterization and etiological classification of Gardnerella in the urinary tract. IMPORTANCE Prior research into the bacterium Gardnerella vaginalis has largely focused on its association with bacterial vaginosis (BV). However, G. vaginalis is also frequently found within the urinary microbiota of women with and without lower urinary tract symptoms as well as individuals with chronic kidney disease, interstitial cystitis, and BV. This prompted our investigation into Gardnerella from the urinary microbiota and all publicly available Gardnerella genomes from the urogenital tract. Our work suggests that while some Gardnerella species can survive in both the urinary tract and vagina, others likely cannot. This study provides the foundation for future studies of Gardnerella within the urinary tract and its possible contribution to lower urinary tract symptoms.

Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome

“…It should also be noted that while 16S rRNA gene sequencing is able to confidently distinguish species with divergent sequences, some members of the urogenital microbiota, namely Gardnerella spp., possess highly similar 16S rRNA sequences and their speciation requires further genetic information. 81 …”

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice

“…It is possible that the inconsistency in associations with lower urinary tract symptoms reflects that different Gardnerella species have greater or less capacity to influence the bladder. It has been noted that G. piotii has not yet been isolated from urine, while most other species and subspecies of Gardnerella have been isolated from both niches ( Putonti et al., 2021 ). However, this could be attributed to differences in the culture techniques that were used in studies isolating Gardnerella from the urine compared to those that isolated Gardnerella from the vagina.…”

Under conditions closely mimicking vaginal fluid, Lactobacillus jensenii strain 62B produces a bacteriocin-like inhibitory substance that targets and eliminates Gardnerella species

“…In fact, the Gardnerella test strain JCP8151B used in the majority of described experiments is now considered to be G. piotii () [27–29, 52]. Urinary isolates (four species of Gram-positive cocci, four species of Gram-negative bacilli, and one yeast species) were obtained from patients with urinary tract infections seen at the Texas Tech University Health Sciences Centre Urology Clinic under an IRB approved protocol and deidentified prior to use in this study ().…”

“…At the time of acquisition, all Gardnerella strains were identified as G. vaginalis by the repositor; however, the published emended descriptions [29] and resolution of species [27] have indicated that our strains include three G. vaginalis, three G. piotii, one G. leopoldii, and one Gardnerella gsp12 (Table 1). In fact, the Gardnerella test strain JCP8151B used in the majority of described experiments is now considered to be G. piotii (Table 1) [27][28][29]52]. Urinary isolates (four species of Gram-positive cocci, four species of Gram-negative bacilli, and one yeast species) were obtained from patients with urinary tract infections seen at the Texas Tech University Health Sciences Centre Urology Clinic under an IRB approved protocol and deidentified prior to use in this study (Table 1).…”