Abstract Vulvovaginal candidiasis is one of the most common vaginal and fungal infections. The majority of infections are successfully treated with antifungal drugs. However, ∼8% of cases lead to chronic recurrent vulvovaginal candidiasis (“RVVC”), and approximately half of RVVC cases are idiopathic. Previous research has generally found closely-related isolates within vaginal and rectal populations and between subsequent infections. However, their coarse methods preclude assessing the fine-scale relationships among closely related isolates and measuring standing genetic variation, a fundamental property of populations with implications for evolutionary potential. To address this gap, we isolated 12 vaginal and 12 rectal yeast isolates during symptomatic relapse from four individuals with a history of RVVC. Three participants had Candida albicans infections, while the fourth had Nakaseomyces glabratus . All isolates were whole-genome sequenced and phenotyped. The isolates were placed into the global phylogenies, which included constructing an updated N. glabratus tree containing over 500 isolates. Multiple analyses were consistent with frequent migration between sites. Although there are extremely few comparables, C. albicans population nucleotide diversity was similar to most commensal oral and rectal populations, while N. glabratus was similar to some bloodstream infections, yet higher than others. Diversity was largely driven by single nucleotide changes; no aneuploidies were found, and although loss-of-heterozygosity tracts were common in the populations, only a single region on chr1L varied among isolates from one participant. There was very little phenotypic diversity for drug response or growth and no consistent difference between isolates from different sites for invasive growth. Combined, this study provides baseline measurements and describes analysis techniques to quantify within-population diversity. We highlight a critical need for comparable studies that use the same sampling effort, sequencing, and analysis methods to understand the interplay between selection, drift, and migration in shaping fungal microbial communities in this and other important contexts. Author Summary Recurrent vaginal yeast infections are relatively common, and we do not understand why some people experience these chronic infections when many others will have a single infection that is successfully treated and cleared. Many open questions remain about the basic biology of the yeast populations involved. We quantified diversity using modern sequencing technology within vaginal and rectal yeast populations from four individuals with a history of recurrent yeast infections experiencing symptoms. Three participants had a Candida albicans infection (the most common causative species), while the fourth had a Nakaseomyces glabratus infection (the second most common and increasingly implicated). We found that vaginal and rectal isolates were closely related, indicating the same population is present at the two sites. We found, surprisingly, that diversity was similar to the yeast populations found at other body sites in healthy people. Our study highlights a critical need for additional studies to be done following the same methods in different contexts to understand better the fungal microbial populations that reside in our bodies.

Genotypic and phenotypic homogeneity of vaginal and rectal yeast isolates from recurrent vulvovaginal candidiasis