Homogeneity Between Cervical and Vaginal Microbiomes and the Diagnostic Limitations of 16S Sequencing for STI Pathogens at Higher Ct Values

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Understanding the interactions between the cervico-vaginal microbiome, immune responses, and sexually transmitted infections (STIs) is crucial for developing targeted diagnostic and therapeutic strategies. Although microbiome analyses are not yet standard practice, integrating them into routine diagnostics could enhance personalized medicine and therapies. We investigated the extent to which partial 16S short-read amplicon microbiome analyses could inform on the presence of six commonly encountered STI-causing pathogens in a patient cohort referred for colposcopy, and whether relevant taxonomic or diagnostic discrepancies occur when using vaginal rather than cervical swabs. The study cohort included cervical and vaginal samples collected from women referred for colposcopy at the University Hospital Bonn between November 2021 and February 2022, due to an abnormal PAP smear or positive hrHPV results. 16S rRNA gene sequencing libraries were prepared targeting the V1–V2 and V4 regions of the 16S RNA gene and sequenced on the Illumina MiSeq. PCR diagnostics for common STI-causing pathogens were conducted using the Allplex STI Essential Assay Kit (Seegene, Seoul, Republic of Korea). Concerning the bacterial microbiome, no significant differences were found between vaginal and cervical samples in terms of prevalence of taxa present or diversity. A total of 95 patients and 171 samples tested positive for at least one among Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis, Mycoplasma genitalium, Chlamydophila trachomatis or Neisseria gonorrhoeae. Sequencing the V1–V2 region enabled detection of one-third to half of the PCR-positive samples, with the detection likelihood increasing at lower cycle threshold (Ct) values. In contrast, sequencing the V4 region was less effective overall, yielding fewer species-level identifications and a higher proportion of undetermined taxa. We demonstrate that the vaginal microbiome closely mirrors the cervical microbiome, a relationship that has not been explored previously, but which broadens the possibilities for microbiome analysis and pathogen detection and establishes vaginal swabs as a reliable method for detecting the investigated pathogens, with sensitivities comparable with or superior to endocervical swabs. On the other hand, the sensitivity of partial 16S amplicon sequencing appears insufficient for effective STI diagnostics, as it fails to reliably identify or even detect pathogens at higher Ct values.

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