Comparing Swab Methods For Vaginal Microbiome Analysis
Traditionally, 16S rRNA gene sequencing has been considered the gold standard for characterizing the vaginal microbiome using swabs. However, this technique is relatively expensive and time-consuming. Recent studies have evaluated faster and cheaper alternative methods for analyzing vaginal swabs, while maintaining high accuracy compared to sequencing.
A 2023 study by Short et al. directly compared vaginal swabs to menstrual cups for collecting vaginal fluid, followed by 16S rRNA gene sequencing. Both sampling methods gave very similar results for factors like DNA yield, bacterial load, alpha diversity, and ability to distinguish community state types. The menstrual cup provided some advantages, including larger volume of undiluted sample and potential for self-collection away from a clinic.
Another approach is direct on-swab metabolic profiling by desorption electrospray ionization mass spectrometry (DESI-MS), as described in a 2021 study by Pruski et al. This rapid method can analyze a vaginal swab in less than 3 minutes. DESI-MS of vaginal swabs could predict vaginal microbiome composition and inflammatory status. Predictive models were validated in over 1000 samples across two independent cohorts. Importantly, DESI-MS metabolic signatures were associated with preterm birth risk.
A third study by Singer et al. in 2021 compared 16S rRNA gene sequencing to IS-pro analysis of vaginal swabs. IS-pro is a PCR-based technique that profiles the 16S-23S rRNA intergenic spacer region. It was faster and cheaper than sequencing in this study. Results between IS-pro and sequencing showed very high correlation (median Pearson's R2 = 0.97).
In summary, while 16S rRNA gene sequencing remains the gold standard, emerging methods like direct swab DESI-MS and IS-pro enable rapid, cost-effective analysis of vaginal swabs. These approaches generate results consistent with sequencing, but in a fraction of the time. DESI-MS can provide results in minutes, while IS-pro has a turnaround time of approximately 4 hours. The quick analysis time and lower costs of new techniques may facilitate large-scale studies and potential clinical applications.
As research continues, faster and cheaper techniques that maintain accuracy compared to sequencing will likely become increasing popular. Ultimately, approaches like DESI-MS and IS-pro could enable point-of-care testing to guide clinical decision making related to vaginal health.
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1. Short CS, Quinlan R, Lee YS, Preda VG, Smith A, Marchesi JR, Shattock R, Bennett PR, MacIntyre DA, Taylor GP. Comparative analysis of vaginal microbiota sampling using menstrual cups and high vaginal swabs in pregnant women living with HIV-1 infection. Front Cell Infect Microbiol. 2023 May 9;13:1190160. doi: 10.3389/fcimb.2023.1190160. PMID: 37228662; PMCID: PMC10204588.
2. Pruski, P., Correia, G.D.S., Lewis, H.V. et al. Direct on-swab metabolic profiling of vaginal microbiome host interactions during pregnancy and preterm birth. Nat Commun 12, 5967 (2021). https://doi.org/10.1038/s41467-021-26215-w
3. Singer M, Koedooder R, Bos MP, Poort L, Schoenmakers S, Savelkoul PHM, Laven JSE, de Jonge JD, Morré SA, Budding AE. The profiling of microbiota in vaginal swab samples using 16S rRNA gene sequencing and IS-pro analysis. BMC Microbiol. 2021 Mar 31;21(1):100. doi: 10.1186/s12866-021-02149-7. PMID: 33789573; PMCID: PMC8015044.