Comparison of vaginal microbiota sampling techniques: cytobrush versus swab

Sci Rep. 2017 Aug 29;7(1):9802. doi: 10.1038/s41598-017-09844-4.


Evidence suggests the vaginal microbiota (VM) may influence risk of persistent Human Papillomavirus (HPV) infection and cervical carcinogenesis. Established cytology biobanks, typically collected with a cytobrush, constitute a unique resource to study such associations longitudinally. It is plausible that compared to rayon swabs; the most commonly used sampling devices, cytobrushes may disrupt biofilms leading to variation in VM composition. Cervico-vaginal samples were collected with cytobrush and rayon swabs from 30 women with high-grade cervical precancer. Quantitative PCR was used to compare bacterial load and Illumina MiSeq sequencing of the V1-V3 regions of the 16S rRNA gene used to compare VM composition. Cytobrushes collected a higher total bacterial load. Relative abundance of bacterial species was highly comparable between sampling devices (R2 = 0.993). However, in women with a Lactobacillus-depleted, high-diversity VM, significantly less correlation in relative species abundance was observed between devices when compared to those with a Lactobacillus species-dominant VM (p = 0.0049). Cytobrush and swab sampling provide a comparable VM composition. In a small proportion of cases the cytobrush was able to detect underlying high-diversity community structure, not realized with swab sampling. This study highlights the need to consider sampling devices as potential confounders when comparing multiple studies and datasets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Bacterial Load
  • Computational Biology / methods
  • Cytodiagnosis / methods
  • Female
  • Humans
  • Metagenome
  • Metagenomics / methods
  • Microbiological Techniques*
  • Microbiota*
  • Middle Aged
  • RNA, Ribosomal, 16S
  • Specimen Handling / methods
  • Vagina / microbiology*
  • Vaginal Smears / methods
  • Young Adult


  • RNA, Ribosomal, 16S