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Comparison of shipping versus immediate freezer storage of vaginal samples for vaginal microbiota assessment
  1. Susan Tuddenham1,
  2. Pawel Gajer2,
  3. Johanna B Holm2,
  4. Sarah Elizabeth Brown2,3,
  5. Larry Forney4,
  6. Jacques Ravel2,5,
  7. Khalil G Ghanem1,
  8. Rebecca M Brotman2,3
  1. 1Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  2. 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
  3. 3Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
  4. 4Initiative for Bioinformatics and Evolutionary Studies (iBEST), University of Idaho, Moscow, Idaho, USA
  5. 5Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
  1. Correspondence to Dr Rebecca M Brotman, University of Maryland School of Medicine, Baltimore, USA; rbrotman{at}som.umaryland.edu

Objectives

We evaluated how storing vaginal samples at room temperature in stabilising solutions versus immediate freezing affects 16S rRNA gene amplicon sequencing-based microbiota studies, aiming to simplify home and field collection.

Methods Twenty participants self-collected six mid-vaginal swabs that were stored in two nucleic acid preservatives (three in modified Solution C2 (Qiagen) and three in Amies/RNALater (Sigma)) in January-February 2016. From each set, two were immediately frozen (−80°C) and one was shipped to the University of Idaho (Moscow, Idaho) with return shipping to the Institute for Genome Sciences (Baltimore, Maryland). Amplicon sequencing of the 16S rRNA gene was used to characterise the vaginal microbiota, VALENCIA was used to assign community state types (CSTs), and quantitative PCR (qPCR) of 16S rRNA genes was used to estimate bacterial abundance. Cohen’s Kappa statistic was used to assess within-participant agreement. Bayesian difference of means models assessed within-participant comparisons between shipped and immediately frozen samples.

Results There were 115 samples available for analysis. Average duration of transit for shipped samples was 8 days (SD: 1.60, range: 6–11). Within-participant comparisons of CSTs between shipped and immediately frozen samples revealed complete concordance (kappa: 1.0) for both preservative solutions. No significant differences comparing shipped and immediately frozen samples were found with taxon-level comparisons or bacterial abundances based on pan-bacterial qPCR.

Conclusions Short-term room temperature shipping of vaginal swabs placed in stabilising solutions did not affect vaginal microbiota composition. Home collection with mail-in of vaginal samples may be a reasonable approach for research and clinical purposes to assess the vaginal microbiota.

  • MICROBIOLOGY
  • REPRODUCTIVE HEALTH
  • Vaginosis, Bacterial
  • WOMEN

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Footnotes

  • Handling editor Erica L Plummer

  • X @symbiologyst

  • Contributors KGG supervised the recruitment of the participants. JR supervised sequencing of samples. PG, RMB, SEB and JBH conducted the analysis. RMB and ST drafted the paper. ST, SEB and JBH contributed to the figures. All authors contributed to data interpretation and revision of the paper. RMB is the guarantor.

  • Funding Research reported in this publication was supported in part by the National Institute for Allergy and Infectious Disease of the National Institute for Health under award numbers R01AI089878 (Ghanem), R01AI119012 (Brotman), K23AI125715 (Tuddenham), F32AI136400 (Holm) and the National Institute for Nursing Research of the National Institute of Health under award number R01NR015495. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

  • Competing interests JR is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutics drugs. ST has been a consultant for Biofire Diagnostics, Roche Molecular Diagnostics and Luca Biologics, receives royalties from UPTODATE and has received speaker honoraria from Roche Molecular Diagnostics and Medscape/WebMD. ST, KG, RB and JR participate in research supported by in-kind donation of test kits by Hologic. JH has been a consultant for Intralytix Inc. LJF consults with Psomagen, Inc. to evaluate factors that influence the outcome of in vitro fertilisation.

  • Provenance and peer review Not commissioned; externally peer-reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.