TY - JOUR
T1 - Comparison of shipping versus immediate freezer storage of vaginal samples for vaginal microbiota assessment
AU - Tuddenham, Susan
AU - Gajer, Pawel
AU - Holm, Johanna B.
AU - Brown, Sarah Elizabeth
AU - Forney, Larry
AU - Ravel, Jacques
AU - Ghanem, Khalil G.
AU - Brotman, Rebecca M.
N1 - Publisher Copyright:
© Author(s) (or their employer(s)) 2024.
PY - 2024/8/19
Y1 - 2024/8/19
N2 - 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.
AB - 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.
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U2 - 10.1136/sextrans-2023-056100
DO - 10.1136/sextrans-2023-056100
M3 - Article
C2 - 38960602
AN - SCOPUS:85197631723
SN - 1368-4973
VL - 100
SP - 368
EP - 370
JO - Sexually transmitted infections
JF - Sexually transmitted infections
IS - 6
ER -