The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
20 08 2024
20 08 2024
Historique:
received:
12
02
2024
accepted:
16
08
2024
medline:
21
8
2024
pubmed:
21
8
2024
entrez:
20
8
2024
Statut:
epublish
Résumé
The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear. As part of planning for the Generation Victoria population-based cohort study beginning in pregnancy, we assessed the utility and reliability of residual clinical GBS vaginal/vaginal-rectal swabs for generating late pregnancy microbiome data. We carried out a two-phased pilot study. Phase one assessed the level of microbial diversity apparent in 'residual' clinical vaginal/vaginal-rectal swabs post clinical testing and storage for 7-10 days at 4 °C (routine clinical practice). Phase two directly assessed the impact of storage time and temperature on the microbial composition of vaginal/vaginal-rectal swabs collected specifically for research purposes. The microbiota composition in the 'residual' clinical swabs aligned with published studies. The 'research' swabs, stored at 4 °C for up to ten days, showed minimal changes in microbiota profile, compared to swabs examined on the day of collection. In contrast, significant variation in diversity was seen in swabs stored at room temperature for up to 48 h. Residual clinical material from swabs collected primarily for GBS screening in late pregnancy represent a reliable and abundant source of material for assessing the late pregnancy maternal microbiome for research purposes. This represents a low-burden opportunity for population-representative pregnancy studies to assess the potential of late pregnancy microbiome for prediction and understanding maternal and child health outcomes.
Identifiants
pubmed: 39164578
doi: 10.1038/s41598-024-70431-5
pii: 10.1038/s41598-024-70431-5
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
19318Informations de copyright
© 2024. Crown.
Références
Fliegner, J. R. & Garland, S. M. Perinatal mortality in victoria, Australia: Role of group B streptococcus. Am. J. Obstet. Gynecol. 163, 1609–1611 (1990).
doi: 10.1016/0002-9378(90)90638-N
pubmed: 2240114
Centers for Disease Control and Prevention. Prevention of perinatal group B streptococcal disease: a public health perspective. MMWR Recomm. Rep. 45, 1–24 (1996).
Schrag, S., Gorwitz, R., Fultz-Butts, K. & Schuchat, A. Prevention of perinatal group B streptococcal disease. Revised guidelines from CDC. MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports / Centers for Disease Control 51, 1–22 (2002).
Australian Government Department of Health. Clinical Practice Guidelines: Pregnancy Care. https://www.health.gov.au/resources/pregnancy-care-guidelines/part-f-routine-maternal-health-tests/group-b-streptococcus (2020).
Albert, A. Y. K. et al. A study of the vaginal microbiome in healthy Canadian women utilizing cpn60-based molecular profiling reveals distinct gardnerella subgroup community state types. PLoS One 10, e0135620 (2015).
doi: 10.1371/journal.pone.0135620
pubmed: 26266808
pmcid: 4534464
Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. U.S.A. 108, 4680–4687 (2011).
doi: 10.1073/pnas.1002611107
pubmed: 20534435
Romero, R. et al. The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome https://doi.org/10.1186/2049-2618-2-10 (2014).
doi: 10.1186/2049-2618-2-10
pubmed: 24987521
pmcid: 4066267
Fettweis, J. M. et al. The vaginal microbiome and preterm birth. Nat. Med. 25(6), 1012–1021 (2019).
doi: 10.1038/s41591-019-0450-2
pubmed: 31142849
pmcid: 6750801
Safer Care Victoria. Group B streptococcus (GBS) – screening and management. https://www.safercare.vic.gov.au/best-practice-improvement/clinical-guidance/maternity/group-b-streptococcus-gbs-screening-and-management (2019).
Verani, J. R., McGee, L., Schrag, S. J., Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC). Prevention of perinatal group B streptococcal disease–revised guidelines from CDC, 2010. MMWR Recomm. Rep. 59, 1–36 (2010).
pubmed: 21088663
Bai, G. et al. Comparison of storage conditions for human vaginal microbiome studies. PLoS One 7, e36934 (2012).
doi: 10.1371/journal.pone.0036934
pubmed: 22655031
pmcid: 3360033
Wagner, J. et al. Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol. 16, 1–17 (2016).
doi: 10.1186/s12866-016-0891-4
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
doi: 10.1038/nmeth.3869
pubmed: 27214047
pmcid: 4927377
McLaren, M. R. & Callahan, B. J. Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2. 10.5281/ZENODO.4587955. (2021).
Callahan, B. RDP taxonomic training data formatted for DADA2 (RDP trainset 18/release 11.5). 10.5281/ZENODO.4310151. (2020).
Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinform. 10, 421 (2009).
doi: 10.1186/1471-2105-10-421
Schoch, C. L. et al. NCBI taxonomy: A comprehensive update on curation, resources and tools. Database 2020, baaa062 (2020).
doi: 10.1093/database/baaa062
pubmed: 32761142
pmcid: 7408187
McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).
doi: 10.1371/journal.pone.0061217
pubmed: 23630581
pmcid: 3632530
Schliep, K. P. Phangorn: Phylogenetic analysis in R. Bioinformatics 27, 592–593 (2011).
doi: 10.1093/bioinformatics/btq706
pubmed: 21169378
Bodenhofer, U., Bonatesta, E., Horejš-Kainrath, C. & Hochreiter, S. msa: An R package for multiple sequence alignment. Bioinformatics 31, 3997–3999 (2015).
doi: 10.1093/bioinformatics/btv494
pubmed: 26315911
Oksanen, J. et al. vegan: Community Ecology Package. Preprint at https://cran.r-project.org/package=vegan (2020).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
doi: 10.1186/s13059-014-0550-8
Wickham, H. Ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2006).
Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).
Murphy, M. A., Evans, J. S. & Storfer, A. Quantifying Bufo boreas connectivity in yellowstone national park with landscape genetics. Ecology 91, 252–261 (2010).
doi: 10.1890/08-0879.1
pubmed: 20380214
Choo, J. M., Leong, L. E. X. & Rogers, G. B. Sample storage conditions significantly influence faecal microbiome profiles. Sci. Rep. https://doi.org/10.1038/srep16350 (2015).
doi: 10.1038/srep16350
pubmed: 26666970
pmcid: 4678330
Shaw, A. G. et al. Latitude in sample handling and storage for infant faecal microbiota studies: The elephant in the room?. Microbiome 4, 1–14 (2016).
doi: 10.1186/s40168-016-0186-x
Liang, Y. et al. Systematic analysis of impact of sampling regions and storage methods on fecal gut microbiome and metabolome profiles. mSphere https://doi.org/10.1128/mSphere.00763-19 (2020).
doi: 10.1128/mSphere.00763-19
pubmed: 33148824
pmcid: 7643832
El Aila, N. A. et al. Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women. BMC Infect. Dis. 10, 285 (2010).
doi: 10.1186/1471-2334-10-285
pubmed: 20920213
pmcid: 2956727
Hiller, J. E., McDonald, H. M., Darbyshire, P. & Crowther, C. A. Antenatal screening for group B Streptococcus: A diagnostic cohort study. BMC Pregnancy Childbirth 5, 12 (2005).
doi: 10.1186/1471-2393-5-12
pubmed: 16042773
pmcid: 1190189
El Aila, N. A. et al. Genotyping of Streptococcus agalactiae (group B streptococci) isolated from vaginal and rectal swabs of women at 35–37 weeks of pregnancy. BMC Infect. Dis. 9, 153 (2009).
doi: 10.1186/1471-2334-9-153
pubmed: 19747377
pmcid: 2753344
El Aila, N. A. et al. Identification and genotyping of bacteria from paired vaginal and rectal samples from pregnant women indicates similarity between vaginal and rectal microflora. BMC Infect. Dis. 9, 167 (2009).
doi: 10.1186/1471-2334-9-167
pubmed: 19828036
pmcid: 2770471
Daniels, J. et al. Rapid testing for group B streptococcus during labour: A test accuracy study with evaluation of acceptability and cost-effectiveness. Health Technol. Assess (Rockv) 13, 1–178 (2009).
Wylie, K. M., Blankenship, S. A., Tuuli, M. G., Macones, G. A. & Stout, M. J. Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy. BMC Res. Notes 11, 1–7 (2018).
doi: 10.1186/s13104-018-3809-4