{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,28]],"date-time":"2024-08-28T13:55:21Z","timestamp":1724853321807},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T00:00:00Z","timestamp":1724112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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 \u2018residual\u2019 clinical vaginal\/vaginal-rectal swabs post clinical testing and storage for 7\u201310\u00a0days at 4\u00a0\u00b0C (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 \u2018residual\u2019 clinical swabs aligned with published studies. The \u2018research\u2019 swabs, stored at 4\u00a0\u00b0C 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\u00a0h. 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.<\/jats:p>","DOI":"10.1038\/s41598-024-70431-5","type":"journal-article","created":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T18:03:21Z","timestamp":1724177001000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy"],"prefix":"10.1038","volume":"14","author":[{"given":"Laura K.","family":"Boelsen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melanie J.","family":"Williams","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yeukai TM.","family":"Mangwiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herah","family":"Hansji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Czajko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa","family":"Marcelino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Forster","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanne M.","family":"Said","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"Satzke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Saffery","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"key":"70431_CR1","doi-asserted-by":"publisher","first-page":"1609","DOI":"10.1016\/0002-9378(90)90638-N","volume":"163","author":"JR Fliegner","year":"1990","unstructured":"Fliegner, J. R. & Garland, S. M. Perinatal mortality in victoria, Australia: Role of group B streptococcus. Am. J. Obstet. Gynecol. 163, 1609\u20131611 (1990).","journal-title":"Am. J. Obstet. Gynecol."},{"key":"70431_CR2","first-page":"1","volume":"45","author":"Centers for Disease Control and Prevention","year":"1996","unstructured":"Centers for Disease Control and Prevention. Prevention of perinatal group B streptococcal disease: a public health perspective. MMWR Recomm. Rep. 45, 1\u201324 (1996).","journal-title":"MMWR Recomm. Rep."},{"key":"70431_CR3","doi-asserted-by":"crossref","unstructured":"Schrag, S., Gorwitz, R., Fultz-Butts, K. & Schuchat, A. Prevention of perinatal group B streptococcal disease. Revised guidelines from CDC. MMWR. Recommendations and reports\u202f: Morbidity and mortality weekly report. Recommendations and reports \/ Centers for Disease Control 51, 1\u201322 (2002).","DOI":"10.1891\/0730-0832.22.1.23"},{"key":"70431_CR4","unstructured":"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)."},{"key":"70431_CR5","doi-asserted-by":"publisher","first-page":"e0135620","DOI":"10.1371\/journal.pone.0135620","volume":"10","author":"AYK Albert","year":"2015","unstructured":"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).","journal-title":"PLoS One"},{"key":"70431_CR6","doi-asserted-by":"publisher","first-page":"4680","DOI":"10.1073\/pnas.1002611107","volume":"108","author":"J Ravel","year":"2011","unstructured":"Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. U.S.A. 108, 4680\u20134687 (2011).","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"70431_CR7","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-10","author":"R Romero","year":"2014","unstructured":"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).","journal-title":"Microbiome"},{"issue":"6","key":"70431_CR8","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1038\/s41591-019-0450-2","volume":"25","author":"JM Fettweis","year":"2019","unstructured":"Fettweis, J. M. et al. The vaginal microbiome and preterm birth. Nat. Med. 25(6), 1012\u20131021 (2019).","journal-title":"Nat. Med."},{"key":"70431_CR9","unstructured":"Safer Care Victoria. Group B streptococcus (GBS) \u2013 screening and management. https:\/\/www.safercare.vic.gov.au\/best-practice-improvement\/clinical-guidance\/maternity\/group-b-streptococcus-gbs-screening-and-management (2019)."},{"key":"70431_CR10","first-page":"1","volume":"59","author":"JR Verani","year":"2010","unstructured":"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\u2013revised guidelines from CDC, 2010. MMWR Recomm. Rep. 59, 1\u201336 (2010).","journal-title":"MMWR Recomm. Rep."},{"key":"70431_CR11","doi-asserted-by":"publisher","first-page":"e36934","DOI":"10.1371\/journal.pone.0036934","volume":"7","author":"G Bai","year":"2012","unstructured":"Bai, G. et al. Comparison of storage conditions for human vaginal microbiome studies. PLoS One 7, e36934 (2012).","journal-title":"PLoS One"},{"key":"70431_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12866-016-0891-4","volume":"16","author":"J Wagner","year":"2016","unstructured":"Wagner, J. et al. Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol. 16, 1\u201317 (2016).","journal-title":"BMC Microbiol."},{"key":"70431_CR13","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581\u2013583 (2016).","journal-title":"Nat. Methods"},{"key":"70431_CR14","unstructured":"McLaren, M. R. & Callahan, B. J. Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2. 10.5281\/ZENODO.4587955. (2021)."},{"key":"70431_CR15","unstructured":"Callahan, B. RDP taxonomic training data formatted for DADA2 (RDP trainset 18\/release 11.5). 10.5281\/ZENODO.4310151. (2020)."},{"key":"70431_CR16","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinform. 10, 421 (2009).","journal-title":"BMC Bioinform."},{"key":"70431_CR17","doi-asserted-by":"publisher","first-page":"baaa062","DOI":"10.1093\/database\/baaa062","volume":"2020","author":"CL Schoch","year":"2020","unstructured":"Schoch, C. L. et al. NCBI taxonomy: A comprehensive update on curation, resources and tools. Database 2020, baaa062 (2020).","journal-title":"Database"},{"key":"70431_CR18","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217 (2013).","journal-title":"PLoS One"},{"key":"70431_CR19","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","volume":"27","author":"KP Schliep","year":"2011","unstructured":"Schliep, K. P. Phangorn: Phylogenetic analysis in R. Bioinformatics 27, 592\u2013593 (2011).","journal-title":"Bioinformatics"},{"key":"70431_CR20","doi-asserted-by":"publisher","first-page":"3997","DOI":"10.1093\/bioinformatics\/btv494","volume":"31","author":"U Bodenhofer","year":"2015","unstructured":"Bodenhofer, U., Bonatesta, E., Horej\u0161-Kainrath, C. & Hochreiter, S. msa: An R package for multiple sequence alignment. Bioinformatics 31, 3997\u20133999 (2015).","journal-title":"Bioinformatics"},{"key":"70431_CR21","unstructured":"Oksanen, J. et al. vegan: Community Ecology Package. Preprint at https:\/\/cran.r-project.org\/package=vegan (2020)."},{"key":"70431_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1\u201321 (2014).","journal-title":"Genome Biol."},{"key":"70431_CR23","volume-title":"Ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2006","unstructured":"Wickham, H. Ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2006)."},{"key":"70431_CR24","first-page":"18","volume":"2","author":"A Liaw","year":"2002","unstructured":"Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18\u201322 (2002).","journal-title":"R News"},{"key":"70431_CR25","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1890\/08-0879.1","volume":"91","author":"MA Murphy","year":"2010","unstructured":"Murphy, M. A., Evans, J. S. & Storfer, A. Quantifying Bufo boreas connectivity in yellowstone national park with landscape genetics. Ecology 91, 252\u2013261 (2010).","journal-title":"Ecology"},{"key":"70431_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/srep16350","author":"JM Choo","year":"2015","unstructured":"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).","journal-title":"Sci. Rep."},{"key":"70431_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-016-0186-x","volume":"4","author":"AG Shaw","year":"2016","unstructured":"Shaw, A. G. et al. Latitude in sample handling and storage for infant faecal microbiota studies: The elephant in the room?. Microbiome 4, 1\u201314 (2016).","journal-title":"Microbiome"},{"key":"70431_CR28","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00763-19","author":"Y Liang","year":"2020","unstructured":"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).","journal-title":"mSphere"},{"key":"70431_CR29","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1186\/1471-2334-10-285","volume":"10","author":"NA El Aila","year":"2010","unstructured":"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).","journal-title":"BMC Infect. Dis."},{"key":"70431_CR30","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1471-2393-5-12","volume":"5","author":"JE Hiller","year":"2005","unstructured":"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).","journal-title":"BMC Pregnancy Childbirth"},{"key":"70431_CR31","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1471-2334-9-153","volume":"9","author":"NA El Aila","year":"2009","unstructured":"El Aila, N. A. et al. Genotyping of Streptococcus agalactiae (group B streptococci) isolated from vaginal and rectal swabs of women at 35\u201337 weeks of pregnancy. BMC Infect. Dis. 9, 153 (2009).","journal-title":"BMC Infect. Dis."},{"key":"70431_CR32","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1186\/1471-2334-9-167","volume":"9","author":"NA El Aila","year":"2009","unstructured":"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).","journal-title":"BMC Infect. Dis."},{"key":"70431_CR33","first-page":"1","volume":"13","author":"J Daniels","year":"2009","unstructured":"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\u2013178 (2009).","journal-title":"Health Technol. Assess (Rockv)"},{"key":"70431_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13104-018-3809-4","volume":"11","author":"KM Wylie","year":"2018","unstructured":"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\u20137 (2018).","journal-title":"BMC Res. Notes"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70431-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70431-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70431-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,20]],"date-time":"2024-08-20T18:10:10Z","timestamp":1724177410000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-70431-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,20]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["70431"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-70431-5","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,20]]},"assertion":[{"value":"12 February 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"CS is lead investigator on a Merck Investigator Studies Program grant funded by MSD on pneumococcal serotype epidemiology in children and is an investigator on a clinical research collaboration on PCV vaccination in Mongolia, funded by Pfizer. CS has received consulting fees from Merck. LKB, MJW, YTMM, HH, AC, VM, SF, JMS and RS declare no potential competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"19318"}}