{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:10:46Z","timestamp":1772169046103,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/gatesopenres.14041.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T00:00:00Z","timestamp":1724976000000}}],"reference-count":56,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T00:00:00Z","timestamp":1724976000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI133080"],"award-info":[{"award-number":["R01AI133080"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1105094"],"award-info":[{"award-number":["OPP1105094"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21AI154387"],"award-info":[{"award-number":["R21AI154387"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32GM100842"],"award-info":[{"award-number":["T32GM100842"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["gatesopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Gates Open Res"],"abstract":"\n Background Previous studies of infants born to HIV-positive mothers have linked HIV exposure to poor outcomes from gastrointestinal and respiratory illnesses, and to overall increased mortality rates. The mechanism behind this is unknown, but it is possible that differences in the nasopharyngeal (NP) microbiome between infants who are HIV-unexposed or HIV-exposed could play a role in perpetuating some outcomes. Methods We conducted a longitudinal analysis of 170 NP swabs of healthy infants who are HIV-exposed (n=10) infants and their HIV(+) mothers, and infants who are HIV-unexposed, uninfected (HUU; n=10) .and their HIV(-) mothers. These swabs were identified from a sample library collected in Lusaka, Zambia between 2015 and 2016. Using 16S rRNA gene sequencing, we characterized the maturation of the microbiome over the first 14 weeks of life to determine what quantifiable differences exist between HIV-exposed and HUU infants, and what patterns are reflected in the mothers' NP microbiomes. Results In both HIV-exposed and HUU infants,\n Staphylococcus<\/ns4:italic>\n and\n Corynebacterium<\/ns4:italic>\n began as primary colonizers of the NP microbiome but were in time replaced by\n Dolosigranulum<\/ns4:italic>\n ,\n Streptococcus<\/ns4:italic>\n ,\n Moraxella<\/ns4:italic>\n and\n Haemophilus<\/ns4:italic>\n . When evaluating the interaction between HIV exposure status and time of sampling among infants, the microbe\n Staphylococcus haemolyticus<\/ns4:italic>\n showed a distinctive high association with HIV exposure at birth. When comparing infants to their mothers with paired analyses, HIV-exposed infants\u2019 NP microbiome composition was only slightly different from their HIV(+) mothers at birth or 14 weeks, including in their carriage of\n S. pneumoniae<\/ns4:italic>\n ,\n H. influenzae<\/ns4:italic>\n , and\n S. haemolyticus<\/ns4:italic>\n . Conclusions Our analyses indicate that the HIV-exposed infants in our study exhibit subtle differences in the NP microbial composition throughout the sampling interval. Given our results and the sampling limitations of our study, we believe that further research must be conducted in order to confidently understand the relationship between HIV exposure and infants\u2019 NP microbiomes.\n <\/ns4:p>","DOI":"10.12688\/gatesopenres.14041.2","type":"journal-article","created":{"date-parts":[[2024,8,30]],"date-time":"2024-08-30T09:35:09Z","timestamp":1725010509000},"page":"143","update-policy":"https:\/\/doi.org\/10.12688\/gatesopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants"],"prefix":"10.12688","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7113-7598","authenticated-orcid":false,"given":"Aubrey R.","family":"Odom","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3353-0617","authenticated-orcid":false,"given":"Christopher J.","family":"Gill","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1514-5320","authenticated-orcid":false,"given":"Rachel","family":"Pieciak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4672-5915","authenticated-orcid":false,"given":"Arshad","family":"Ismail","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donald","family":"Thea","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8003-8874","authenticated-orcid":false,"given":"William B.","family":"MacLeod","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W. Evan","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rotem","family":"Lapidot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2024,8,30]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"S187-95","DOI":"10.1097\/QAD.0000000000000090","article-title":"HIV-exposed infants: rethinking care for a lifelong condition.","volume":"27 Suppl 2","author":"N Sugandhi","year":"2013","journal-title":"AIDS."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"2368-79","DOI":"10.1056\/NEJMoa1108275","article-title":"Three postpartum antiretroviral regimens to prevent intrapartum HIV infection.","volume":"366","author":"K Nielsen-Saines","year":"2012","journal-title":"N Engl J Med."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"2351-60","DOI":"10.1097\/QAD.0000000000001211","article-title":"A meta-analysis assessing all-cause mortality in HIV-exposed uninfected compared with HIV-unexposed uninfected infants and children.","volume":"30","author":"A Brennan","year":"2016","journal-title":"AIDS."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"1-8","DOI":"10.1097\/QAI.0000000000002097","article-title":"A meta-analysis assessing diarrhea and pneumonia in HIV-Exposed Uninfected Compared with HIV-Unexposed Uninfected infants and children.","volume":"82","author":"A Brennan","year":"2019","journal-title":"J Acquir Immune Defic Syndr."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"1696-702","DOI":"10.1056\/NEJM199312023292304","article-title":"A prospective study of diarrhea and HIV-1 infection among 429 zairian infants.","volume":"329","author":"D Thea","year":"1993","journal-title":"N Engl J Med."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"562-9","DOI":"10.1086\/519847","article-title":"Infant morbidity, mortality, and breast milk immunologic profiles among breast-feeding HIV-infected and HIV-uninfected women in Botswana.","volume":"196","author":"R Shapiro","year":"2007","journal-title":"J Infect Dis."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"1346-56","DOI":"10.1093\/cid\/civ059","article-title":"Increased risk for and mortality from invasive pneumococcal disease in HIV-exposed but uninfected infants aged <1 year in South Africa, 2009-2013.","volume":"60","author":"C von Mollendorf","year":"2015","journal-title":"Clin Infect Dis."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"191-199","DOI":"10.1016\/j.jpeds.2016.09.040","article-title":"High burden of morbidity and mortality but not growth failure in infants exposed to but uninfected with human immunodeficiency virus in Tanzania.","volume":"180","author":"L Locks","year":"2017","journal-title":"J Pediatr."},{"key":"ref-9","first-page":"401-409","article-title":"Infectious disease morbidity and growth among young HIV-exposed uninfected children in Jamaica.","volume":"40","author":"R Pierre","year":"2016","journal-title":"Rev Panam Salud Publica."},{"key":"ref-10","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.13.21264939","article-title":"Nasopharyngeal dysbiosis precedes the development of lower respiratory tract infections in young infants: a longitudinal infant cohort study.","author":"R Lapidot","year":"2021","journal-title":"medRxiv."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"298-308","DOI":"10.1164\/rccm.201401-0073OC","article-title":"The impact of breastfeeding on nasopharyngeal microbial communities in infants.","volume":"190","author":"G Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"1094","DOI":"10.3389\/fimmu.2019.01094","article-title":"Dysregulation of intestinal epithelial cell RIPK pathways promotes chronic inflammation in the IBD gut.","volume":"10","author":"R Garcia-Carbonell","year":"2019","journal-title":"Front Immunol."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"853-8","DOI":"10.1016\/s0022-3476(05)83170-1","article-title":"Invasive pneumococcal disease among infected and uninfected children of mothers with human immunodeficiency virus infection.","volume":"124","author":"J Farley","year":"1994","journal-title":"J Pediatr."},{"key":"ref-14","doi-asserted-by":"publisher","first-page":"286-295","DOI":"10.1111\/tmi.12057","article-title":"Dynamics of nasopharyngeal bacterial colonisation in HIV-exposed young infants in Tanzania.","volume":"18","author":"G Kinabo","year":"2013","journal-title":"Trop Med Int Health."},{"key":"ref-15","doi-asserted-by":"publisher","first-page":"656-662","DOI":"10.1097\/00006454-199707000-00007","article-title":"Nasopharyngeal pneumococcal colonization among Kenyan children: antibiotic resistance, strain types and associations with human immunodeficiency virus type 1 infection.","volume":"16","author":"I Rusen","year":"1997","journal-title":"Pediatr Infect Dis J."},{"key":"ref-16","doi-asserted-by":"publisher","first-page":"211-215","DOI":"10.1016\/s1201-9712(99)90027-9","article-title":"Nasopharyngeal carriage of multidrug-resistant Streptococcus pneumoniae in institutionalized HIV-infected and HIV-negative children in northeastern Romania.","volume":"3","author":"E Leibovitz","year":"1999","journal-title":"Int J Infect Dis."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"608-612","DOI":"10.1097\/00006454-200007000-00005","article-title":"Colonization by Streptococcus penumoniae in human immunodeficiency virus-infected children.","volume":"19","author":"F Polack","year":"2000","journal-title":"Pediatr Infect Dis J."},{"key":"ref-18","doi-asserted-by":"publisher","first-page":"S154-S164","DOI":"10.1093\/cid\/ciw526","article-title":"Incidence of severe and nonsevere pertussis among HIV-exposed and -unexposed Zambian infants through 14 weeks of age: results from the Southern Africa Mother Infant Pertussis Study (SAMIPS), a longitudinal birth cohort study.","volume":"63","author":"C Gill","year":"2016","journal-title":"Clin Infect Dis."},{"key":"ref-19","doi-asserted-by":"publisher","DOI":"10.1186\/s13006-015-0033-x","article-title":"Infants and young children feeding practices and nutritional status in two districts of Zambia.","volume":"10","author":"M Katepa-Bwalya","year":"2015","journal-title":"Int Breastfeed J."},{"key":"ref-20","doi-asserted-by":"publisher","DOI":"10.7448\/IAS.20.1.21251","article-title":"Postnatal HIV transmission in breastfed infants of HIV-infected women on ART: a systematic review and meta-analysis.","volume":"20","author":"S Bispo","year":"2017","journal-title":"J Int AIDS Soc."},{"key":"ref-21","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.","volume":"41","author":"A Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref-22","article-title":"FastQC: a quality control tool for high throughput sequence data.","author":"S Andrews","year":"2010"},{"key":"ref-23","doi-asserted-by":"publisher","first-page":"2114-2120","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data.","volume":"30","author":"A Bolger","year":"2014","journal-title":"Bioinformatics."},{"key":"ref-24","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-33","article-title":"PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.","volume":"2","author":"C Hong","year":"2014","journal-title":"Microbiome."},{"key":"ref-25","article-title":"Aubreyodom\/HIV_exposed_infants: initial release.","year":"2022","journal-title":"Zenodo."},{"key":"ref-26","doi-asserted-by":"publisher","first-page":"13-22","DOI":"10.1093\/biomet\/73.1.13","article-title":"Longitudinal data analysis using generalized linear models.","volume":"73","author":"K Liang","year":"1986","journal-title":"Biometrika."},{"key":"ref-27","doi-asserted-by":"publisher","DOI":"10.1002\/0471249688","article-title":"Categorical data analysis.","author":"A Agresti","year":"2002"},{"key":"ref-28","doi-asserted-by":"publisher","first-page":"79-107","DOI":"10.1146\/annurev.clinpsy.032408.153550","article-title":"Advances in analysis of longitudinal data.","volume":"6","author":"R Gibbons","year":"2010","journal-title":"Annu Rev Clin Psychol."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.3390\/genes13071183","article-title":"A distribution-free model for longitudinal metagenomic count data.","volume":"13","author":"D Luo","year":"2022","journal-title":"Genes (Basel)."},{"key":"ref-30","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac149","article-title":"Detecting sparse microbial association signals adaptively from longitudinal microbiome data based on generalized estimating equations.","volume":"23","author":"H Sun","year":"2022","journal-title":"Brief Bioinform."},{"key":"ref-31","doi-asserted-by":"publisher","first-page":"1-11","DOI":"10.18637\/jss.v015.i02","article-title":"The R package geepack for generalized estimating equations.","volume":"15","author":"S H\u00f8jsgaard","year":"2006","journal-title":"Journal of statistical software."},{"key":"ref-32","doi-asserted-by":"publisher","DOI":"10.1002\/9781118391686","article-title":"Methods of multivariate analysis","author":"A Rencher","year":"2012"},{"key":"ref-33","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaf5103","article-title":"Maternal HIV infection influences the microbiome of HIV-uninfected infants.","volume":"8","author":"J Bender","year":"2016","journal-title":"Sci Transl Med."},{"key":"ref-34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0080299","article-title":"Breast milk and gut microbiota in African mothers and infants from an area of high HIV prevalence.","volume":"8","author":"R Gonz\u00e1lez","year":"2013","journal-title":"PLoS One."},{"key":"ref-35","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-22244-6","article-title":"HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort.","volume":"8","author":"S Claassen-Weitz","year":"2018","journal-title":"Sci Rep."},{"key":"ref-36","doi-asserted-by":"publisher","first-page":"655-665","DOI":"10.1038\/s41396-021-01108-4","article-title":"Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy.","volume":"16","author":"M Kelly","year":"2022","journal-title":"ISME J."},{"key":"ref-37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005975","article-title":"A longitudinal study of the infant nasopharyngeal microbiota: the effects of age, illness and antibiotic use in a cohort of South East Asian children.","volume":"11","author":"S Salter","year":"2017","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-38","doi-asserted-by":"publisher","first-page":"704-715","DOI":"10.1016\/j.chom.2015.03.008","article-title":"The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development.","volume":"17","author":"S Teo","year":"2015","journal-title":"Cell Host Microbe."},{"key":"ref-39","doi-asserted-by":"publisher","DOI":"10.1101\/2022.07.27.501757","article-title":"Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.","author":"T Faits","year":"2022","journal-title":"bioRxiv."},{"key":"ref-40","doi-asserted-by":"publisher","first-page":"7292-7308","DOI":"10.1128\/JB.187.21.7292-7308.2005","article-title":"Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species.","volume":"187","author":"F Takeuchi","year":"2005","journal-title":"J Bacteriol."},{"key":"ref-41","doi-asserted-by":"publisher","first-page":"166-168","DOI":"10.1128\/JCM.05563-11","article-title":"Staphylococcus haemolyticus as an important hospital pathogen and carrier of methicillin resistance genes.","volume":"50","author":"E Barros","year":"2012","journal-title":"J Clin Microbiol."},{"key":"ref-42","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2024.127652","article-title":"Staphylococcus haemolyticus: an updated review on nosocomial infections, antimicrobial resistance, virulence, genetic traits, and strategies for combating this emerging opportunistic pathogen.","volume":"282","author":"C Rossi","year":"2024","journal-title":"Microbiol Res."},{"key":"ref-43","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10061130","article-title":"Clinical infections, antibiotic resistance, and pathogenesis of Staphylococcus haemolyticus.","volume":"10","author":"H Eltwisy","year":"2022","journal-title":"Microorganisms."},{"key":"ref-44","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2334-13-572","article-title":"Molecular epidemiology of coagulase-negative Staphylococcus carriage in neonates admitted to an intensive care unit in Brazil.","volume":"13","author":"Y Ternes","year":"2013","journal-title":"BMC Infect Dis."},{"key":"ref-45","doi-asserted-by":"publisher","first-page":"458-469","DOI":"10.1016\/j.jinf.2015.06.010","article-title":"Nasopharyngeal bacterial burden and antibiotics: influence on inflammatory markers and disease severity in infants with respiratory syncytial virus bronchiolitis.","volume":"71","author":"M Su\u00e1rez-Arrabal","year":"2015","journal-title":"J Infect."},{"key":"ref-46","doi-asserted-by":"publisher","first-page":"611-615","DOI":"10.1136\/thx.2005.048397","article-title":"High incidence of pulmonary bacterial co-infection in children with severe Respiratory Syncytial Virus (RSV) bronchiolitis.","volume":"61","author":"K Thorburn","year":"2006","journal-title":"Thorax."},{"key":"ref-47","doi-asserted-by":"publisher","first-page":"1924-1928","DOI":"10.1093\/infdis\/jiw456","article-title":"Differences in the nasopharyngeal microbiome during acute respiratory tract infection with human rhinovirus and respiratory syncytial virus in infancy.","volume":"214","author":"C Rosas-Salazar","year":"2016","journal-title":"J Infect Dis."},{"key":"ref-48","doi-asserted-by":"publisher","first-page":"1232-1234","DOI":"10.4103\/jfmpc.jfmpc_111_19","article-title":"Increased household exposure to respiratory pathogens in HIV exposed uninfected children due to maternal HIV.","volume":"8","author":"T Khan","year":"2019","journal-title":"J Family Med Prim Care."},{"key":"ref-49","doi-asserted-by":"publisher","first-page":"e00852-20","DOI":"10.1128\/mSphere.00852-20","article-title":"Dolosigranulum pigrum cooperation and competition in human nasal microbiota.","volume":"5","author":"S Brugger","year":"2020","journal-title":"mSphere."},{"key":"ref-50","doi-asserted-by":"publisher","first-page":"1104-1115","DOI":"10.1164\/rccm.201602-0220OC","article-title":"Nasopharyngeal microbiota, host transcriptome, and disease severity in children with respiratory syncytial virus infection.","volume":"194","author":"W de Steenhuijsen Piters","year":"2016","journal-title":"Am J Respir Crit Care Med."},{"key":"ref-51","doi-asserted-by":"publisher","first-page":"634","DOI":"10.3390\/pathogens10060634","article-title":"Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells.","volume":"10","author":"M Islam","year":"2021","journal-title":"Pathogens."},{"key":"ref-52","doi-asserted-by":"publisher","first-page":"e211-e218","DOI":"10.1097\/INF.0000000000001607","article-title":"The nasopharyngeal microbiota of children with respiratory infections in Botswana.","volume":"36","author":"M Kelly","year":"2017","journal-title":"Pediatr Infect Dis J."},{"key":"ref-53","doi-asserted-by":"publisher","first-page":"1329-1339","DOI":"10.1183\/13993003.00152-2016","article-title":"Association of nasopharyngeal microbiota profiles with bronchiolitis severity in infants hospitalised for bronchiolitis.","volume":"48","author":"K Hasegawa","year":"2016","journal-title":"Eur Respir J."},{"key":"ref-54","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-22","article-title":"Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge.","volume":"2","author":"E Allen","year":"2014","journal-title":"Microbiome."},{"key":"ref-55","doi-asserted-by":"publisher","first-page":"1447-1453","DOI":"10.1007\/s12098-012-0762-4","article-title":"Associations between potential bacterial pathogens in the nasopharynx of HIV infected children.","volume":"79","author":"S Bhattacharya","year":"2012","journal-title":"Indian J Pediatr."},{"key":"ref-56","doi-asserted-by":"publisher","first-page":"220-230","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota.","volume":"489","author":"C Lozupone","year":"2012","journal-title":"Nature."}],"container-title":["Gates Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T02:10:15Z","timestamp":1727316615000},"score":1,"resource":{"primary":{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,30]]},"references-count":56,"URL":"https:\/\/doi.org\/10.12688\/gatesopenres.14041.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/gatesopenres.14041.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/gatesopenres.17682.r37923","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/gatesopenres.17682.r37848","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/gatesopenres.17682.r37848","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/gatesopenres.17682.r37923","asserted-by":"object"}]},"ISSN":["2572-4754"],"issn-type":[{"value":"2572-4754","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,30]]},"assertion":[{"value":"Indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/gatesopenres.15340.r33429, Christiana Smith, University of Colorado, Aurora, CO, 16 Jun 2023, version 1, 2 approved with reservations","URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v1#referee-response-33429","order":0,"name":"referee-response-33429","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Aubrey Odom-Mabey<\/b>; \nPosted: 13 Aug 2024<\/i>; Reviewer 1 \nComment 1-1<\/u>: This is a well-written description of a very small study comparing the nasopharyngeal microbiome of Zambian HEU infants (and their mothers) to HUU infants (and their mothers) over the first 14 weeks of life. The hypothesis that the maternal or infant microbiome plays a key role in the increased morbidity\/mortality observed in HEU infants has been under-explored in the literature, justifying the indication for the study. However, the differences identified between HEU and HUU infants in this study were rather minimal (the authors use the word \u201csubtle\u201d), which diminishes the overall impact\/significance of the publication. Strengths of the study include that the participants were followed longitudinally over time, and the HEU and HUU cohorts were well-matched and recruited from the same physical location. \nResponse 1-1<\/u>: We appreciate the reviewer\u2019s summary and thank the reviewer for providing their feedback for this paper. \nComment 1-2<\/u>: The two major limitations of the study, which are described appropriately by the authors, are: 1) the small sample size results in very limited power to identify differences between HEU and HUU infants, leading to \u201cuncertain evidence that there is an HIV exposure effect on the NP microbiome...\u201d and 2) no information is provided on the immune status of the HIV+ mothers (viral load, CD4) or the HIV infection status of the HIV-exposed infants (i.e. HIV NAAT results after birth), which are likely very important contributors to the NP microbiome. For example \u2013 a person with poorly controlled HIV and low CD4 count is at risk of opportunistic respiratory infections (TB, PJP, MAC) which would likely influence the composition of their NP microbiome. Was there really no information available to the study authors that could be included to better describe the health of the mothers and infants (any maternal viral loads or CD4 counts, known maternal comorbidities, infant dried blood spot testing at birth, etc.)? \nResponse 1-2<\/u>: We agree that information on the immune status of the HIV+ mothers is indeed integral to identifying additional factors in the composition of their NP microbiota. We regrettably did not have access to this data as detailed HIV status information was not collected as part of the SAMIPS study, which was focused on Pertussis incidence. It was not optimally designed to look at the impact of HIV exposure as the original study purpose and did not seek to characterize the mothers HIV health status nor collect breastfeeding information. Neither viral load nor CD4 testing were routinely performed in Lusaka at this time and neither of these were deemed essential for the purposes of the original study beyond noting the mothers\u2019 HIV status. We have clarified this point further in the Methods section on line 118, and in the discussion on lines 492-494 (\u201cseveral key variables were not measured that would have been informative as potential confounders in our study results\u201d). \nComment 1-3<\/u>: Person-first language should be used throughout the abstract and manuscript. It is probably fine to use the abbreviations as-is (HIV+, HEU, HUU), but phrases such as \u201cHIV-positive mothers\u201d or \u201cHIV-infected women\u201d should be changed to \u201cwomen\/mothers with HIV\u201d or \u201cwomen\/mothers living with HIV.\u201d The term \u201cmother-to-child transmission\u201d is also outdated and should be changed to \u201cvertical transmission\u201d or \u201cperinatal transmission.\u201d For more information on why this matters, please see: Dilmitis \net al.<\/i> (2012\n1<\/sup>). \nReferences<\/b> 1. Dilmitis S, Edwards O, Hull B, Margolese S, et al.: Language, identity and HIV: why do we keep talking about the responsible and responsive use of language? Language matters. \nJournal of the International AIDS Society<\/i>. 2012; \n15<\/b> (4(Suppl 2)). Publisher Full Text \nResponse 1-3<\/u>: We thank the reviewer for their attentiveness to this matter. We have implemented person-first identifying language throughout the manuscript. \nComment 1-4<\/u>: Introduction, paragraph 2: the authors reference \u201cthe HEU phenomenon\u201d several times without really explaining what \u201cthe phenomenon\u201d is. Are they referring to the increased morbidity and mortality observed in this population? Please be more specific. \nResponse 1-4<\/u>: The reviewer\u2019s inclination is correct; we are referring to the increased morbidity and mortality rates observed in HEU infants. We have altered the manuscript to read more clearly in the introduction, by removing one instance and clarifying in another case the \u201cHEU \u2018phenomenon\u2019 of increased morbidity and\/or mortality rates\u201d (see lines 51, 64, 66). In lines 511-513 of the Conclusions, we altered a sentence reading \u201cThis warrants further research and discussion regarding the phenomenon\u201d to \u201cThe effects we have found here warrant further research and discussion regarding the role HIV exposure plays in infant health before readily affirming or denying that HIV exposure affects infants\u2019 NP microbiomes.\u201d \nComment 1-5<\/u>: Introduction, paragraph 4: The authors state that their study might \u201cprovide insight into the presence or absence of immunological factors distinguishing [HEU vs. HUU infants].\u201d However, differences in the microbiome do not necessarily indicate differences in \u201cimmunological factors.\u201d Recommend revising the text appropriately. \nResponse 1-5<\/u>: We agree with the reviewer\u2019s reasoning that differences present in the microbiome do not necessarily correlate to immunological differences. We made a jump in reasoning that can only be made with something akin to an analysis of host-microbe interactions, which was not conducted here. We have altered the sentence to read, \u201cWe reasoned that by characterizing quantifiable differences in NP microbiota distinguishing these two groups, this pilot study could indicate differences encouraging future immunology-focused studies\u201d (lines 82-83). \nComment 1-6<\/u>: Methods, paragraph 1: it is necessary to state whether all infants breastfed or whether some infants consumed any foods other than breast milk in the first 14 weeks of life, as nutrition sources have a profound ability to impact the microbiome. \nResponse 1-6<\/u>: We agree that information on breastfeeding would be extremely relevant for the purposes of microbiome analysis. After reviewing the case report forms, we found that the study did not assess and collect breast feeding status. For purposes of this study, we can clarify that formula is rarely used and breastfeeding is nearly universal. We have clarified this in the manuscript and added a relevant citation (lines 123-125). \nComment 1-7<\/u>: There are several examples where the manuscript is organized in a non-standard way: Tables containing data (such as Table 1 and Table 2) belong in the results section, not the methods section. Recommend moving these tables, and the text describing them, to the beginning of Results. \nResponse 1-7<\/u>: We have moved the tables and appropriate text descriptions to the beginning of the Results section (lines 267-273). \nComment 1-8<\/u>: The text in the methods section describing the reasons that some samples were excluded (beginning with \u201cSome missingness in the data is present\u2026\u201d) also belongs in results, not methods. \nResponse 1-8<\/u>: We have moved the description of the excluded samples to the beginning of the Results section (line 268). \nComment 1-9<\/u>: There are some \u201ceditorial\u201d comments in the results section, which really belong in the discussion instead. For example, page 7, last paragraph: \u201c\u2026which may in part be the result of the mothers\u2019 acquired immunity over time and therefore lower overall NP carriage;\u201d page 8, 3\nrd<\/sup> to last paragraph: \u201cThese transitional patterns align with those found in a longitudinal East Asian infant cohort.\u201d \nResponse 1-9<\/u>: We have moved the comments in question to the Discussion section, including the larger paragraph on parallel findings from previous studies (lines 285-287; 421-422; other comments were also moved when relevant). \nComment 1-10<\/u>: Table 1 is very confusing and poorly organized: The headers often do not apply to the rows beneath them (male sex and median age should not be categorized under \u201cplace of birth;\u201d median birth weight and twin births should not be categorized under \u201cgestational age;\u201d number of mothers, mothers age, married, father lives with child should not be categorized under \u201cimmunizations at birth;\u201d etc. There are many rows for which the result is 0 in every column, or for which there are apparently no data. These rows should be removed from the table completely. For example, why is the Chilenje clinic described in table when only the Chawama clinic is described in the text? Why is \u201cother place of birth\u201d listed in the table if none of the infants were born in an \u201cother place\u201d? Why are \u201cfather lives with child\u201d and \u201ctrimester initiated ART\u201d included in the table if there are no data for these variables? The L&D complications that did not occur in any infants (obstructed labor, sepsis, hemorrhage, other) can be removed and a sentence could be added to the text that says \u201cnone of these complications occurred: X,Y,Z.\u201d The table shows one infant with birth asphyxia. This infant should be further described in the text. How severe was the birth asphyxia? Did the infant require respiratory support, intubation, oxygen, etc. (since respiratory instrumentation could potentially have impacted this infant\u2019s respiratory microbiome)? \nResponse 1-10<\/u>: We thank the reviewer for their attention to this oversight. We have reordered the rows to clearly define parameter sections, and removed all rows for which the parameter did not apply to the infant demographics. We have added the following sentence in place of the excluded rows: \u201cNone of the mothers in this cohort experienced obstructed labor, sepsis, or hemorrhage complications during the labor and delivery period\u201d (lines 97-99). During the SAMIPS data collection procedures, each mother was asked whether they had any complications with labor and delivery. This was a closed ended question with five possible responses: obstructed labor, birth asphyxia, sepsis, hemorrhage, or other. Follow-up questions about severity or treatment were not asked. Given that the study eligibility criteria limited enrollment to healthy infants with no acute or chronic medical conditions, it is unlikely that the birth asphyxia was severe. However, we cannot rule out the use of respiratory instrumentation that could impact the infant\u2019s respiratory microbiome. We have noted this clarification in our study limitations of the Discussion section (lines 502-503). \nComment 1-11<\/u>: Table 2: The text states that two of 20 mothers lacked swabs at both the t=0 and t=6 time points. However, the table shows all 20 mothers had a swab at t=0 and 2 were missing swabs at t=6. Either the text or table should be revised so that they harmonize. It would be preferred if the table could be stratified by HIV status at each time point, rather than consolidating all of the HEU and HUU results at the bottom. This way it would be easy to see whether either group was over-represented at any one given time point. \nResponse 1-11<\/u>: We appreciate the reviewer\u2019s attention to this discrepancy. We verified that the table contains an accurate summary of the data and updated the text to reflect the table (line 273). We have also updated Table 2 to delineate each status\/subject group per time point. \nComment 1-12<\/u>: Table 3: please standardize the number of decimal points across columns (some columns have 2 decimal points, others have none). \nResponse 1-12:<\/u> We have adjusted the table to have one decimal point standardized across the columns and right-justified the entries (now Table 7). \nComment 1-13<\/u>: Table 4: several columns describe \u201cadjusted p-values\u201d but there is no description of what variables were adjusted for. The reader should not have to refer back to the methods section to understand the statistical analysis. This is also a problem in Table 7. Please add a description of what variables the analyses were adjusted for to the Table heading or to a footnote for each table. \nResponse 1-13:<\/u> We thank the reviewer for their comment. We acknowledge that there may also be some confusion as to what we mean by adjusted p-values. The concept of adjusting p-values is widely used in \u2018omics analysis, and stems from the application of a correction to limit the Type I error (false positive) inflation in multiple hypothesis testing. There are several techniques that can be used for this purpose; we used the Bonferroni correction which is the most conservative. The actual implementation of this correction is to identify a corrected significance level, \u03b1, so each p-value is compared to this new value resulting in an adjusted p-value. We have clarified language throughout the manuscript and caption for Table 7 (now Table 6) by changing to the following language: \u201cA Bonferroni correction was applied to account for multiple hypothesis testing.\u201d (lines 753-754). We recognize that Table 4 (now Table 3) is especially confusing given the different variables. We have rearranged the columns to list the coefficient estimate followed by the unadjusted and adjusted p-values for each variable included in the model. \nComment 1-14<\/u>: Table 6: I believe there is a typo in the table; the two time points being compared are t=0 and t=6 according to the text; however, the table shows t=0 and t=1. \nResponse 1-14<\/u>: We have adjusted Table 6 accordingly (now Table 5). \nComment 1-15<\/u>: Table 7: It is very difficult to understand this table without reading the text. Specifically, what direction is indicated by the positive and negative numbers in the column titled \u201cmean of differences\u201d (higher abundance in infants or higher abundance in mothers)? After a long period of scrutiny, I was able to determine that negative numbers mean higher abundance in infants, but it should be immediately apparent to the reader. Please explain this in the Table heading or in a footnote. \nResponse 1-15<\/u>: We agree that the mean of differences column is not well explained. We have gone ahead and corrected the table caption and heading to explain the sign directionality for mean of differences values for Table 7 (now Table 6). \nComment 1-16<\/u>: Also related to Table 7, in the results section, page 12, paragraph 2: The authors describe that the purpose of the analysis in Table 7 is to compare the abundance of 3 particular bacterial species between the mothers and infants within each cohort (HIV+\/HEU and HIV-\/HUU), and that this comparison will help explain why HEU infants may be more susceptible to morbidity\/mortality. It is not clear how comparing the abundance of these bacteria between mothers vs. infants WITHIN each cohort would help explain the HEU infants\u2019 increased susceptibility to morbidity\/mortality. It seems that to answer this question, it would be more valuable to compare the abundance of bacteria between HEU vs. HUU infants (or between HIV+ vs. HIV- mothers). Please clarify how you expect this analysis to answer the question proposed or modify\/remove the language describing the reason for this analysis. \nResponse 1-16:<\/u> We agree that the justification for performing this set of tests is invalid as written, and so we have rewritten the test justification as follows (see lines 363-366): \u201cAlthough all infants in our cohort were free from illness, we found that certain pathogenic species were present in modest abundance across samples. To ascertain the possibility of HIV-exposed infants acquiring pathogens from their HIV(+) mothers, we conducted paired t-tests for three well-known pathogenic species: Streptococcus pneumoniae; Haemophilus influenzae; and Staphylococcus haemolyticus.\u201d \nComment 1-17<\/u>: Discussion: The authors should add to the list of limitations that their results may not be generalizable to HEU infants around the globe, given that all samples were collected from participants living in a single African country. \nResponse 1-17:<\/u> We agree with this limitation and have added it to our conclusion accordingly on lines 490-491. (\u201cSecond, given that all samples were collected from participants born in Zambia, these results may not be generalizable to HIV-exposed infants in other countries.\u201d) \nComment 1-18<\/u>: Discussion, page 14: There is some redundancy between the last 2 sentences of the first paragraph, and the 6\nth<\/sup> paragraph, both of which describe differences in bacterial diversity between HIV+ and HIV- mothers. \nResponse 1-18:<\/u> We have relocated the sentence referring to Figure 1B (\u201cFrom Figure 1B, we observed that\u2026\u201d) to lines 478-479 and removed the repetitive sentence referring to increased microbial diversity. \nComment 1-19<\/u>: There are several typos in the manuscript. For example, page 11, paragraph 3: \u201cThe same test for all infant samples at time point six was contrastingly showed\u2026.\u201d Also Conclusions: \u201cour findings may suggest that that sociological\u2026.\u201d \nResponse 1-19:<\/u> We have made the appropriate corrections throughout the manuscript and thank the reviewer for their attention to this matter.","URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2#referee-comment-3708","order":1,"name":"referee-comment-3708","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/gatesopenres.17682.r37848, Bryan Vonasek, Michigan State University College of Osteopathic Medicine (Ringgold ID: 43977), East Lansing, Michigan, 24 Sep 2024, version 2, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2#referee-response-37848","order":2,"name":"referee-response-37848","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/gatesopenres.17682.r37923, Rupert Kaul, University of Toronto, Toronto, Ontario, 26 Sep 2024, version 2, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-143\/v2#referee-response-37923","order":3,"name":"referee-response-37923","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the Bill and Melinda Gates Foundation [OPP1105094] who funded the Southern Africa Mother Infant Pertussis Study: Phase I (SAMIPS-1) and also by the NIAID of the NIH under grant R01AI133080 to C.G. W.E.J and A.R.O.M. were supported in part by the NIH under grant R21AI154387. A.R.O.M. was supported in part by the NIGMS of the NIH under grant T32GM100842.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}