{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:27:56Z","timestamp":1792787276478,"version":"4.5.0"},"reference-count":45,"publisher":"BMJ","issue":"9","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"unspecified","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Ineos Oxford Institute for Antimicrobial Research, University of Oxford","award":["INEOS Oxbridge Doctoral Initiative"],"award-info":[{"award-number":["INEOS Oxbridge Doctoral Initiative"]}],"id":[{"id":"https:\/\/ror.org\/052gg0110","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["BMJ Open"],"accepted":{"date-parts":[[2026,8,13]]},"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Participants<\/jats:title>\n                    <jats:p>A total of 107 mother\u2013infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings to date<\/jats:title>\n                    <jats:p>Baseline characteristics of 98\/107 mother\u2013infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54\/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (&lt;2500\u2009g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6\u2009months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Future plan<\/jats:title>\n                    <jats:p>Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1136\/bmjopen-2026-120775","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T13:30:36Z","timestamp":1789738236000},"page":"e120775","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":0,"title":["Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort"],"prefix":"10.1136","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-7636-4527","authenticated-orcid":false,"given":"Rida","family":"Toufiq","sequence":"first","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alizay","family":"Shahid","sequence":"additional","affiliation":[{"name":"Department of Biology, Quaid-i-Azam University, Islamabad, Islamabad Capital Territory, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rabaab","family":"Zahra","sequence":"additional","affiliation":[{"name":"Department of Biology, Quaid-i-Azam University, Islamabad, Islamabad Capital Territory, Pakistan"},{"name":"Trinity College Dublin, Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aditya Kumar","family":"Lankapalli","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jared","family":"Oduwo","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8014-7306","authenticated-orcid":false,"given":"Edward Otieno","family":"Owinoh","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadia","family":"Aftab","sequence":"additional","affiliation":[{"name":"Pakistan Institute of Medical Sciences, Islamabad, Islamabad Capital Territory, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brekhna","family":"Hassan","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Cardiff University, Cardiff, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Thomson","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy R","family":"Walsh","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsty","family":"Sands","sequence":"additional","affiliation":[{"name":"Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK"},{"name":"Department of Medical Microbiology, Cardiff University, Cardiff, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"239","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"2026091806301750000_16.9.e120775.1","doi-asserted-by":"publisher","DOI":"10.5483\/BMBRep.2023-0114"},{"key":"2026091806301750000_16.9.e120775.2","doi-asserted-by":"crossref","unstructured":"Stiemsma LT , Michels KB . The Role of the microbiome in the developmental origins of health and disease. Pediatrics 2018;141. doi:10.1542\/PEDS.2017-2437\/37739","DOI":"10.1542\/peds.2017-2437"},{"key":"2026091806301750000_16.9.e120775.3","doi-asserted-by":"crossref","first-page":"224","DOI":"10.3345\/cep.2023.00598","article-title":"Influence of infant microbiome on health and development","volume":"67","author":"Younge","year":"2024","journal-title":"Clin Exp Pediatr"},{"key":"2026091806301750000_16.9.e120775.4","doi-asserted-by":"publisher","DOI":"10.1002\/phar.2731"},{"key":"2026091806301750000_16.9.e120775.5","doi-asserted-by":"crossref","first-page":"8787","DOI":"10.3748\/wjg.v21.i29.8787","article-title":"Role of the normal gut microbiota","volume":"21","author":"Jandhyala","year":"2015","journal-title":"WJG"},{"key":"2026091806301750000_16.9.e120775.6","doi-asserted-by":"publisher","DOI":"10.1007\/s00394-017-1445-8"},{"key":"2026091806301750000_16.9.e120775.7","doi-asserted-by":"crossref","unstructured":"Spragge F , Bakkeren E , Jahn MT , et al . Microbiome diversity protects against pathogens by nutrient blocking. Science 2023;382. doi:10.1126\/science.adj3502","DOI":"10.1126\/science.adj3502"},{"key":"2026091806301750000_16.9.e120775.8","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad9378"},{"key":"2026091806301750000_16.9.e120775.9","doi-asserted-by":"crossref","first-page":"102150","DOI":"10.1016\/j.mib.2022.102150","article-title":"Antibiotic resistance in the commensal human gut microbiota","volume":"68","author":"Lamberte","year":"2022","journal-title":"Curr Opin Microbiol"},{"key":"2026091806301750000_16.9.e120775.10","doi-asserted-by":"crossref","unstructured":"Dongre DS , Saha UB , Saroj SD . Exploring the role of gut microbiota in antibiotic resistance and prevention. Ann Med 2025;57. doi:10.1080\/07853890.2025.2478317","DOI":"10.1080\/07853890.2025.2478317"},{"key":"2026091806301750000_16.9.e120775.11","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3151"},{"key":"2026091806301750000_16.9.e120775.12","doi-asserted-by":"crossref","unstructured":"Bilal H , Khan MN , Rehman T , et al . Antibiotic resistance in Pakistan: a systematic review of past decade. BMC Infect Dis 2021;21. doi:10.1186\/s12879-021-05906-1","DOI":"10.1186\/s12879-021-05906-1"},{"key":"2026091806301750000_16.9.e120775.13","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(24)01867-1\/ATTACHMENT\/4F9FA746-A486-4BC0-BF71-075D4D1D6D56\/MMC3.PDF"},{"key":"2026091806301750000_16.9.e120775.14","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1186\/s12879-021-06795-0","article-title":"Antimicrobial resistance among GLASS priority pathogens from Pakistan: 2006\u20132018","volume":"21","author":"Saeed","year":"2021","journal-title":"BMC Infect Dis"},{"key":"2026091806301750000_16.9.e120775.15","doi-asserted-by":"crossref","unstructured":"Samarra A , Esteban-Torres M , Cabrera-Rubio R , et al . Maternal-infant antibiotic resistance genes transference: what do we know? Gut Microbes 2023;15. doi:10.1080\/19490976.2023.2194797","DOI":"10.1080\/19490976.2023.2194797"},{"key":"2026091806301750000_16.9.e120775.16","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1007\/s00248-017-0985-z","article-title":"The Threat of Antimicrobial Resistance on the Human Microbiome","volume":"74","author":"Brinkac","year":"2017","journal-title":"Microb Ecol"},{"key":"2026091806301750000_16.9.e120775.17","doi-asserted-by":"crossref","first-page":"122","DOI":"10.29271\/jcpsp.2025.01.122","article-title":"Gaps and Barriers to the Implementation of Antimicrobial Stewardship Programmes in Hospitals of Pakistan","volume":"35","author":"Khan","year":"2025","journal-title":"J Coll Physicians Surg Pak"},{"key":"2026091806301750000_16.9.e120775.18","doi-asserted-by":"crossref","first-page":"37265987","DOI":"10.1093\/jacamr\/dlad062","article-title":"Drivers of inappropriate antibiotic use in low- and middle-income countries","volume":"5","author":"Otaigbe","year":"2023","journal-title":"JAC-Antimicrobial Resistance"},{"key":"2026091806301750000_16.9.e120775.19","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1038\/s41372-025-02209-0","article-title":"A systematic review of Perinatal Antibiotic Stewardship - where we are, where to go?","volume":"45","author":"Winteler","year":"2025","journal-title":"J Perinatol"},{"key":"2026091806301750000_16.9.e120775.20","unstructured":"Pakistan (PAK) - Demographics, Health &amp; Infant Mortality - UNICEF DATA. 2026. Available: https:\/\/data.unicef.org\/country\/pak\/"},{"key":"2026091806301750000_16.9.e120775.21","doi-asserted-by":"publisher","DOI":"10.2147\/IDR.S294156"},{"key":"2026091806301750000_16.9.e120775.22","doi-asserted-by":"crossref","unstructured":"Patangia DV , Grimaud G , Wang S , et al . Influence of age, socioeconomic status, and location on the infant gut resistome across populations. Gut Microbes 2024;16. doi:10.1080\/19490976.2023.2297837","DOI":"10.1080\/19490976.2023.2297837"},{"key":"2026091806301750000_16.9.e120775.23","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1016\/j.tim.2025.05.008","article-title":"Analyzing human gut microbiome data from global populations: challenges and resources","volume":"33","author":"Arif","year":"2025","journal-title":"Trends Microbiol"},{"key":"2026091806301750000_16.9.e120775.24","doi-asserted-by":"crossref","unstructured":"Luchen CC , Chibuye M , Spijker R , et al . Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review. PLoS Med 2023;20. doi:10.1371\/journal.pmed.1004235","DOI":"10.1371\/journal.pmed.1004235"},{"key":"2026091806301750000_16.9.e120775.25","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1016\/j.tim.2025.07.003","article-title":"Antibiotic effects on the gut microbiome across diverse geographies","volume":"33","author":"Jaya","year":"2025","journal-title":"Trends Microbiol"},{"key":"2026091806301750000_16.9.e120775.26","doi-asserted-by":"crossref","first-page":"8139","DOI":"10.1038\/s41467-025-63401-6","article-title":"Temporal dynamics and microbial interactions shaping the gut resistome in early infancy","volume":"16","author":"Chatzigiannidou","year":"2025","journal-title":"Nat Commun"},{"key":"2026091806301750000_16.9.e120775.27","doi-asserted-by":"crossref","first-page":"11536","DOI":"10.1038\/s41467-025-66497-y","article-title":"Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother\u2019s milk","volume":"16","author":"Ferretti","year":"2025","journal-title":"Nat Commun"},{"key":"2026091806301750000_16.9.e120775.28","doi-asserted-by":"crossref","first-page":"105630","DOI":"10.1016\/j.ebiom.2025.105630","article-title":"Dynamics of gut resistome and mobilome in early life: a meta-analysis","volume":"114","author":"Bargheet","year":"2025","journal-title":"EBioMedicine"},{"key":"2026091806301750000_16.9.e120775.29","doi-asserted-by":"crossref","first-page":"935","DOI":"10.3390\/microorganisms12050935","article-title":"Improving Bacterial Metagenomic Research through Long-Read Sequencing","volume":"12","author":"Greenman","year":"2024","journal-title":"Microorganisms"},{"key":"2026091806301750000_16.9.e120775.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02262-1"},{"key":"2026091806301750000_16.9.e120775.31","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1038\/s41564-022-01184-y","article-title":"Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries","volume":"7","author":"Carvalho","year":"2022","journal-title":"Nat Microbiol"},{"key":"2026091806301750000_16.9.e120775.32","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2025-111007"},{"key":"2026091806301750000_16.9.e120775.33","unstructured":"BARNARDS . Ineos Oxford Institute. 2026. Available: https:\/\/www.ineosoxford.ox.ac.uk\/barnards [Accessed 3 Mar 2026]."},{"key":"2026091806301750000_16.9.e120775.34","doi-asserted-by":"crossref","DOI":"10.1186\/s13006-020-00295-8","article-title":"Prelacteal feeding practices in Pakistan: a mixed-methods study","volume":"15","author":"Asim","year":"2020","journal-title":"Int Breastfeed J"},{"key":"2026091806301750000_16.9.e120775.35","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1186\/s12889-025-21947-6","article-title":"Community health needs assessment: findings from a community-university partnership strengthening program on maternal and child health in Pakistan","volume":"25","author":"Zakar","year":"2025","journal-title":"BMC Public Health"},{"key":"2026091806301750000_16.9.e120775.36","doi-asserted-by":"crossref","first-page":"100398","DOI":"10.1016\/j.microb.2025.100398","article-title":"Comparative evaluation of DNA extraction protocols for neonatal gut microbiota profiling in a resource-limited setting","volume":"7","author":"Akpulu","year":"2025","journal-title":"The Microbe"},{"key":"2026091806301750000_16.9.e120775.37","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/s41385-022-00548-1","article-title":"The rise to power of the microbiome: power and sample size calculation for microbiome studies","volume":"15","author":"Ferdous","year":"2022","journal-title":"Mucosal Immunol"},{"key":"2026091806301750000_16.9.e120775.38","doi-asserted-by":"crossref","unstructured":"Silverman JD , Shenhav L , Halperin E , et al . Statistical considerations in the design and analysis of longitudinal microbiome studies. bioRxiv [Preprint] 2018. doi:10.1101\/448332","DOI":"10.1101\/448332"},{"key":"2026091806301750000_16.9.e120775.39","unstructured":"The DHS Program - Pakistan: DHS, 2017-18 - Final Report (English). 2026. Available: https:\/\/dhsprogram.com\/publications\/publication-fr354-dhs-final-reports.cfm [accessed 7 Jul 2026]"},{"key":"2026091806301750000_16.9.e120775.40","doi-asserted-by":"crossref","first-page":"169","DOI":"10.5005\/jp-journals-10006-1485","article-title":"Birth Weight for Gestational Age Centile Charts for Low-risk Population of Islamabad Capital Territory: A Hospital-based Study and Cross-country Comparison","volume":"9","author":"Tasnim","year":"2017","journal-title":"Journal of South Asian Federation of Obstetrics and Gynaecology"},{"key":"2026091806301750000_16.9.e120775.41","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1186\/s12874-023-02116-y","article-title":"Height-for-age and weight-for-age growth charts for Pakistani infants under six months: derived from a novel case selection method using multiple indicator cluster survey data","volume":"23","author":"Aasim","year":"2023","journal-title":"BMC Med Res Methodol"},{"key":"2026091806301750000_16.9.e120775.42","unstructured":"WHO EMRO - WHO: breastfeeding critical for public health and preventing annual losses of US$2.8 billion in Pakistan. Available: https:\/\/www.emro.who.int\/pak\/pakistan-news\/who-breastfeeding-critical-for-public-health-and-preventing-annual-losses-of-us-2-8-billion-in-pakistan.html?utm_source=chatgpt.com [Accessed 13 Jun 2026]."},{"key":"2026091806301750000_16.9.e120775.43","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2019.1581063"},{"key":"2026091806301750000_16.9.e120775.44","doi-asserted-by":"crossref","first-page":"e0244866","DOI":"10.1371\/journal.pone.0244866","article-title":"Treatment outcomes, antibiotic use and its resistance pattern among neonatal sepsis patients attending Bahawal Victoria Hospital, Pakistan","volume":"16","author":"Atif","year":"2021","journal-title":"PLoS One"},{"key":"2026091806301750000_16.9.e120775.45","unstructured":"Manuals of Emergency Obstetric and Newborn Care | NCMNH. Available: https:\/\/ncmnh.org.pk\/publications\/safe-motherhood\/manuals-of-emergency-obstetric-and-newborn-care\/ [Accessed 9 Mar 2026]."}],"container-title":["BMJ Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1136\/bmjopen-2026-120775","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T13:30:46Z","timestamp":1789738246000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmjopen.bmj.com\/lookup\/doi\/10.1136\/bmjopen-2026-120775"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":45,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,18]]},"published-print":{"date-parts":[[2026,9]]}},"alternative-id":["10.1136\/bmjopen-2026-120775"],"URL":"https:\/\/doi.org\/10.1136\/bmjopen-2026-120775","relation":{},"ISSN":["2044-6055","2044-6055"],"issn-type":[{"value":"2044-6055","type":"print"},{"value":"2044-6055","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9]]}}}