Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort

Toufiq, Rida, Shahid, Alizay, Zahra, Rabaab, Lankapalli, Aditya Kumar, Oduwo, Jared, Owinoh, Edward Otieno, Aftab, Sadia, Hassan, Brekhna, Thomson, Kathryn, Walsh, Timothy R and Sands, Kirsty 2026. Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort. BMJ Open 16 (9) , e120775. 10.1136/bmjopen-2026-120775

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Abstract

Purpose 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. Participants A total of 107 mother–infant 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. Findings to date Baseline characteristics of 98/107 mother–infant 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 (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime. Future plan 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.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Schools > Medicine
Publisher:	BMJ Publishing Group
ISSN:	2044-6055
Date of First Compliant Deposit:	30 September 2026
Date of Acceptance:	13 August 2026
Last Modified:	30 Sep 2026 11:55
URI:	https://orca.cardiff.ac.uk/id/eprint/189906

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