The INBUGS-P longitudinal birth cohort 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, recruiting 107 mother-infant pairs at a Pakistani hospital with 10 predefined follow-up timepoints from birth to 12 months.
The INBUGS-P cohort recruited 107 mother-infant pairs at the Pakistan Institute of Medical Sciences between December 2023 and June 2024.
A large volume of biological and environmental samples were collected across the follow-up period.
The cohort reflects an urban low-income population in Pakistan.
Caesarean section was the predominant mode of delivery in the cohort.
A notable proportion of infants in the cohort were late preterm or had low birth weight.
Exclusive breastfeeding from birth to 6 months was uncommon despite breastfeeding being the predominant feeding mode.
Antibiotic exposure was near-universal for mothers postpartum and common among infants during follow-up.
Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and antimicrobial resistance genes.
This research describes the setup and baseline characteristics of a new study called INBUGS-P, which is tracking the gut bacteria and antibiotic resistance genes in Pakistani infants during their first year of life. The researchers recruited 107 mothers and their babies at a hospital in Islamabad, Pakistan, and collected hundreds of stool, breast milk, maternal, and environmental samples at regular intervals from birth to 12 months. The families involved were predominantly urban and low-income, with a median household income of roughly US$170 per month. The study found that more than half of deliveries in this group were by caesarean section, about 1 in 8 infants were born preterm, and only around 24 out of 98 babies were exclusively breastfed for the recommended first six months. Crucially, nearly all mothers received antibiotics after giving birth, and 19 infants were also given antibiotics during the first year — most commonly a combination of amikacin and ceftazidime. These factors — delivery mode, feeding practices, and antibiotic use — are all known to influence the development of an infant's gut microbiome and can affect how antibiotic-resistant bacteria become established. This research matters because low- and middle-income countries like Pakistan carry a disproportionate burden of antibiotic resistance and infant infections, yet relatively little is known about how the gut microbiome and resistance genes develop in these settings during early life. By sequencing the collected samples using advanced genomic techniques, the INBUGS-P team aims to provide detailed insight into how early exposures shape the infant gut, with potential implications for understanding and ultimately reducing antibiotic resistance in vulnerable populations.
Toufiq R, Shahid A, Zahra R, Lankapalli A, Oduwo J, Owinoh E, et al.. (2026). Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.. BMJ open. https://doi.org/10.1136/bmjopen-2026-120775