A Prospective Multisite Investigation of the Neonatal Gut Resistome Development and Its Association with Sepsis Outcomes in Nigerian Neonatal Intensive Care Units

The development of the neonatal gut resistome in the first weeks of life is shaped by birth mode, antibiotic exposure, feeding practices, and environmental colonization sources, with emerging evidence that early resistome establishment has lasting consequences for infection susceptibility and sepsis outcomes. This critical research question has not been investigated in Nigerian neonatal intensive care units (NICUs), where antibiotic use intensity is high and infection rates are severe. This prospective multisite cohort study characterized neonatal gut resistome development and its association with late-onset sepsis outcomes in NICUs at Ahmadu Bello University Teaching Hospital (Zaria), University of Ilorin Teaching Hospital, and Lagos Island General Hospital over 18 months. Serial rectal swabs from 150 NICU-admitted neonates were collected at days 1, 3, 7, 14, and 28 of life. Shotgun metagenomics and 16S rRNA sequencing were simultaneously applied to characterize resistome composition and gut microbial community dynamics. Clinical data including antibiotic exposure history, mode of delivery, gestational age, feeding type, and sepsis episodes were recorded. Late-onset sepsis (LOS) was diagnosed by positive blood culture after 72 hours of life. Results showed rapid resistome expansion in antibiotic-exposed neonates, with blaNDM, blaTEM, and tetracycline resistance genes appearing within 72 hours of aminoglycoside-carbapenem therapy in 76 percent of exposed infants. Resistome beta-diversity at day 7 significantly differentiated neonates who subsequently developed LOS from those who did not. Gut microbiome diversity at day 3 was a stronger predictor of LOS than antibiotic exposure alone. These findings constitute an original longitudinal resistome contribution to neonatal microbiology in Nigeria and identify the NICU gut resistome as a modifiable risk factor for sepsis outcomes. Keywords: neonatal resistome, NICU, sepsis, gut microbiome, longitudinal metagenomics.