Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of preterm infants (isolate genomes)

Preterm infants (<37 weeks gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe infections, including necrotising enterocolitis and sepsis. However, antibiotics can disrupt the development of early-life microbiota, potentially impairing gut immunity and colonisation resistance. Evidence shows that probiotics (e.g., Bifidobacterium) may help restore healthy gut microbiota. In this study, we examined the effects of probiotics and antibiotics on the preterm gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants (moderate to very preterm), with one cohort receiving probiotics. Within each group, some infants were treated with antibiotics (benzylpenicillin and/or gentamicin) while others served as controls. We performed shotgun metagenome sequencing on 93 longitudinal faecal samples, generated >300 metagenome-assembled genomes, and obtained ~90 isolate genomes through targeted culturomics, enabling analysis of the microbiome/resistome at species and strain levels. Additionally, we investigated in vitro horizontal gene transfer (HGT) capacity of the multidrug-resistant (MDR) pathogen Enterococcus via infant gut models. Overall, probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and helped restore a typical early-life microbiota. However, the persistence of MDR pathogens like Enterococcus, with high HGT potential, highlights the need for ongoing surveillance in neonatal care. Our findings underscore the complex interactions among antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.