Impact of Commonly Prescribed Antibiotics on Preterm Gut Microbiome in Necrotising Enterocolitis and Late Onset Sepsis

Background: Antibiotics are usually prescribed to preterm infants during their early days of life in neonatal intensive care units. The effects of this intervention on the developing gut microbiome are poorly understood but might have important consequences for health. We aimed to explore the routinely used antibiotics in a neonatal intensive care unit and to what extent this intervention alters the preterm gut microbiome. Methods: The three most commonly prescribed antibiotic combinations were analysed VCM (Vancomycin, Ceftazidine and Metronidazole), VC (Vancomycin and Ceftazidine) and AFG (Amoxicillin, Flucloxacillin, and Gentamicin). Sampling was performed at four time points: 2-3 days before course started (Pre), last day of administration (During), 1-2 days after antibiotic was given (After), and one week later than or as late as possible before next antibiotic course. In total, 141 stool samples were collected from 38 patients and bacterial profiling was performed by 16SrRNA gene sequencing (Miseq, Illumina) Results: Bacterial diversity increased significantly after the VC course was stopped (P=0.1). Diversity was reduced for all antibiotic treatment during their administration (P>0.05). Generally, VCM and VC were comparable with lower bacterial taxa when compared to AFG which recorded higher bacterial taxa. The result also showed that VC and VCM recovered but AFG does not. Conclusion: The three antibiotics courses differentially affected the preterm gut microbiome, causing reductions in the diversity. Further work is necessary to determine the contribution of these changes to health and how medical intervention can be tailored to achieve optimal outcomes for preterm infants.