Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial

• DOI: 10.1038/s41467-022-28525-z
• Publication Date: 2022-02-16T11:03:04Z
• Authors: Marta Reyman; Marlies A. van Ho...; Rebecca L. Watson; Mei Ling J. N. Chu; Kayleigh Arp; Wouter J. de Waal; Irene Schiering; Frans B. Plötz; Rob J. L. Willems; Willem van Schaik; Elisabeth A. M. S...; Debby Bogaert
• Keywords: Resistome

Broad-spectrum antibiotics for suspected early-onset neonatal sepsis (sEONS) may have pronounced effects on gut microbiome development and selection of antimicrobial resistance when administered in the first week life, during assembly phase microbiome. Here, 147 infants born at ≥36 weeks gestational age, requiring broad-spectrum treatment sEONS their life were randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations, namely penicillin + gentamicin, co-amoxiclav gentamicin or amoxicillin cefotaxime (ZEBRA study, Trial Register NL4882). Average duration was 48 hours. A subset 80 non-antibiotic treated from a healthy birth cohort served as controls (MUIS NL3821). Rectal swabs and/or faeces collected before immediately after treatment, 1, 4 12 months life. Microbiota characterized by 16S rRNA-based sequencing panel 31 genes tested using targeted qPCR. Confirmatory shotgun metagenomic executed samples. The overall microbial community composition gene profile majorly shift directly following (R2 = 9.5%, adjusted p-value 0.001 R2 7.5%, 0.001, respectively) normalize over 1.1%, 0.03 0.6%, 0.23, respectively). We find decreased abundance Bifidobacterium spp. increased Klebsiella Enterococcus compared controls. Amoxicillin shows largest both profile, whereas exhibits least effects. These data suggest that choice empirical is relevant adverse ecological side-effects.