Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infantsOriginal paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This study examined how early-life antibiotics and probiotics shape the gut microbiome and resistome of preterm infants. Researchers used shotgun metagenomics with genome-resolved and strain-level analysis. They compared probiotic-supplemented and non-supplemented cohorts, and within each, infants given antibiotics versus none. They reconstructed metagenome-assembled genomes and cultured isolate genomes. They also ran an ex vivo infant gut model to test horizontal transfer of antibiotic-resistance plasmids between Enterococcus strains. The goal was to disentangle probiotic and antibiotic effects on resistance-gene carriage.
Who was studied?
The study analyzed 34 very-low-birth-weight, human-milk-fed preterm infants, all under 34 weeks gestation, drawn from a larger observational cohort in UK neonatal units. Samples came from two hospital sites. One cohort received a probiotic (Infloran) containing Bifidobacterium bifidum and Lactobacillus acidophilus; the other did not. Some infants in each cohort received benzylpenicillin and/or gentamicin. Weekly fecal samples spanned the first three weeks of life. In total, 92 longitudinal samples were sequenced, yielding over 300 metagenome-assembled genomes and around 90 isolate genomes.
What were the most important findings?
Probiotic-supplemented infants had significantly fewer antibiotic resistance genes than non-supplemented infants across the first three weeks, and fewer ARG types in weeks 2 and 3. Their guts were dominated by actively replicating Bifidobacterium, which suppressed pathobionts. From 411 genomes, 195 dereplicated strains were analyzed. Enterococcus, Klebsiella, Escherichia, and Staphylococcus were the most resistant genera. None of the probiotic-cohort Klebsiella or Escherichia genomes were multidrug-resistant. In the gut model, a roughly 137 kb Enterococcus mega-plasmid carrying an aminoglycoside resistance gene transferred to a susceptible strain, conferring gentamicin resistance.
What are the greatest implications of this study?
The findings support probiotics as a tool for antimicrobial stewardship in preterm infants, since supplementation lowered resistance-gene and multidrug-resistant pathogen burden while normalizing the microbiome. This matters for a population routinely exposed to broad-spectrum antibiotics. However, persistent Enterococcus with high plasmid-carriage and demonstrated transfer capacity shows probiotics do not prevent horizontal gene transfer. Shared strains across unrelated infants suggested nosocomial transmission. The short three-week window and two-site design limit long-term conclusions. The authors call for continued surveillance and longer, larger studies.