Metagenomic analysis reveals reduction in antibiotic resistance genes in breastfed infants fed Bifidobacterium longum subsp. infantis EVC001

Purpose: The rapid emergence of antibiotic-resistant pathogens is a major public health concern. Each year more than two million people in the United States develop antibiotic-resistant infections, and at least 23,000 die as a result. Furthermore, it is estimated that over 70% of bacteria responsible for nosocomial infections are resistant to at least one of the antibiotics used worldwide as first-line therapy. Drug-resistant bacterial infections require longer periods of treatment costing the US health care system an estimated $5 billion annually. Recent studies have focused on the early infant gut microbiome showing that antibiotic resistance genes (ARGs) can be acquired in early life and may have long term sequelae. Currently, there are limited means by which the spread of ARGs, or the organisms that harbor them, can be restricted. We recently demonstrated extensive and durable modification of the infant gut microbiome following a three-week course of the activated probiotic strain B. infantis EVC001 for a year. Here, we used shotgun metagenomics to characterize the effect of B. infantis EVC001 modulation of the microbiome on the abundance of ARGs in breastfed infants. Methods: Subjects were randomized to receive either lactation support and a commercial preparation of activated Bifidobacterium longum subsp. infantis EVC001 (n = 29 samples) or lactation support alone (n = 31 samples). Infants were fed EVC001 for two weeks starting at day 7. Stool samples were collected at day 21 and processed for shotgun metagenomics. Bacterial strain-level analysis showed that infants fed EVC001 had a significant increase of B. infantis EVC001, and a decreased number of potentially enteropathogenic bacteria (e.g. E. coli, Klebsiella, Clostridium, Staphylococcus, and Streptococcus). Results: The EVC001-fed group showed a significant decrease of 87.5% in ARGs compared to controls. 38 ARGs were significantly reduced in the EVC001-fed infants. These genes are associated with resistance to a wide range of drugs including β-lactams, fluoroquinolones, and macrolides. EVC001-fed infants presented less overall resistance genes, and to fewer drug classes than the control infants, which harbored a wide array of genes conferring resistance to clinically-associated antibiotics. Confirmation of antibiotic-resistant genotype and phenotype was assessed via minimum inhibitory concentrations (MICs) analysis from bacterial isolates. Conclusion: In this study we demonstrated that even in the absence of antibiotic selective pressure the healthy term infant gut of a Northern America population harbors a variety of genes encoding resistance to several antibiotic classes. Colonization by an activated Bifidobacterium longum subsp. infantis EVC001 resulted in a stable and rapid colonization of this single strain, which dominated the bacterial gut community in breastfed infants. EVC001 colonization had profound impacts on the infant gut microbiome, reducing the number and diversity of ARGs and revealing immediate clinically relevant benefits in the treatment of nosocomial infections.