Characterization of vancomycin-resistance gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.

OBJECTIVES

To characterize vancomycin-resistance gene clusters and potential -carrying bacteria in the intestinal microbiota of healthy volunteers exposed or not to β-lactam antibiotics.

METHODS

Stool samples were collected before and after 7 days of cefprozil β-lactam antibiotic exposure of 18 participants and six control participants who were not exposed to the antibiotic at the same time points. Metagenomic sequencing and culture-enriched metagenomic sequencing (with and without β-lactam selection) were used to characterize gene clusters and determine potential -carrying bacteria. Alteration by antimicrobials was also examined.

RESULTS

Culture enrichment allowed detection of genes in a large number of participants (11/24; 46%) compared to direct metagenomics (2/24; 8%). genes were detected in stool cultures only following β-lactam exposure, either after β-lactam treatment of participants or after culture of stools with β-lactam selection. Six types of gene clusters were identified. Two types of cluster highly similar to those of enterococci were found in two participants. Other genes or clusters were nearly identical to those identified in commensal anaerobic bacteria of the families Lachnospiraceae and Oscillospiraceae and/or bordered by genomic sequences similar or related to these anaerobes, suggesting that they are the origin or carriers of .

CONCLUSIONS

This study showed that culture-enriched metagenomics allowed detection of genes not detected by direct metagenomics and revealed collateral enrichment of bacteria containing vancomycin-resistance genes following exposure to β-lactams, with a higher prevalence of the most likely gut commensal anaerobes carrying . These commensal anaerobes could be the reservoir of genes carried by enterococci.