Novel bacteriophage-mediated β-lactamase-encoding genes and their risk assessment in environmental communities

Abstract

Bacteria can obtain antibiotic resistance genes (ARGs) through multiple transmission routes, including horizontal gene transfer mediated by phages. Sequence-based metagenomics can detect novel phage-derived ARGs and avoid spending a great deal of time on phage isolation. Here, a metagenomic method was applied to explore the presence of ARGs in phages in freshwater samples. Two novel β-lactamase-encoding genes, blaORF88 and blaORF47, were identified and characterized in phage genomes for the first time in this study. Phylogenetic analyses indicated that blaORF88 is a member of the class C β-lactamase family, while blaORF47 formed an independent branch away from the class C β-lactamases. The average absolute abundance of blaORF88 in phage DNA and bacterial DNA was as high as 5.14 log GC/100 ml and 5.73 log GC/ml, respectively. The blaORF47 gene detected in bacterial DNA was found at the highest concentration, particularly in urban sewage samples, with 5.32 log GC/ml. Our findings raise concerns that phages might carry unknown or novel ARGs, which may spread into bacteria, leading to the emergence of antibiotic-resistant bacteria in the environment, and we urgently need effective strategies to avoid the health risks caused by ARGs.