The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs

The role of bacteriophages in the spread of antimicrobial resistance genes (ARGs) has been debated over the past decade. Several questions regarding the ARG dissemination potential of bacteriophages remain unanswered. For example, what is the frequency of acquisition of ARGs in phages? Are phages selective in acquiring the ARGs compared to other host genes? What is the predominant mechanism of transferring ARGs to phages? To address these questions, we thoroughly analyzed the available phage genomes, viromes, temperate phage, and prophage sequences for the presence of all known ARGs. Out of the 38,861 phage genome sequences we analyzed, only 182 phages contained a total of 314 ARGs. Interestingly, a few of the Streptococcus and Acinetobacter phages were found to carry an ARG cluster with four or more genes. One of the uncharacterized Myoviridae phages was found to carry the entire vancomycin operon. Furthermore, based on the presence of lysogenic marker sequences, the terminal location of ARGs on phage genomes, and complete ARG clusters transferred to phages, we suggest that ARGs are predominantly acquired from hosts by temperate phages via specialized transduction. The close association of most phage ARGs with lysogenic markers and mobile genetic elements (MGEs) also points towards specialized transduction as a potent mechanism of acquisition of ARGs by phages. Our study further suggests that the acquisition of ARGs by phages occurs by chance rather than through a selective process. Taken together, the limited presence of ARGs in phages, alongside various transfer bottlenecks, significantly restricts the role of phages in the dissemination of ARGs.