Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

Abstract

Background: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. Results: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e −5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases bla HRV-1 and bla HRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring bla HRV-1 and bla HRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow-and extendedspectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.

Phages as a Cohesive Prophylactic and Therapeutic Approach in Aquaculture Systems

“…It is worth noting that the role of phages in spreading antibiotic resistance genes has been raised in a growing number of articles as well, which clearly reflects an increased interest in phage-based therapeutics in general [57][58][59][60]. Metagenomic studies have confirmed the presence of such genes in phages isolated from a vast range of environments, which is in line with their ability to transfer genetic material between hosts.…”

“…In fact, a recent study detected that environmental waters contain a large reservoir of resistance genes, conferring resistance to tetracyclines and β-lactamases. Those genes, detected in phage DNA, were isolated from freshwater, water treatment plants, and oceans [57,59]. Aquatic environments may promote dissemination and acquisition of antibiotic resistance genes [61], which should be taken into consideration in aquacultures.…”

Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

“…The virome data can also be used to predict putative host-phage systems by matching virome sequences to the CRISPR array sequences of bacterial CRISPR-Cas systems 7,8 or bacterial signature genes 9,10 . Virome sequences are also very useful for the discovery of novel phage genes, including antibiotic resistance genes, that are carried by uncultured phages 11,12 .…”

Horizontal Transfer Mediated Proliferation of Antibiotic Resistance Genes in High-Fat Diet Induced Obesity Mice

“…Horizontal gene transfer (HGT) has regarded as the major pathway of ARGs transmission, which includes conjugation, transformation and transduction [9]. As a dominant pathway of HGT, conjugation is the transfer of ARGs through a pilin bridge between a donor and a recipient, which is usually achieved via mobile genetic elements (MGEs), such as plasmids (pMV158oriT), insertion sequences (IS613), integrons (intI-1), transposons (tnpA-03), and phages [10,11]. HGT can occur in any environment, especially where bacterial densities are high, such as in soil [12], in the gut microbiome of humans and animals [4]; and it has been shown to provide microbes with a wide variety of adaptive traits for microbial survival and proliferation under the pressure of antibiotics, heavy metals and other environmental contaminants [13].…”