Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes.
A metagenomics approach was applied to explore the presence of antibiotic resistance genes (ARGs) in bacteriophages from hospital wastewater. Metagenomic analysis showed that most phage sequences affiliated to the order Caudovirales, comprising the tailed phage families Podoviridae, Siphoviridae and Myoviridae. Moreover, the relative abundance of ARGs in the phage DNA fraction (0.26%) was higher than in the bacterial DNA fraction (0.18%). These differences were particularly evident for genes encoding ATP-binding cassette (ABC) and resistance-nodulation-cell division (RND) proteins, phosphotransferases, β-lactamases and plasmid-mediated quinolone resistance. Analysis of assembled contigs also revealed that blaOXA-10, blaOXA-58 and blaOXA-24 genes belonging to class D β-lactamases as well as a novel blaTEM (98.9% sequence similarity to the blaTEM-1 gene) belonging to class A β-lactamases were detected in a higher proportion in phage DNA. Although preliminary, these findings corroborate the role of bacteriophages as reservoirs of resistance genes and thus highlight the necessity to include them in future studies on the emergence and spread of antibiotic resistance in the environment.
Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
Jéssica
J
Subirats
Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
Alexandre
A
Sànchez-Melsió
Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain.
Carles M
CM
Borrego
Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain. Electronic address: jlbalcazar@icra.cat.
José Luis
JL
Balcázar
École Centrale de Lyon, Université de Lyon, Écully, France.
Pascal
P
Simonet
D001419:Bacteria / Q000187:drug effects / Q000821:virology*; D001435:Bacteriophages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017899:Caudovirales / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D005814:Genes, Viral; D006761:Hospitals; D056186:Metagenomics; D062065:Wastewater / Q000821:virology*
D062065:Wastewater
Antibiotic resistance genes; Bacteriophages; Horizontal gene transfer