Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China)

Abstract

In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.

Keywords: Antibiotic Resistance Gene (ARG); Beta-lactamase; Coastal marine aquaculture; Metagenome; Multi-drug resistant organisms (MDROs).