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Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

Journal article
Authors Johan Bengtsson-Palme
Fredrik Boulund
Jerker Fick
Erik Kristiansson
D. G. Joakim Larsson
Published in Frontiers in Microbiology
Volume 5
Issue 648
ISSN 1664-302X
Publication year 2014
Published at Department of Mathematical Sciences, Mathematical Statistics
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links dx.doi.org/10.3389/fmicb.2014.00648
https://gup-server.ub.gu.se/v1/asse...
Keywords antibiotic resistance, horizontal gene transfer, lake sediment, metagenomics, mobile genetic elements, pharmaceutical pollution, plasmids
Subject categories Biological Sciences, Genetics, Bioinformatics and Systems Biology, Other Natural Sciences

Abstract

There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.

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