Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India
Journal article, 2014

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.

mobile genetic elements

lake sediment

antibiotic resistance

pharmaceutical pollution

metagenomics

plasmids

horizontal gene transfer

Author

Johan Bengtsson-Palme

University of Gothenburg

Fredrik Boulund

Chalmers, Mathematical Sciences, Mathematical Statistics

University of Gothenburg

Jerker Fick

Umeå University

Erik Kristiansson

Chalmers, Mathematical Sciences, Mathematical Statistics

University of Gothenburg

D. G. Joakim Larsson

University of Gothenburg

Frontiers in Microbiology

1664-302X (ISSN)

Vol. 5 648 648

Subject Categories

Biological Sciences

Bioinformatics and Systems Biology

Other Natural Sciences

Genetics

DOI

10.3389/fmicb.2014.00648

More information

Latest update

2/27/2018