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Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Journal article
Authors Nachiket Marathe
Anders Janzon
Stathis Kotsakis
Carl-Fredrik Flach
Mohammad Razavi
Fanny Berglund
Erik Kristiansson
D. G. Joakim Larsson
Published in Environment International
Volume 112
Pages 279-286
ISSN 0160-4120
Publication year 2018
Published at Department of Mathematical Sciences
Institute of Biomedicine, Department of Infectious Medicine
Centre for antibiotic resistance research, CARe
Pages 279-286
Language en
Links https://doi.org/10.1016/j.envint.20...
Keywords Antibiotic pollution, Antibiotic resistance, ESBL, Functional metagenomics, Novel resistance gene
Subject categories Bioinformatics (Computational Biology), Microbiology, Bacteriology

Abstract

© 2017 Elsevier Ltd Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, bla RSA1 and bla RSA2 , were phylogenetically close to clinically important ESBLs like bla GES , bla BEL and bla L2 , and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.

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