Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
Journal article, 2019

Background: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases. Results: Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and bla RSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli. Conclusion: By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.

Hidden Markov model

Antibiotic resistance

Carbapenemase

Hospital effluent

India

Pathogens

Author

Nachiket Marathe

Havforskningsinstituttet

University of Gothenburg

Fanny Berglund

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Mohammad Razavi

University of Gothenburg

C. Pal

Ministry of Agriculture and Forestry - New Zealand

University of Gothenburg

Johannes Dröge

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Sharvari Samant

Mahatma Gandhi Mission's Dental College and Hospital

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

D. G. Joakim Larsson

University of Gothenburg

Microbiome

2049-2618 (eISSN)

Vol. 7 1 97

Subject Categories

Microbiology

Medical Genetics

Genetics

DOI

10.1186/s40168-019-0710-x

PubMed

31248462

More information

Latest update

10/1/2019