Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
Artikel i vetenskaplig tidskrift, 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
blaRSA1. 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.

Hospital effluent

Antibiotic resistance




Hidden Markov model


Nachiket P. Marathe

Sahlgrenska akademin

Fanny Berglund

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Mohammad Razavi

Sahlgrenska akademin

Chandan Pal

Johannes Dröge

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Sharvari Samant

Erik Kristiansson

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

D. G. Joakim Larsson

Sahlgrenska akademin


2049-2618 (eISSN)

Vol. 7 97 97-



Medicinsk genetik

Bioinformatik och systembiologi



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