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

Abstract

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.

The Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Bacteria from Hospital Sewage, Treated Effluents and Receiving Rivers

“…NDM was identified to be the most prevalent carbapenemase and it was commonly harbored in Enterobacteriaceae, as well as in some non-Enterobacteriaceae families (Acinetobacter spp., Aeromonas spp., and Pseudomonas spp.). Our results are consistent with previous studies, showing that bla NDM has occurred in many unrelated species and is spreading rapidly in different environmental compartments [15,18,32]. The genus Acinetobacter, which is widespread in nature and particularly abundant in wastewater, has been recognized in recent years as a universal threat to public health [10].…”

Metagenomics Reveals Impact of Urbanisation in Central India on the Human Gut Microbiome and its Antimicrobial Resistance Profiles

“…The co-occurrence of pathogens and AMR genes for critically important antibiotics offers increased opportunities for unwanted horizontal gene transfer events [26]. Perhaps of most concern, the Ambler class B metallo-beta-lactamase NDM which was detected in only 1 of 35 rural subjects was found in 32/70 urban subjects, and also supports clinical data detecting carbapenemase producing pathogens from Mumbai [29] and another recent study showing that NDM-1 is also common in hospital effluent from Delhi [30].…”

“…Inadequate public health infrastructure, poor sanitation, and infection control practices in the primary healthcare system increase demand for parallel markets and further contribute to the overuse of antibiotics. Antibiotic resistance is also being driven environmentally by untreated urban waste, sewage effluent from Indian hospitals [26] and pharmaceutical pollution of waterways [27]. Indiscriminate use of beta-lactam antibiotics in both the community setting and hospitals has given rise to the presence of antibiotic-resistant Enterobacteriaceae in healthy human faecal samples in North India [28].…”

Prevalence of Colistin-Resistant, Carbapenem-Hydrolyzing Proteobacteria in Hospital Water Bodies and Out-Falls of West Bengal, India

“…Along similar lines, neighboring countries, such as Bangladesh and Singapore, have also reported prevalence of bla NDM harboring bacteria in hospital wastewater and water collected from hospital-adjacent areas [14,15]. In the Indian context, reports are few and restricted to one or two hospitals [16][17][18]. So far, the spread of carbapenem-resistant Enterobacteriaceae and New Delhi Metallo-β lactamase-1 (NDM-1) in hospital wastewater out-falls has been explicitly probed only in New Delhi [19,20].…”