Detection and characterization of ESBL-producing Enterobacteriaceae from the gut of subsistence farmers, their livestock, and the\xa0surrounding environment in rural Nepal

Bharat Prasad Baral,Yang Metok,Indira Bairy,Supram Hosuru Subramanya,Dipendra Gautam,Niranjan Nayak

doi:10.1038/s41598-021-81315-3

Abstract

The increasing trend of gut colonization by extended-spectrum β-lactamase (ESBL) producing Enterobacterales has been observed in conventional farm animals and their owners. Still, such colonization among domesticated organically fed livestock has not been well studied. This study aimed to determine the gut colonization rate of ESBL-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae (CPE) among rural subsistence farming communities of the Kaski district in Nepal. Rectal swabs collected by systematic random sampling from 128 households of subsistence farming communities were screened for ESBL-producing Enterobacteriaceae and CPE by phenotypic and molecular methods. A total of 357 (57%) ESBL-producing Enterobacteriaceae isolates were obtained from 626 specimens, which included 97 ESBL-producing Enterobacteriaceae (75.8%) from 128 adult humans, 101 (79.5%) from 127 of their children, 51 (47.7%) from 107 cattle, 26 (51%) from 51 goats, 30 (34.9%) from 86 poultry and 52 (42%) from 127 environmental samples. No CPE was isolated from any of the samples. blaCTX-M-15 was the most predominant gene found in animal (86.8%) and human (80.5%) isolates. Out of 308 Escherichia coli isolates, 16 human and two poultry isolates were positive for ST131 and were of clade C. Among non-cephalosporin antibiotics, the resistance rates were observed slightly higher in tetracycline and ciprofloxacin among all study subjects. This is the first one-health study in Nepal, demonstrating the high rate of CTX-M-15 type ESBL-producing Enterobacteriaceae among gut flora of subsistence-based farming communities. Gut colonization by E. coli ST131 clade C among healthy farmers and poultry birds is a consequential public health concern.

Highlights

Abbreviations MDR Multi-drug resistant/resistance ESBL Extended-spectrum β-lactamase carbapenemase-producing Enterobacteriaceae (CPE) Carbapenemase-producing Enterobacteriaceae PCR Polymerase chain reaction MLST Multilocus sequence typing Village Development Committees (VDCs) Village development committees AmpC Ambler class C IQR Interquartile range Double Disc Synergy Test (DDST) Double disc synergy test CLSI Clinical & Laboratory Standards Institute ATCC American type culture collection
The emergence of such resistant traits was restricted to healthcare-associated isolates confined within the clinical s ettings[8]. This trend shifted towards community-associated clinical isolates, and ESBL-producing Enterobacteriaceae have been disseminating to the community inhabitants, including the gut flora of healthy humans and animals
The population structure of ESBL producing E. coli is influenced by ST131 clones, which are the quintessential examples of successful high-risk clones disseminating globally in human clinical isolates[9]

Summary

Introduction

The rates of multi-drug resistance in human and animal pathogens are steadily rising around the globe. The emergence of such resistant traits was restricted to healthcare-associated isolates confined within the clinical s ettings[8] This trend shifted towards community-associated clinical isolates, and ESBL-producing Enterobacteriaceae have been disseminating to the community inhabitants, including the gut flora of healthy humans and animals. Acquisition of ESBL/carbapenemase genes among these gut flora plays a central role in the spread of MDR bacteria among humans, animals, and the environment via the food chain. The gut colonization with ESBL-producing Enterobacteriaceae/CRE may serve as a vivacious source for horizontal transmission and endogenous infections[10] Such resistant gut flora can no longer be considered as innocent bystanders. The population structure of ESBL producing E. coli is influenced by ST131 clones (typical extra-intestinal pathogenic E. coli clone), which are the quintessential examples of successful high-risk clones disseminating globally in human clinical isolates[9]

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