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

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.

Multi-Drug Resistant Escherichia coli, Biosecurity and Anti-Microbial Use in Live Bird Markets, Abeokuta, Nigeria

“…AMR E. coli are commonly found in food producing animals such as in the gastrointestinal tract of chickens and facilities in which these chickens are housed [ 17 , 18 , 19 ]. The presence and persistence of resistance in commensal E. coli is a significant biomarker for the selective pressure enforced by antibiotic use and subsequent resistance predicted in other potentially pathogenic bacteria [ 20 ]. The high prevalence of MDR E. coli in poultry has been evaluated and reported in several countries including Nigeria [ 5 , 21 , 22 , 23 , 24 , 25 ].…”

Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia

“…The Centers for Disease Control and Prevention (CDC) has classified extended-spectrum ß-lactamase (ESBL) expression in Enterobacteriaceae as a serious threat to public health due to limited therapeutic options and challenges in controlling its transmission [ 1 ]. The surveillance of ESBL is complicated by the commensal and hardy nature of Enterobacteriaceae, where ESBL has been reported not only from the clinical setting but also in asymptomatic community dwellers [ 2 – 4 ], wastewater [ 5 , 6 ], farm animals and pets [ 7 , 8 ], and even natural environments [ 9 , 10 ]. Notably, these nonclinical settings often lack regular antibiotic surveillance and monitoring, rendering them reservoirs for ESBL and other antibiotic resistance genes which can potentially supply these resistance determinants to virulent and pathogenic strains.…”

“…Additionally, ST131 is also frequently associated with fluoroquinolone resistance, either through the carriage of plasmid-mediated quinolone resistance (PMQR) genes such as qnrS or quinolone resistance determining region (QRDR) chromosomal mutations, such as gyrA and parC [ 14 , 17 ]. Nevertheless, ESBL dissemination can also be carried and disseminated by commensal strains through horizontal gene transfer of plasmids carrying the ESBL gene [ 18 ], as observed in community studies (e.g., [ 2 , 7 ]).…”

Occurrence of Multi-Drug-Resistant Escherichia coli in Chickens, Humans, Rodents and Household Soil in Karatu, Northern Tanzania

“…Escherichia coli is the major cause of urinary tract infections and neonatal meningitis in humans [3], and it also causes avian colibacillosis, a serious infectious disease in poultry [4]. Other conditions caused by E. coli in chickens include yolk sac infections, pericarditis, peritonitis and osteomyelitis [5]. E. coli is a commensal microbe in humans and chickens that carries and spreads resistance genes to other pathogens [6], threatening public health.…”