Detection and characterization of ESBL-producing Enterobacteriaceae from the gut of healthy chickens, Gallus gallus domesticus in rural Nepal: Dominance of CTX-M-15-non-ST131 Escherichia coli clones.

Niranjan Nayak,Rajesh Amberpet,Brijesh Sathian,Indira Bairy,Yang Metok,Grzegorz Woźniakowski,Supram Hosuru Subramanya,Shashiraj Padukone,Dharm Raj Bhatta

doi:10.1371/journal.pone.0227725

Abstract

The surge in the prevalence of drug-resistant bacteria in poultry is a global concern as it may pose an extended threat to humans and animal health. The present study aimed to investigate the colonization proportion of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae (EPE and CPE, respectively) in the gut of healthy poultry, Gallus gallus domesticus in Kaski district of Western Nepal. Total, 113 pooled rectal swab specimens from 66 private household farms and 47 commercial poultry farms were collected by systematic random sampling from the Kaski district in western Nepal. Out of 113 pooled samples, 19 (28.8%) samples from 66 backyard farms, and 15 (31.9%) from 47 commercial broiler farms were positive for EPE. Of the 38 EPE strains isolated from 34 ESBL positive rectal swabs, 31(81.6%) were identified as Escherichia coli, five as Klebsiella pneumoniae (13.2%), and one each isolate of Enterobacter species and Citrobacter species (2.6%). Based on genotyping, 35/38 examined EPE strains (92.1%) were phylogroup-1 positive, and all these 35 strains (100%) had the CTX-M-15 gene and strains from phylogroup-2, and 9 were of CTX-M-2 and CTX-M-14, respectively. Among 38 ESBL positive isolates, 9 (23.7%) were Ambler class C (Amp C) co-producers, predominant were of DHA, followed by CIT genes. Two (6.5%) E. coli strains of ST131 belonged to clade C, rest 29/31 (93.5%) were non-ST131 E. coli. None of the isolates produced carbapenemase. Twenty isolates (52.6%) were in-vitro biofilm producers. Univariate analysis showed that the odd of ESBL carriage among commercial broilers were 1.160 times (95% CI 0.515, 2.613) higher than organically fed backyard flocks. This is the first study in Nepal, demonstrating the EPE colonization proportion, genotypes, and prevalence of high-risk clone E. coli ST131 among gut flora of healthy poultry. Our data indicated that CTX-M-15 was the most prevalent ESBL enzyme, mainly associated with E. coli belonging to non-ST131clones and the absence of carbapenemases.

Highlights

The family Enterobacteriaceae exhibit antimicrobial resistance mainly due to the production of extended-spectrum β-lactamases (ESBL), AmpC β-lactamases, and carbapenemases [1]
Superbugs that are resistant to multiple classes of antibiotics like tetracycline, fluoroquinolone, trimethoprim owing to the acquisition of ESBL genes have increased rapidly worldwide
The present study aimed to investigate the colonization proportion of extended-spectrum β-lactamase-producing Enterobacteriaceae (EPE) and carbapenemase-producing Enterobacteriaceae (CPE) in the gut of healthy poultry, Gallus gallus domesticus in Kaski district, western Nepal

Summary

Introduction

The family Enterobacteriaceae exhibit antimicrobial resistance mainly due to the production of extended-spectrum β-lactamases (ESBL), AmpC β-lactamases, and carbapenemases [1]. Food-producing animals are considered to be an important reservoir of various multidrug-resistant (MDR) microbes [2]. Animal-derived Enterobacteriaceae, Escherichia coli, can be pathogenic to humans and may act as a donor of resistance genes to other pathogens. Among ESBL genes, CTX-M-15 producing E. coli sequence type 131 (ST131) is a well-established pandemic clone causing significant extraintestinal infections in humans [3]. Poultry and other food-producing animals harboring E. coli ST131 clones can spread to humans either directly via consumption or through environmental pathways. The emergence and rapid spread of ESBLs’ among Enterobacteriaceae is a major hurdle in treating severe infections of livestock as well as humans [4]

Methods

Findings

Discussion

Conclusion