First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh

Abstract

Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4-8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.

Keywords: Bangladesh; Colistin resistance; E. coli; MDR; Plasmid; mcr-1.