A nationwide survey of antimicrobial resistance of Escherichia coli isolated from broiler chickens in Malawi

Abstract

Background: Antimicrobial resistance is a global health challenge with profound implications across sectors. Livestock, a significant field at the One Health interface, lacks sufficient information, particularly in low-resource settings such as Malawi. Objectives: We determined the antimicrobial resistance rates of Escherichia coli isolated from broiler chickens in Malawi and explored the relationship between resistance genes across sectors using genomic analysis. Methods: In 2023, we isolated 115 E. coli strains from 116 faecal and caecal samples from broiler chickens across Malawi. Antimicrobial susceptibility tests were performed using agar dilution method according to the Clinical Laboratory Standard Institute guidelines. Whole-genome sequencing was performed using Illumina sequencing. Results: Notably, 50 isolates (44%) were resistant to cefotaxime. We detected ESBL blaCTX-M genes (blaCTX-M-55, blaCTX-M-14, blaCTX-M-65, blaCTX-M-27, blaCTX-M-15, blaCTX-M-1, and blaCTX-M-3) in 48 cefotaxime-resistant isolates, which exhibited higher resistance rates to levofloxacin than non-ESBL-encoding isolates (29/48; 60% versus 20/67; 30%). All isolates were susceptible to colistin and carbapenems. High resistance rates were observed for tetracycline and co-trimoxazole commonly used in broiler chickens (90% and 70%, respectively). Sequence type 206 and phylogroup A were predominant (14% and 65%, respectively). In the genetic context of blaCTX-M genes, whole-genome alignment of the ESBL-producing isolates with reference plasmids from E. coli of various origins indicated significant similarity. Conclusions: Antimicrobial resistance is highly prevalent among E. coli from broiler chickens in Malawi. Genomic analysis suggests potential transmission pathways for ESBL genes across sectors, necessitating further studies from One Health perspective.