Draft genome sequences and resistome analysis of multidrug-resistant and mcr-1-harboring E. coli isolated from preharvest poultry in Lebanon

J Glob Antimicrob Resist. 2021 Mar 21:S2213-7165(21)00066-7. doi: 10.1016/j.jgar.2021.03.001. Online ahead of print.


OBJECTIVES: Antibiotic resistance pauses a serious risk to Lebanon, a country with challenges in infrastructure and antibiotic stewardship. Recently, a high prevalence of multidrug-resistant E. coli harboring the mobile-colistin-resistance gene (mcr-1) was reported in fecal matter of poultry in Lebanon. Some of these isolates exhibited also resistance to important antibiotics, including cephalosporins and carbapenems. Here, we performed whole genome sequence (WGS) analysis to further analyze the genetic determinants of resistance and the sequence types (ST) of five of these isolates.

METHODS: WGS was performed with a MiSeq sequencer. Draft genomes were assembled using SPAdes v3.9.0. ResFinder (v.3.0) and PlasmidFinder (v1.3) databases were used to analyze the resistome and the plasmid types, respectively. STs were determined with the MLST software.

RESULTS: WGS analysis revealed that the strains harbored 9 to 19 antibiotic resistance genes, including mcr-1.1 and others that encode resistance to important antibiotics used in agriculture and human medicine. In each strain, the mcr-1.1 was located on the same contigs with IncX4 plasmid sequences. Furthermore, the strains belonged to different STs, including those associated with 1) zoonotic transmission from poultry to humans, 2) food contamination, and 3) clinical samples.

CONCLUSIONS: Our analysis revealed diverse genetic resistance determinants in multi-drug resistant and mcr-1-positive E. coli isolated from poultry. Furthermore, these strains belonged to sequence types associated with transmission to humans. Taken together, the occurrence of strains that harbor resistance to critical antibiotics in Lebanese poultry and their potential transmission to humans suggest an urgent need to mitigate the dissemination of antibiotic resistance on poultry farms in Lebanon.

PMID:33762208 | DOI:10.1016/j.jgar.2021.03.001