Genomic landscape of multi-drug resistant avian pathogenic Escherichia coli recovered from broilers

Abstract Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), constitutes a substantial burden to the poultry industry worldwide. APEC has been extensively characterized throughout the world, however, less is known about the genetic background of APEC isolates from Pakistan. In this study, a total of 75 E. coli isolates from colibacillosis affected dead broiler birds in Pakistan were subjected to whole genome sequencing followed by in-silico characterization. These isolates were investigated for virulence and resistance genotypes, serotypes, multi-locus sequence types, plasmid replicon types and single nucleotide polymorphism-based core genome phylogeny. Among the APEC isolates investigated, 14 different sequence types were identified with ST117 (16%), ST2847 (10.7%) and ST48 (5.3%) being the most prevalent. Of the 28 different serotypes identified in this study, O1, O2 and O78 serotypes accounted for 25.3% of the APEC isolates. The most frequently identified virulence-associated genes (VAGs) were increased serum survival gene; iss (100%), glutamate decarboxylase; gad (92%) and the siderophore receptor; iroN (81.3%). According to the previously established definition, 72% of isolates fell within the highly pathogenic APEC category by possessing a combination of VAGs; iss, iroN, iutA, hlyF and ompT simultaneously. Of the 75 APEC isolates, 89.3% contained the genes predicted to encode resistance against aminoglycosides, tetracyclines and sulfonamides. Notably, the acquired colistin resistance gene mcr-1 was found in 38.7% of the APEC isolates. Our findings reveal a diverse genetic background and high virulence and resistance potentials for APEC isolates in Pakistan.