Virulence factor genes analysis of extended spectrum β-Lactamase producing <i>Escherichia coli</i> isolated from broiler chickens in Indonesia

Extended spectrum β-lactamase producing Escherichia coli (ESBL-Ec) is recognized as an opportunistic pathogen with zoonotic potential, posing a threat to public health. This study aimed to identify virulence factor genes (VFGs), determine ESBL-Ec pathotypes and pathovars, and analyze their distribution in isolates from broiler cecum across eight Disease Investigation Center (DIC) areas in Indonesia. A total of 120 ESBL-Ec isolates were proportionally selected based on regional prevalence. The VFGs were detected using Oxford Nanopore Technologies (ONT) MinION sequencing and analyzed with bioinformatics pipelines. Of the total isolates, 113 met the quality threshold. A total of 4,269 non-redundant orthologs and alleles related to VFGs were detected, representing 99 VFG types grouped into 25 clusters, indicating substantial genetic diversity. The fim gene cluster was the most frequently detected (20.1%), whereas the esp cluster exhibited the highest allele diversity (18.2%). The VFGs encoding the ExPEC were predominant (66.7%), while the remaining VFGs encoded the InPEC (33.3%). Each isolate potentially encodes at least two pathovars, with nearly 80% encoding three or more. The diversity of VFGs and pathovar combinations highlights the disease potential and zoonotic risk of ESBL-Ec.