Virulence Factor Genes in ESBL-E.coli

Extended spectrum beta-lactamase producing Escherichia coli (ESBL-Ec) is a key indicator of global antimicrobial resistance (AMR) surveillance and poses a serious threat to public health. This study aimed to identify virulence factor genes (VFGs), ESBL-Ec pathotypes and pathovars, and analyze distribution patterns in isolates from broiler cecum in eight Disease Investigation Center (DIC) working areas in Indonesia. A total of 120 ESBL-Ec isolates were selected proportionally according to region distribution. Virulence factor genes (VFGs) were detected using Oxford Nanopore Technologies (ONT) MinION sequencing, and the results were analyzed using bioinformatics tools. Among the 113 isolates that passed the quality standards, researchers found 99 types of virulence factor genes (VFGs) from 4,269 unique allele genes. In addition, five different pathovars were identified, showing high genetic diversity. The fim gene cluster had the highest frequency (20.1%), while esp showed the most gene cluster diversity (18.2%). The highest prevalence was found in the gene cluster encoding extraintestinal pathogenic/ExPEC pathotypes (ent, fep, fes: 100%) and intestinal pathogenic/InPEC (esp: 96.5%, and yag/ecp: 91%). The virulent gene encoding ExPEC (66.7%) was more dominant than InPEC (33.3%). The gene frequency distribution displayed the highest dominance in Denpasar DIC (20%). All isolates possessed VFGs that potentially encoded a minimum of two pathovars, with nearly 80% encoding three or more. These findings highlight the potential risk of pathogenic ESBL-Ec spreading to both humans and the environment.