Comprehensive assessment of four different molecular genotyping panels to characterize avian pathogenic <i>E. coli</i> (APEC) for epidemiological studies

Avian pathogenic Escherichia coli (APEC) is a leading cause of colibacillosis in poultry worldwide. Molecular genotyping using polymerase chain reaction is a rapid and effective way to separate APEC from commensal E. coli in poultry. This study assessed the accuracy of four different molecular genotyping panels in a head-to-head comparison, using 250 APEC isolates from diseased birds and 106 fecal E. coli (AFEC) isolates from healthy birds. The cut-off value of all four panels was observed and optimal cut-off values with sensitivity and specificity were suggested in this study. The results found that the APECtyper panel had the highest sensitivity (81.2%) being significantly different to the other three panels, while the 9-gene panel demonstrated the highest specificity (89.6%). The cut-off of the 13-gene panel was optimized with a predicted probability of 12%, balancing sensitivity (57.2%) and specificity (75.5%), which was used in this study. Overall, three of the four panels except the 13-gene panel showed good performance with distinct strengths. This research provides valuable insights, but further studies are needed to confirm the reliability and reproducibility of these assays across different geographical regions, various poultry populations, and diverse field conditions.