Understanding the Antimicrobial Resistance and Virulence Potential of Escherichia coli Isolated from Poultry Environment and Fecal Material

Abstract

Escherichia coli is among the leading cause of infections in healthcare facilities and community settings, and has become a threat to health globally and a One Health challenge. Poultry houses have been proposed as a reservoir for these virulent and drug resistant E. coli. Several of these E. coli isolates from poultry fecal matter and the surrounding environment may contain ExPEC and DEC associated virulence genes, thus tend to be potentially harmful and can spread to humans via contaminated poultry meat consumption and through hand-mouth transmission during handling. However, limited information is available about the actual potential of poultry-sourced E. coli to cause extraintestinal infections. Treatment for such infections include antimicrobial therapy that has become further challenging by the emergence of multidrug-resistant (MDR) E. coli that possess resistance to colistin, a last resort option for MDR infections. The aim of this study was to understand the virulence potential, resistance profiles and sequence features of 146 E. coli isolates from poultry environment. By means of whole Genome Sequencing (WGS) and screening for virulence genes, 33% poultry fecal sourced E. coli isolates were categorized into ExPEC, 34% as DEC and 20% as hybrid (ExPEC/DEC) strains. Among the ExPEC isolates, 10% were UPEC and 5% were SEPEC based on the results of in vitro screening (growth in human urine and complement resistance). These isolates were further tested in vivo for disease-causing ability in mouse models and were able to induce Urinary Tract Infection (UTI) and sepsis. Furthermore, the findings revealed that 91% of the isolates were MDR. Moreover, poultry environmental E. coli isolates were also found to possess a significant diversity of biocide, disinfectant, and heavy metal resistance genes. The highly prevalent serotypes were O8 and O9 and the dominant phylogroups included A and B1. High-risk pandemic lineages, such as ST10, ST155, ST410, ST457, and ST69 were frequently identified in the poultry environment. According to pangenome estimations, the genomic diversity of E. coli corresponds to an open pangenome with a reservoir of over 18,000 genes. In summary, this study presents a thorough genomic analysis of E. coli and highlights the prospective role of poultry environment as a potential health hazard to humans and other animals via zoonosis and dissemination of antibiotic resistance genes.