Comparative Resistome and Virulome Analysis of Poultry Gut Colonized Escherichia coli Isolates with Clinical Human Isolates

Abstract

The limited knowledge regarding the genomic diversity of drug-resistant bacteria, particularly in food-producing animals such as poultry in Pakistan, has hindered accurate hazard assessment and the establishment of crucial control measures to protect public health. Escherichia coli, an exemplar of a 'One Health organism,' is prevalent in both food products and natural environments. Alarmingly, certain strains of Escherichia coli have acquired resistance to multiple drugs, rendering them multidrug-resistant (MDR). Additionally, some Escherichia coli strains have the potential to cause severe human diseases, underscoring their significance as significant human pathogens. However, the transmission dynamics of E. coli between clinical settings and poultry farms remain obscure. This study aims to investigate antibiotic-resistant E. coli using whole genome sequencing data obtained from two distinct sources: poultry and humans. A total of ten E. coli isolates were procured from chicken cecal samples. These isolates underwent antibiotic susceptibility testing against 13 antimicrobial agents, encompassing β-lactams, aminoglycosides, tetracycline, fluoroquinolones, and polymyxin E (colistin), to assess their phenotypic resistance. Among the ten isolates, three displayed resistances to three or more antimicrobial classes, classifying them as multi-drug resistant strains. Whole genome sequencing was performed on these three multi-drug resistant E. coli isolates (TK.2.1, TK.3.1, and TK.4.1) sourced from poultry in Rawalpindi. This sequencing aimed to establish correlations between resistant phenotypes and potential antimicrobial resistance-related genes. Comparative genomic analysis was conducted by comparing these isolates with 140 publicly available genomes from poultry and human sources in Pakistan, China, and India. This analysis sought to investigate the transmission and diversity of Escherichia coli. The comparative analysis unveiled that poultry isolates exhibited similar resistance and virulence profiles as previously reported human clinical isolates. Furthermore, phylogenetic analysis indicated significant diversities in phylogenetic group distribution among Escherichia coli strains originating from both poultry and clinical human sources. These genetic insights hold promise for the development of effective control measures 2 against this pathogen, both in healthcare provision and within research and development (R&D) organizations. Curtailing antibiotic usage in poultry farming is imperative, as poultry-derived E. coli strains harbor antibiotic resistance genes. The dissemination of these resistant bacteria to humans poses a potential threat to public health, emphasizing the importance of reducing antibiotic usage in poultry farming to mitigate this issue.