Evaluation of Escherichia coli Isolates from Bovine Fecal Matter to Determine their Potential Risk to Bovine and Human Health

Abstract

Escherichia coli, a microorganism that acts as a commensal as well as an opportunistic pathogen, is the most studied microorganism worldwide. Its role in One Health is significant, especially in the context of human dominated ecosystems such as dairy farms. The cattle release large quantities of E. coli along with feces into the environment and studies have shown that these E. coli strains may contain virulence and resistance genes. The bovine fecal matter ultimately goes into the sewage or may be used as fertilizer. Therefore, if proper hygienic measures are not maintained, the virulent E. coli from bovine feces may contaminate the milk, meat or even the crops that are consumed by humans. It is therefore necessary to conduct surveillance studies to keep track of the emerging virulence and resistance gene patterns in the bovine sourced E. coli. This study aimed to evaluate the virulence potential, resistance profiles and the genetic diversity of 87 E. coli isolates from bovine fecal matter using their WGS data. The screening for virulence genes showed that the bovine fecal E. coli comprised of 6.9% ExPEC, 5.7% DEC and only 1.15% hybrid (ExPEC/DEC) strains. Among the ExPEC, 50% were UPEC and 50% were SEPEC based on the results of in vitro results (growth in human urine and complement resistance) and VAGs screening. These bacterial strains were tested in vivo for understanding their disease-causing capacity in mouse models and were able to cause urinary tract infection and sepsis, respectively. Furthermore, the findings revealed that 100% of the isolates were MDR with all the strains being resistant to macrolide, cephalosporin, and polymyxin B. The correlation between genotypic and phenotypic resistance showed high specificity to aminoglycoside and tetracycline, whereas high sensitivity to colistin was observed. Strain typing studies showed that most strains (62.02%) belonged to phylogroup B1. The highest prevailing serotypes were O8, O88, and O146 while the dominant sequence types were ST10, ST58, and ST155. The pan vs core-genome analysis showed the open pangenome of E. coli isolates to comprise 14,188 genes. Moreover, it indicated a high degree of genomic plasticity with the capacity for adaptability and functional variety. The visualization of the phylogenetic tree further elaborated the diversity within the isolates. In summary, this study presents a diverse genomic approach to analyze the E. coli isolates from bovine fecal matter to estimate their probable risk to the animals and humans interacting in a farm environment.