Occurrence of virulence genes in multidrug-resistant Escherichia coli isolates from humans, animals, and the environment: One health perspective

Escherichia coli is one of the critical One Health pathogens due to its vast array of virulence and antimicrobial resistance genes. This study used multiplex PCR to determine the occurrence of virulence genes bfp, ompA, traT, eaeA, and stx1 among 50 multidrug-resistant (MDR) E. coli isolates from humans (n = 15), animals (n = 29), and the environment (n = 6) in Dar es Salaam, Tanzania. Their association with antimicrobial-resistant genes (ARGs) was determined using Principal Component Analysis (PCA). All 50/50 (100%) MDR E. coli isolates carried at least one virulence gene, with 19/50 (38%) carrying four genes, bfp + traT + eaeA + ompA. The findings showed a high occurrence of virulence genes bfp (82%), traT (82%), eaeA (78%), and ompA (72%); the study detected no stx1 in any of the isolates. In humans, the most detected virulence genes were bfp and traT 14/15 (93.3%); for poultry, it was eaeA 13/14 (92.9%); for pigs, was bfp and traT 13/15 (86.7%); while for river water, it was eaeA 6/6 (100%). The study observed no significant association between virulence genes and ARGs. PCA results show the genes ompA, traT, eaeA, and bfp contributed to the virulence of the isolates, and blaTEM, blaCTX-M, and qnrs contributed to ARGs. The PCA ellipses show that isolates from pigs had more virulence genes than those isolated from poultry, river water, and humans. The high frequency of numerous virulence genes in MDR E. coli isolates from humans, animals, and the environment indicates that these isolates have a very high potential to cause diseases that are difficult to treat because they are MDR.

Rabbits as a Reservoir of Multidrug-Resistant Escherichia coli: Clonal Lineages and Public Health Impact

Escherichia coli, including extended-spectrum β-lactamases (ESBL)-producing strains, poses a global health threat due to multidrug resistance, compromising food safety and environmental integrity. In industrial settings, rabbits raised for meat have the highest consumption of antimicrobial agents compared to other food-producing animals. The European Union is facing challenges in rabbit farming as rabbit consumption declines and antibiotic-resistant strains of E. coli cause enteric diseases. The aim of this study was to investigate the antibiotic resistance profile, genetic diversity, and biofilm formation in cefotaxime-resistant E. coli strains isolated from twenty rabbit farms in Northern Portugal to address the effect of the pressing issue of antibiotic resistance in the rabbit farming industry. Resistance to critically antibiotics was observed, with high levels of resistance to several categories, such as tetracycline, ampicillin, aztreonam, and streptomycin. However, all isolates were susceptible to cefoxitin and imipenem. Multidrug resistance was common, with strains showing resistance to all antibiotics tested. The blaCTX-M variants (blaCTX-3G and blaCTX-M9), followed by the tetracycline resistance genes, were the most frequent resistance genes found. ST10 clones exhibiting significant resistance to various categories of antibiotics and harboring different resistance genes were detected. ST457 and ST2325 were important sequence types due to their association with ESBL-E. coli isolates and have been widely distributed in a variety of environments and host species. The strains evaluated showed a high capacity for biofilm formation, which varied when they were grouped by the number of classes of antibiotics to which they showed resistance (i.e., seven different classes of antibiotics, six classes of antibiotics, and three/four/five classes of antibiotics). The One Health approach integrates efforts to combat antimicrobial resistance in rabbit farming through interdisciplinary collaboration of human, animal, and environmental health. Our findings are worrisome and raise concerns. The extensive usage of antibiotics in rabbit farming emphasizes the urgent need to establish active surveillance systems.

The Multi-Omics Analysis Revealed Microbiological Regulation of Rabbit Colon with Diarrhea Fed an Antibiotic-Free Diet

Diarrhea symptoms appeared after antibiotics were banned from animal feed based on the law of the Chinese government in 2020. The colon and its contents were collected and analyzed from diarrheal and healthy rabbits using three omics analyses. The result of the microbial genomic analysis showed that the abundance of Bacteroidetes and Proteobacteria increased significantly (p-value < 0.01). Transcriptomes analysis showed that differentially expressed genes (DEGs) are abundant in the IL-17 signaling pathway and are highly expressed in the pro-inflammatory pathway. The metabolome analysis investigated differential metabolites (DMs) that were mainly enriched in tryptophan metabolism and bile secretion, which were closely related to the absorption and immune function of the colon. The results of correlation analysis showed that Bacteroidetes was positively correlated with 4-Morpholinobenzoic acid, and 4-Morpholinobenzoic acid could aggravate inflammation through its influence on the bile secretion pathway. The enriched DMs L-Tryptophan in the tryptophan metabolism pathway will lead to the functional disorder of inhibiting inflammation by affecting the protein digestion and absorption pathway. Thus, the colonic epithelial cells were damaged, affecting the function of the colon and leading to diarrhea in rabbits. Therefore, the study provided an idea for feed development and a theoretical basis for maintaining intestinal tract fitness in rabbits.