Genome-Based Characterization of Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains Isolated in South Korea, 2016-2020

Genetic and virulence characteristics of hybrid Shiga toxin-producing and atypical enteropathogenic Escherichia coli strains isolated in South Korea

Introduction

The predominant hybrid pathogenic E. coli, enterohemorrhagic E. coli (EHEC), combines characteristics of Shiga toxin-producing E. coli (STEC) and enteropathogenic E. coli (EPEC), contributing to global outbreaks with severe symptoms including fatal consequences. Since EHEC infection was designated as a notifiable disease in 2000 in South Korea, around 2000 cases have been reported, averaging approximately 90 cases annually.

Aim

In this work, genome-based characteristic analysis and cell-based assay of hybrid STEC/aEPEC strains isolated from livestock feces, animal source foods, and water in South Korea was performed.

Methods

To identify the virulence and antimicrobial resistance genes, determining the phylogenetic position of hybrid STEC/aEPEC strains isolated in South Korea, a combination of real-time PCR and whole-genome sequencing (WGS) was used. Additionally, to assess the virulence of the hybrid strains and compare them with genomic characterization, we performed a cell cytotoxicity and invasion assays.

Results

The hybrid STEC/aEPEC strains harbored stx and eae genes, encoding Shiga toxins and E. coli attachment/effacement related protein of STEC and EPEC, respectively. Furthermore, all hybrid strains harbored plasmid-carried enterohemolysin(ehxCABD), a key virulence factor in prevalent pathogenic E. coli infections, such as diarrheal disease and hemolytic-uremic syndrome (HUS). Genome-wide phylogenetic analysis revealed a close association between all hybrid strains and specific EPEC strains, suggesting the potential acquisition of Stx phages during STEC/aEPEC hybrid formation. Some hybrid strains showed cytotoxic activity against HeLa cells and invasive properties against epithelial cells. Notably, all STEC/aEPEC hybrids with sequence type (ST) 1,034 (n = 11) exhibited higher invasiveness than those with E2348/69. This highlights the importance of investigating potential correlations between STs and virulence characteristics of E. coli hybrid strains.

Conclusion

Through genome-based characterization, we confirmed that the hybrid STEC/aEPEC strains are likely EPEC strains that have acquired STEC virulence genes via phage. Furthermore, our results emphasize the potential increased danger to humans posed by hybrid STEC/aEPEC strains isolated in South Korea, containing both stx and eaeA, compared to STEC or EPEC alone.

Bacillus halotolerans SW207 alleviates enterotoxigenic Escherichia coli-induced inflammatory responses in weaned piglets by modulating the intestinal epithelial barrier, the TLR4/MyD88/NF-κB pathway, and intestinal microbiota

Enterotoxigenic Escherichia coli (ETEC) is one of the major pathogens contributing to piglet diarrhea, with significant implications for both piglet health and the economic aspects of the livestock industry. SW207 is an isolate of Bacillus halotolerans isolated from the cold- and disease-resistant Leixiang pigs in Northeastern China. We have discovered that SW207 can survive in the pig's gastrointestinal fluid and under conditions of high bile salt concentration, displaying potent antagonistic activity against ETEC. In this study, we established a weaned piglet diarrhea model infected with ETEC to investigate the role of SW207 in preventing diarrhea and improving intestinal health. Results indicate that SW207 upregulates the expression of tight junction proteins, including claudin-1, occludin, and zonula occludens-1, at both the transcriptional and translational levels. Furthermore, SW207 reduces serum endotoxin, D-lactic acid, and various oxidative stress markers while enhancing piglet mechanical barrier function. In terms of immune barrier, SW207 suppressed the activation of the TLR4/MyD88/NF-κB pathway, reducing the expression of various inflammatory factors and upregulating the expression of small intestine mucosal sIgA. Concerning the biological barrier, SW207 significantly reduces the content of E. coli in the intestines and promotes the abundance of beneficial bacteria, thereby mitigating the microbiota imbalance caused by ETEC. In summary, SW207 has the potential to prevent weaned piglet diarrhea caused by ETEC, alleviate intestinal inflammation and epithelial damage, and facilitate potential beneficial changes in the intestinal microbiota. This contributes to elucidating the potential mechanisms of host-microbe interactions in preventing pathogen infections.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC) has consistently been one of the significant pathogens causing mortality in weaned piglets in pig farming. The industry has traditionally relied on antibiotic administration to control ETEC-induced diarrhea. However, the overuse of antibiotics has led to the emergence of drug-resistant zoonotic bacterial pathogens, posing a threat to public health. Therefore, there is an urgent need to identify alternatives to control pathogens and reduce antibiotic usage. In this study, we assessed the protective effect of a novel probiotic in a weaned piglet model infected with ETEC and analyzed its mechanisms both in vivo and in vitro. The study results provide theoretical support and reference for implementing interventions in the gut microbiota to alleviate early weaned piglet diarrhea and improve intestinal health.

Levels of Indicator Bacteria and Characteristics of Foodborne Pathogens from Carcasses of Cattle Slaughterhouses in Korea

The initial microbial contamination of carcasses during slaughtering adversely affects spoilage and shelf life and is of global concern for food safety and meat quality. This study evaluated the hygiene and quality using the prevalence of foodborne pathogens and the level of indicator bacteria on 200 carcasses, collecting 10 from each of 20 cattle slaughterhouses in Korea. The distribution of aerobic bacterial count in carcasses was significantly highest at 2.0-3.0 log10 CFU/cm2 (34.1%), whereas the Escherichia coli count was significantly highest at under 1.0 log10 CFU/cm2 (94.0%) (P < 0.05). Clostridium perfringens was most prevalent (60.0% of slaughterhouses; 17.5% of carcasses), followed by Yersinia enterocolitica (30.0% of slaughterhouses; 6.5% of carcasses), Staphylococcus aureus (15.0% of slaughterhouses; 4.0% of carcasses), Listeria monocytogenes 1/2a (5.0% of slaughterhouses; 1.0% of carcasses), Salmonella enterica subsp. enterica serovar Infantis (5.0% of slaughterhouses; 1.0% of carcasses), and Shiga toxin-producing E. coli O:66 (5.0% of slaughterhouses; 0.5% of carcasses). Although 28 C. perfringens isolates from 11 slaughterhouses were divided into 21 pulsotypes, all isolates showed the same toxinotype as type A and only carried the cpa. Interestingly, 83.3% of isolates from two slaughterhouses located in the same province showed resistance to tetracycline. Furthermore, 13 Y. enterocolitica isolates from six slaughterhouses were divided into seven pulsotypes that were divided into biotypes 1A and 2 and serotypes O:5 and O:8, except for isolates that could not be typed. Twelve (92.3%) isolates only carried ystB, but one (7.7%) isolate carried ail and ystA. Moreover, 46.2% of Y. enterocolitica isolates showed multidrug resistance against ampicillin, cefoxitin, and amoxicillin/clavulanic acid. This study supports the need for continuous monitoring of slaughterhouses and hygiene management to improve the microbiological safety of carcasses.

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

ArcA positively regulates the expression of virulence genes and contributes to virulence of porcine Shiga toxin-producing enterotoxigenic Escherichia coli

IMPORTANCE

Enterotoxigenic Escherichia coli (ETEC) cause severe diarrhea in humans and animals, leading to death and huge economic loss worldwide. Thus, elucidation of ETEC's pathogenic mechanisms will provide powerful data for the discovery of drugs serving as prevention or therapeutics against ETEC-caused diarrheal diseases. Here, we report that ArcA plays an essential role in the pathogenicity and virulence regulation in ETEC by positively regulating the expression of several key virulence factors including F18 fimbriae, heat-labile and heat-stable toxins, Shiga toxin 2e, and hemolysin, under microaerobic conditions and in vivo. Moreover, we found that positive regulation of several virulence genes by ArcA requires a global repressor H-NS (histone-like nucleoid structuring), implying that ArcA may exert positive effects by antagonizing H-NS. Collectively, our data established a key role for ArcA in the pathogenicity of porcine ETEC and ETEC strains isolated from human infections. Moreover, our work reveals another layer of regulation in relation to oxygen control of virulence factors in ETEC.

Genomic traits of multidrug resistant enterotoxigenic Escherichia coli isolates from diarrheic pigs

Diarrhea caused by enterotoxigenic Escherichia coli (ETEC) infections poses a significant challenge in global pig farming. To address this issue, the study was conducted to identify and characterize 19 ETEC isolates from fecal samples of diarrheic pigs sourced from large-scale farms in Sichuan Province, China. Whole-genome sequencing and bioinformatic analysis were utilized for identification and characterization. The isolates exhibited substantial resistance to cefotaxime, ceftriaxone, chloramphenicol, ciprofloxacin, gentamicin, ampicillin, tetracycline, florfenicol, and sulfadiazine, but were highly susceptible to amikacin, imipenem, and cefoxitin. Genetic diversity among the isolates was observed, with serotypes O22:H10, O163orOX21:H4, and O105:H8 being dominant. Further analysis revealed 53 resistance genes and 13 categories of 195 virulence factors. Of concern was the presence of tet(X4) in some isolates, indicating potential public health risks. The ETEC isolates demonstrated the ability to produce either heat-stable enterotoxin (ST) alone or both heat-labile enterotoxin (LT) and ST simultaneously, involving various virulence genes. Notably, STa were linked to human disease. Additionally, the presence of 4 hybrid ETEC/STEC isolates harboring Shiga-like toxin-related virulence factors, namely stx2a, stx2b, and stx2e-ONT-2771, was identified. IncF plasmids carrying multiple antimicrobial resistance genes were prevalent, and a hybrid ETEC/STEC plasmid was detected, highlighting the role of plasmids in hybrid pathotype emergence. These findings emphasized the multidrug resistance and pathogenicity of porcine-origin ETEC strains and the potential risk of epidemics through horizontal transmission of drug resistance, which is crucial for effective control strategies and interventions to mitigate the impact on animal and human health.