Isolation, genotyping and antimicrobial resistance of Shiga toxin-producing Escherichia coli

Shiga Toxin-Producing Escherichia coli Testing in New York 2011-2022 Reveals Increase in Non-O157 Identifications

Shiga toxin-producing Escherichia coli (STEC) are an important cause of bacterial enteric infection. STEC strains cause serious human gastrointestinal disease, which may result in life-threatening complications such as hemolytic uremic syndrome. They have the potential to impact public health due to diagnostic challenges of identifying non-O157 strains in the clinical laboratory. The Wadsworth Center (WC), the public health laboratory of the New York State Department of Health, has isolated and identified non-O157 STEC for decades. A shift from initially available enzyme immunoassay testing to culture-independent diagnostic tests (CIDTs) has increased the uptake of testing at clinical microbiology laboratories. This testing change has resulted in an increased number of specimen submissions to WC. During a 12-year period between 2011 and 2022, WC received 5037 broths and/or stool specimens for STEC confirmation from clinical microbiology laboratories. Of these, 3992 were positive for Shiga toxin genes (stx1 and/or stx2) by real-time PCR. Furthermore, culture methods were utilized to isolate, identify, and characterize 2925 STEC from these primary specimens. Notably, WC observed a >200% increase in the number of STEC specimens received in 2021-2022 compared with 2011-2012 and an 18% increase in the number of non-O157 STEC identified using the same methodologies. During the past decade, the WC testing algorithm has been updated to manage the increase in specimens received, while also navigating the novel COVID-19 pandemic, which took priority over other testing for a period of time. This report summarizes updated methods for confirmation, surveillance, and outbreak detection of STEC and describes findings that may be related to our algorithm updates and the increased use of CIDTs, which is starting to elucidate the true incidence of non-O157 STEC.

Shiga toxin-producing Escherichia coli O157:H7 among diarrheic patients and their cattle in Amhara National Regional State, Ethiopia

BACKGROUND

Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7) is a zoonotic pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome worldwide. This study aimed to determine the prevalence, antibiotic susceptibility, and associated risk factors of STEC O157:H7 among diarrheic patients and their cattle.

METHODS

A cross-sectional study was conducted among diarrheic patients and their cattle in Amhara National Regional State, Ethiopia from December- 2020 to June- 2022. A total of 1,149 diarrheic patients and 229 cattle were included in the study. STEC O157:H7 detection was done using culture, latex agglutination test, and polymerase chain reaction on diarrheic stool samples and recto-anal mucosal swabs of cattle. Antibiotic susceptibility tests were performed using disk diffusion techniques. Risk factors association were identified using binary and multivariable logistic regression analysis.

RESULTS

The overall prevalence of STEC O157:H7 in diarrheic patients and their cattle was 11.1% (128/1149) and 14.4% (33/229) respectively. High percentage of the study subjects were found in under-five children (34.5%). Age less than 5 (AOR: 4.02, 95%CI:1.608-10.058,P = 0.003), and greater than 64 years old (AOR:3.36, 95% CI:1.254-8.986, P = 0.016), presence of diarrheic patient in the house (AOR:2.11, 95%CI:1.309-3.390, P = 0.002), availability of cattle in the house (AOR:2.52, 95%CI:1.261-5.049, P = 0.009), and habit of consuming raw foods (AOR:4.35, 95%CI:2.645-7.148, P = 0.000) were risk factors. Antibiotic resistance was shown in 109(85.2%), and 31(93.9%) isolates from diarrheic patients and their cattle respectively. The highest levels of antibiotic resistance were found to tetracycline (54.7%, 69.7%) in diarrheic patients and their cattle respectively. Multiple drug resistance was also observed among 56(43.8%) and 11(33.3%) isolates in diarrheic patients and their cattle respectively.

CONCLUSION

Our study showed high prevalence of STEC O157:H7 in diarrheic patients and their cattle. Therefore, health education should be given to the community on how to care for animals, proper sanitation, and the impact of raw food consumption.

Phage Tail Fiber Protein as a Specific Probe for Recognition of Shiga Toxin-Producing Escherichia coli O91, O103, and O111

The ability to quickly identify specific serotypes of Shiga toxin-producing Escherichia coli (STEC) could facilitate the monitoring and control of STEC pathogens. In this study, we identified the receptors and receptor-binding proteins (RBPs) of three novel phages (pO91, pO103, and pO111) isolated from hospital wastewater. Recombinant versions of these RBPs (pO91-ORF43, pO103-ORF42, and pO111-ORF8) fused to a fluorescent reporter protein were then constructed. Both fluorescence microscopy and transmission electron microscopy showed that all three recombinant RBPs were bound to the bacterial surface. Indirect enzyme-linked immunosorbent assay was used to verify that each recombinant RBP bound specifically to E. coli O91, O103, or O111, but not to any of the 83 strains of E. coli with different O-antigens, nor to 10 other bacterial species that were tested. The recombinant RBPs adsorbed to their respective host bacteria within 10 min of incubation. The minimum concentration of bacteria required for detection by the recombinant RBPs was 33 colony-forming units (CFU)/mL (range: 3.3 × 10 to 3.3 × 108 CFU/mL). Furthermore, each recombinant RBP was also able to detect bacteria in lettuce, chicken breast meat, and infected mice, indicating that their usage will facilitate the detection of STEC and may help to reduce the spread of STEC-related infections and diseases.

The emergence of multi-drug resistant and virulence gene carrying Escherichia coli strains in the dairy environment: a rising threat to the environment, animal, and public health

Escherichia coli is a common inhabitant of the intestinal microbiota and is responsible for udder infection in dairy cattle and gastro-urinary tract infections in humans. We isolated E. coli strains from a dairy farm environment in Xinjiang, China, and investigated their epidemiological characteristics, phenotypic and genotypic resistance to antimicrobials, virulence-associated genes, and phylogenetic relationship. A total of 209 samples were collected from different sources (feces, slurry, water, milk, soil) and cultured on differential and selective agar media (MAC and EMB). The presumptive identification was done by the VITEK2 system and confirmed by 16S rRNA gene amplification by PCR. Antimicrobial susceptibility testing was done by micro-dilution assay, and genomic characterization was done by simple and multiplex polymerase chain reaction (PCR). A total of 338 E. coli strains were identified from 141/209 (67.5%) of the samples. Most of the E. coli strains were resistant to sulfamethoxazole/trimethoprim (62.43%), followed by cefotaxime (44.08%), ampicillin (33.73%), ciprofloxacin (31.36%), tetracycline (28.99%), and a lesser extent to florfenicol (7.99%), gentamicin (4.44%), amikacin (1.77%), and fosfomycin (1.18%). All of the strains were susceptible to meropenem, tigecycline, and colistin sulfate. Among the resistant strains, 44.4% were identified as multi-drug resistant (MDR) showing resistance to at least one antibiotic from ≥3 classes of antibiotics. Eighteen out of 20 antibiotic-resistance genes (ARGs) were detected with sul2 (67.3%), blaTEM (56.3%), gyrA (73.6%), tet(B) (70.4%), aph(3)-I (85.7%), floR (44.4%), and fosA3 (100%, 1/1) being the predominant genes among different classes of antibiotics. Among the virulence-associated genes (VAGs), ompA was the most prevalent (86.69%) followed by ibeB (85.0%), traT (84.91%), ompT (73.96%), fyuA (23.1%), iroN (23.1%), and irp2 gene (21.9%). Most of the E. coli strains were classified under phylogenetic group B1 (75.45%), followed by A (18.34%), C (2.96%), D (1.18%), E (1.18%), and F (0.30%). The present study identified MDR E. coli strains carrying widely distributed ARGs and VAGs from the dairy environment. The findings suggested that the dairy farm environment may serve as a source of mastitis-causing pathogens in animals and horizontal transfer of antibiotic resistance and virulence genes carrying bacterial strains to humans via contaminated milk and meat, surface water and agricultural crops.

Antimicrobial Peptide Mastoparan-AF Kills Multi-Antibiotic Resistant Escherichia coli O157:H7 via Multiple Membrane Disruption Patterns and Likely by Adopting 3-11 Amphipathic Helices to Favor Membrane Interaction

We investigated the antimicrobial activity and membrane disruption modes of the antimicrobial peptide mastoparan-AF against hemolytic Escherichia coli O157:H7. Based on the physicochemical properties, mastoparan-AF may potentially adopt a 3-11 amphipathic helix-type structure, with five to seven nonpolar or hydrophobic amino acid residues forming the hydrophobic face. E. coli O157:H7 and two diarrheagenic E. coli veterinary clinical isolates, which are highly resistant to multiple antibiotics, are sensitive to mastoparan-AF, with minimum inhibitory and bactericidal concentrations (MIC and MBC) ranging from 16 to 32 μg mL^-1 for E. coli O157:H7 and four to eight μg mL^-1 for the latter two isolates. Mastoparan-AF treatment, which correlates proportionally with membrane permeabilization of the bacteria, may lead to abnormal dents, large perforations or full opening at apical ends (hollow tubes), vesicle budding, and membrane corrugation and invagination forming irregular pits or pores on E. coli O157:H7 surface. In addition, mRNAs of prepromastoparan-AF and prepromastoparan-B share a 5'-poly(A) leader sequence at the 5'-UTR known for the advantage in cap-independent translation. This is the first report about the 3-11 amphipathic helix structure of mastoparans to facilitate membrane interaction. Mastoparan-AF could potentially be employed to combat multiple antibiotic-resistant hemolytic E. coli O157:H7 and other pathogenic E. coli.

Pre-treatment with phages achieved greater protection of mice against infection with Shiga toxin-producing Escherichia coli than post-treatment

Shiga toxin-producing Escherichia coli (STEC) is a group of pathogen that can cause various diseases in both humans and animals, such as watery diarrhea, hemorrhagic colitis, and uremia syndrome. Due to the serious situation of antibiotic resistance, phage therapy is considered to have a great potential in combating bacterial diseases. In this study, three phages (NJ-10, NJ-20, and NJ-38) with strong abilities to lyse virulent STEC strain CVCC193 cells in vitro were isolated. Subsequently, the therapeutic effects of the three phages were investigated in mice infected with CVCC193 cells. The results showed that the survival rates of mice injected with the phages at 3 h after challenge with CVCC193 cells were 40%-50%, while the survival rates of mice injected with the phages at 24 h before challenge were 80%-100%, indicating that pre-treatment with phages had better therapeutic effects than post-treatment. Pathological changes, bacterial loads in different organs, and serum levels of inflammatory factors of the infected mice were also detected. The results showed that the mice injected with the phages at 3 h after or 24 h before challenge with CVCC193 cells had significantly decreased organ lesions, bacterial loads, and serum levels of inflammatory factors as compared to infected mice without phage treatment. These results suggested that phages NJ-10, NJ-20, and NJ-38 can potentially protect against STEC infections.

Infectious Diseases Associated with Hydrometeorological Hazards in Europe: Disaster Risk Reduction in the Context of the Climate Crisis and the Ongoing COVID-19 Pandemic

Hydrometeorological hazards comprise a wide range of events, mainly floods, storms, droughts, and temperature extremes. Floods account for the majority of the related disasters in both developed and developing countries. Flooding alters the natural balance of the environment and frequently establish a favorable habitat for pathogens and vectors to thrive. Diseases caused by pathogens that require vehicle transmission from host to host (waterborne) or a host/vector as part of their life cycle (vector-borne) are those most likely to be affected by flooding. Considering the most notable recent destructive floods events of July 2021 that affected several Central Europe countries, we conducted a systematic literature review in order to identify documented sporadic cases and outbreaks of infectious diseases in humans in Europe, where hydrometeorological hazards, mainly floods, were thought to have been involved. The occurrence of water-, rodent-, and vector-borne diseases in several European countries is highlighted, as flooding and the harsh post-flood conditions favor their emergence and transmission. In this context, strategies for prevention and management of infectious disease outbreaks in flood-prone and flood-affected areas are also proposed and comprise pre- and post-flood prevention measures, pre- and post-outbreak prevention measures, as well as mitigation actions when an infectious disease outbreak finally occurs. Emphasis is also placed on the collision of floods, flood-related infectious disease outbreaks, and the evolving COVID-19 pandemic, which may result in unprecedented multi-hazard conditions and requires a multi-hazard approach for the effective disaster management and risk reduction.

Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli derived from cattle farm

Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen, which can cause diseases such as diarrhea, hemorrhagic enteritis, and hemolytic uremic syndrome in humans. Twelve STEC isolates were collected from beeves and feces of commercial animals in China between 2019 and 2020 for this study. In addition to the determination of serotype and Shiga toxin subtype, whole-genome sequencing (WGS) was used for determining phylogenetic relationships, antimicrobial resistance (AMR), virulence genes, and sequence type (ST) of isolates. A total of 27 AMR genes were detected, and each STEC isolate carried more than 10 AMR genes. Eight STEC isolates from ground beef and four STEC isolated from feces were screened. A total of seven serotypes were identified, and one isolate ONT:H10 was undetermined by SeroTypeFinder. Three O157:H7 strains were confirmed and the remaining five serogroups were confirmed as O26:H11, O81:H31, O105:H8, O178:H19, and O136:H12. The phylogenetic analysis showed that STEC isolates of the same serotype or ST were clustered together based on cgMLST. The comparison of the genomes of 157 STEC reference isolates worldwide with our local STEC isolates showed that STEC isolates screened in China represented various collections and could not form a separate cluster but were interspersed among the STEC reference collection, which suggested that several STEC isolates shared a common ancestor irrespective of STEC serotype isolates. cgMLST revealed that isolates of the same O serotype clustered irrespective of their H type. Further investigation is required to determine the pathogenic potential of other serotypes of STEC, particularly in regard to these rare serotypes.

Virulence Genes of Pathogenic Escherichia coli in Wild Red Foxes (Vulpes vulpes)

Simple Summary

Escherichia coli is a commensal of the intestinal tract of humans and animals, but some pathotypes can cause severe infections. Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC), and enterohemorrhagic E. coli (EHEC) are the pathotypes most frequently involved in enteric disorders observed in people and domestic animals. Wildlife may harbor and excrete these pathotypes too, therefore, they may be source of infections for humans and domestic animals. Vulpes vulpes seem to be involved in the epidemiology of pathogenic E. coli strains, and thus they could be a relevant threat mainly when they invade human settlements in rural and urban areas.

Abstract

Different pathotypes of Escherichia coli can cause severe diseases in animals and humans. Wildlife may contribute to the circulation of pathogenic pathotypes, including enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC), and enterohemorrhagic E. coli (EHEC). This study analyzed 109 DNA samples previously extracted from fecal specimens collected from red foxes (Vulpes vulpes) to detect E. coli virulence genes eaeA, hlyA, stx1, and stx2, that characterize the EPEC, STEC, and EHEC strains. Thirty-one (28.4%) samples were positive for at least one investigated virulence gene: eaeA gene was detected in 21 (19.2%) samples, hlyA in 10 (9.1%), stx1 in 6 (5.5%), and stx2 in 4 (3.6%). Nine DNA samples resulted positive for two or three virulence genes: five (4.6%) samples were positive for eaeA and hlyA genes, two (1.8%) for eaeA and stx1, one (0.9%) for hlyA and stx1, one (0.9%) for eaeA, hlyA and stx2. Red foxes seem to be involved in the epidemiology of these infections and their role could be relevant because they may be source of pathogenic E. coli for other wild animals, as well as domestic animals and humans.

Epidemiology of Non-O157 Shiga Toxin-Producing Escherichia coli in the Province of Alberta, Canada, from 2018 to 2021

Non-O157 serogroups contribute significantly to the burden of disease caused by Shiga toxin-producing Escherichia coli (STEC) and have been underrecognized by traditional detection algorithms. We described the epidemiology of non-O157 STEC in Alberta, Canada for the period of 2018 to 2021. All non-O157 STEC isolated from clinical samples were submitted for serotyping and qPCR targeting the stx₁ and stx₂ genes. A total of 729 isolates were identified. Increased detection occurred over the summer months, peaking in July. Patients 18 years and younger made up 42.4% of cases, with 31.1% in those 0–9 years of age. There was a slight female predominance (399/729, 54.7%) A total of 50 different serogroups were detected; the most common were O26 (30.3%), O103 (15.9%), O111 (12.8%), O121 (11.0%), O118 (3.3%) and O71 (2.9%). These six serogroups made up 76.2% of all isolates. In total, 567 (77.8%) were positive for stx₁, 114 (15.6%) were positive for stx₂ and 48 (6.6%) were positive for both stx₁ and stx₂. A wide variety of non-O157 serogroups have been detected in Alberta, with the most frequent serogroups differing from other locations. These results highlight the need for further characterization of their virulence factors and clinical impact.

Droplet Digital PCR (ddPCR) Analysis for Detecting Shiga-Toxin-Producing Escherichia coli (STEC)

Verocytotoxin-producing Escherichia coli, also referred to as Shiga-toxin-producing Escherichia coli (STEC), can be transmitted to humans through person-to-person contact, consumption of contaminated food or water, or by direct contact with animals. Its clinical and economic consequences have prompted the development of alternative approaches to the official method of analysis “UNI CEN ISO/TS 13136: 2012”, which describes the identification of STEC through the detection of its main virulence genes. Recently, droplet digital PCR (ddPCR) has been proposed as a technique for the sequence-specific detection and direct quantification of nucleic acids. The present study aimed to investigate if ddPCR could be able to detect STEC in less time than that required by the official method. This study consisted of the ddPCR of slices of beef contaminated with STEC and of the sponges used for beef official control at the slaughter stage. The results showed the ability of ddPCR to detect STEC in slices of beef already after sample incubation for 7 h at 37 °C while, in the case of sponges used for official controls, 9 h at 37 °C was needed. In this way, the ddPCR could represent an efficient method for detecting STEC and providing results in less time than the official method.

Pathogenic E. coli from Cattle as a Reservoir of Resistance Genes to Various Groups of Antibiotics

Antimicrobial resistance has become a worldwide concern in all public health domains and reducing the spread has become a global priority. Pathogenic E. coli is responsible for a number of illnesses in humans and outbreaks in the past have been correlated with the consumption of contaminated bovine products. This is why surveillance in all the steps of production is essential. This study focused on identifying the pathogenic strains of E. coli in two large bovine abattoirs from Romania and France, and on associating them with the antimicrobial resistance patterns. A total of 250 samples from intestinal content were aseptically collected during the evisceration step of the cattle slaughtering process, from which 242 E. coli strains were isolated. Seventeen percent of all samples tested positive to at least one E. coli isolate carrying eaeA, stx1 and stx2 genes. The most prevalent genetic profile found in the E. coli strains tested was Stx1-positive and Stx2/eaeA-negative. More than 68% of the pathogenic E. coli isolated in Romania showed multi-drug resistance (MDR) and in France, the percentage was significantly lower (38%). The MDR profiles showed a high gene diversity for antibiotic resistance, which represents a great risk for environmental spread and human health. Our results indicate that in Romania, bovines can represent a reservoir for MDR E. coli and, hence, a surveillance system for antimicrobials usage in farm animals is highly needed.

Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?

Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characterized STEC from wildlife (wild boar (n = 56), red deer (n = 101), red fox (n = 37) and otter (n = 92)). Cultivable STEC (n = 52) were isolated from 17% (n = 49) of the faecal samples. All the isolates were non-O157 STEC encoding stx1 (n = 2; 4%) and/or stx2 genes (n = 51; 98%). Only one strain (2%) isolated from red fox had an antibiotic resistant phenotype. However, when the normalized resistance interpretation of epidemiological cutoffs (NRI ECOFFs) were used, 23% (n = 12) of the strains were non-wildtype to at least one of the antibiotics tested. After analysis by pulsed-field gel electrophoresis (PFGE), 20 strains were selected for whole genome sequencing and belonged to the following serotypes: O27:H30 (n = 15), O146:H28 (n = 2), O146:H21 (n = 1), O178:H19 (n = 1), and O103:H2 (n = 1). In addition to stx, all strains encode several virulence factors such as toxins, adhesins, fimbriae and secretion systems, among others. All sequenced genomes carried several mobile genetic elements (MGEs), such as prophages and/or plasmids. The core genome and the phylogenetic analysis showed close evolutionary relationships between some of the STEC recovered from wildlife and strains of clinical origin, highlighting their pathogenic potential. Overall, our results show the zoonotic potential of STEC strains originating from wildlife, highlighting the importance of monitoring their genomic characteristics following a One Health perspective, in which the health of humans is related to the health of animals, and the environment.

Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers

Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.

Validation of post-harvest antimicrobial interventions to control Shiga toxin-producing Escherichia coli (STEC) on market hog carcass surfaces

Although swine are less associated with STEC foodborne disease outbreaks, the potential for swine to serve as a source of STEC infections in human beings cannot be disregarded. This study compared eight USDA-approved antimicrobial intervention technologies to quantify their ability to reduce STEC contamination on market hog carcasses. Hogs were harvested to provide skin-on carcass sides, and eight sides (per three replications) were inoculated with a 7-strain STEC cocktail (ca. 5 log CFU/cm² across all external and body cavity surfaces). Each side was randomly assigned to a final pre-chill wash treatment administered in a commercial Chad carcass cabinet using a low-volume spray [3% lactic acid (lLA; 130 °F), 400 ppm peracetic acid (lPAA), or acidified 400 ppm peracetic acid (laPAA)] or a high-volume wash [ambient water (hAW), 400 ppm PAA (hPAA), 400 or 600 ppm hypobromous acid (hDBDMH), or 71 °C water (hHW)] treatment according to a randomized complete block study design. Post-treatment (after a 10-min hanging drip) and post-chilling (18 h at 2 °C) STEC reductions were compared for external skin-on surfaces and internal body cavity lean surface tissue. Post-treatment color changes were determined for lean, adipose, and skin carcass surfaces before and after chilling. When applied to the external, skin-on surface, the hHW, hPAA, and hDBDMH₆₀₀ deluge washes were significantly (P ≤ 0.05) more effective than the other intervention technologies, achieving STEC reductions of 3.8, 3.4, and 3.2 log CFU/cm², respectively. In comparison, the hAW control reduced STEC by 1.7-log CFU/cm² on the external, skin-on surface. The carcass interventions were less effective at reducing STEC populations attached to interior body cavity (diaphragm region), with post-chill populations reduced by 0.9-2.2 log cycles, while the hAW control wash achieved a 0.6-log reduction. None of the treatments negatively impacted instrumental carcass color. While all market hog carcass interventions reduced STEC populations, larger reductions were observed when applied to the external, skin-on surface, with the largest reductions achieved by the hHW, hPAA, and hDBDMH₆₀₀ deluge washes. These data equip pork processors with the information necessary to support decision-making when selecting an intervention technology.

Attachment of Shiga Toxin-Producing Escherichia coli (STEC) to Pre-Chill and Post-Chill Beef Brisket Tissue

Shiga toxin-producing Escherichia coli (STEC) has caused numerous foodborne illness outbreaks where beef was implicated as the contaminated food source. Understanding how STEC attach to beef surfaces may inform effective intervention applications at the abattoir. This simulated meat processing conditions to measure STEC attachment to adipose and lean beef tissue. Beef brisket samples were warmed to a surface temperature of 30 °C (warm carcass), while the remaining samples were maintained at 4 °C (cold carcass), prior to surface inoculation with an STEC cocktail (O26, O45, O103, O111, O121, O145, and O157:H7). Cocktails were grown in either tryptic soy broth (TSB) or M9 minimal nutrient medium. Loosely and firmly attached cells were measured at 0, 3, 5, and 20 min and 1, 3, 8, 12, 24 and 48 h. TSB-grown STEC cells became more firmly attached throughout storage and a difference in loosely versus firmly attached populations on lean and adipose tissues was observed. M9-grown STEC demonstrated a 0.2 log₁₀ CFU/cm² difference in attachment to lean versus adipose tissue and variability in populations was recorded throughout sampling. Future research should investigate whether a decrease in intervention efficacy correlates to an increase in firmly attached STEC cells on chilled carcasses and/or subprimals, which has been reported.

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Simple Summary

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause food-borne diseases in humans, where cattle and derived products play a key role as reservoirs and vehicles. We analyzed the genomic data of STEC strains circulating at the livestock-food-human interface in South America, extracting clinically and epidemiologically relevant information (serotypes, virulome, resistance genes, sequence types, and phylogenomics). This study included 130 STEC genomes obtained from cattle (n = 51), beef (n = 48), and human (n = 31) samples. The successful expansion of O157:H7 (ST11) and non-O157 (ST16, ST21, ST223, ST443, ST677, ST679, ST2388) clones is highlighted, suggesting common activities, such as multilateral trade and travel. Circulating STEC strains analyzed exhibit high genomic diversity and harbor several genetic determinants associated with severe illness in humans, highlighting the need to establish official surveillance of this pathogen that should be focused on detecting molecular determinants of virulence and clonal relatedness, in the whole beef production chain.

Abstract

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens responsible for causing food-borne diseases in humans. While South America has the highest incidence of human STEC infections, information about the genomic characteristics of the circulating strains is scarce. The aim of this study was to analyze genomic data of STEC strains isolated in South America from cattle, beef, and humans; predicting the antibiotic resistome, serotypes, sequence types (STs), clonal complexes (CCs) and phylogenomic backgrounds. A total of 130 whole genome sequences of STEC strains were analyzed, where 39.2% were isolated from cattle, 36.9% from beef, and 23.8% from humans. The ST11 was the most predicted (20.8%) and included O-:H7 (10.8%) and O157:H7 (10%) serotypes. The successful expansion of non-O157 clones such as ST16/CC29-O111:H8 and ST21/CC29-O26:H11 is highlighted, suggesting multilateral trade and travel. Virulome analyses showed that the predominant stx subtype was stx2a (54.6%); most strains carried ehaA (96.2%), iha (91.5%) and lpfA (77.7%) genes. We present genomic data that can be used to support the surveillance of STEC strains circulating at the livestock-food-human interface in South America, in order to control the spread of critical clones “from farm to table”.

Genomic features and antimicrobial resistance patterns of Shiga toxin-producing Escherichia coli strains isolated from food in Chile

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes severe illness in humans, often associated with foodborne outbreaks. Antimicrobial resistance among foodborne E. coli has increased over the last decades becoming a public health issue. In this study, the presence and features of STEC were investigated in samples of meat, seafood, vegetables and ready-to-eat street-vended food collected in Chile, using a genomic and microbiological approach. Phenotypic and genotypic antimicrobial resistance profiles were determined, and serotype, phylogroup, sequence type (ST) and phylogenomics were predicted using bioinformatic tools. Three thousand three hundred samples collected in 2019 were screened, of which 18 were positive for STEC strains (0.5%), with stx2a (61.1%) being the predominant stx subtype. The presence of the virulence genes lpfA (100%), iha and ehaA (94.4%), and ehxA, hlyA and saa (83.3%) was confirmed among the STEC strains; the Locus of adhesion and autoaggregation (LAA) was predicted in 14 (77.8%) strains. Strains displayed resistance to colistin (100%), and intermediate resistance to enrofloxacin (11.1%) and chloramphenicol (5.6%). In this regard, mutations in the two-component regulatory system genes pmrA (S29G), pmrB (D283G) and phoP (I44L), and the presence of the qnrB19 gene were confirmed. STEC strains belonged to ST11231 (38.9%), ST297 and ST58 (16.7% each), and ST1635, ST11232, ST446, ST442 and ST54 (5.6% each), and the most frequently detected serotypes were O113:H21 (44.4%), O130:H11 and O116:H21 (16.7% each), and O174:H21 (11.1%). Strains belonging to the international ST58 showed genomic relatedness with worldwide strains from human and non-human sources. Our study reports for the first time the genomic profile of STEC strains isolated from food in Chile, highlighting the presence of international clones and sequence types commonly associated with human infections in different geographical regions, as well as the convergence of virulence and resistance in STEC lineages circulating in this country.

Virulence Characteristics and Antibiotic Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Diverse Sources

Shiga toxin-producing Escherichia coli (STEC) is an enteric pathogen that causes several gastrointestinal ailments in humans across the world. STEC’s ability to cause ailment is attributed to the presence of a broad range of known and putative virulence factors (VFs) including those that encode Shiga toxins. A total of 51 E. coli strains belonging to serogroups O26, O45, O103, O104, O113, O121, O145, and O157 were tested for the presence of nine VFs via PCR and for their susceptibility to 17 frequently used antibiotics using the disc diffusion method. The isolates belonged to eight different serotypes, including eight O serogroups and 12 H types. The frequency of the presence of key VFs were stx1 (76.47%), stx2 (86.27%), eae (100%), ehxA (98.03%), nleA (100%), ureC (94.11%), iha (96.07%), subA (9.80%), and saa (94.11%) in the E. coli strains. All E. coli strains carried seven or more distinct VFs and, among these, four isolates harbored all tested VFs. In addition, all E. coli strains had a high degree of antibiotic resistance and were multidrug resistant (MDR). These results show a high incidence frequency of VFs and heterogeneity of VFs and MDR profiles of E. coli strains. Moreover, half of the E. coli isolates (74.5%) were resistant to > 9 classes of antibiotics (more than 50% of the tested antibiotics). Thus, our findings highlight the importance of appropriate epidemiological and microbiological surveillance and control measures to prevent STEC disease in humans worldwide.

Characterization and molecular subtyping of Shiga toxin-producing Escherichia coli strains in provincial abattoirs from the Province of Buenos Aires, Argentina, during 2016-2018

We characterized Shiga toxin-producing Escherichia coli (STEC) O157 (n = 20) and non-O157 (n = 68) isolated from carcasses (n = 54), the environment (n = 20), head meat (n = 3) and viscera washing and chilling water (n = 11) in provincial abattoirs before and after implementing improvement actions. The strains were tested for eae, saa, ehxA and fliC_H7 genes. Variants stx₁ and stx₂ were also determined. Pulsed-field gel electrophoresis (PFGE) was carried out with restriction enzymes XbaI and BlnI. All twenty O157 STEC strains [H7; H21; HNM] carried genes rfb_O157 and ehxA; 90.0 % were positive for eae and 15.0 % were negative for fliC_H7 and positive for saa. Results of PFGE showed 17 XbaI patterns, of which 14 were unique and three formed clusters. From the 68 non-O157 STEC strains, 66.2 %, 55.9 % and 2.9 % were positive for ehxA, saa and eae genes, respectively. Fifty-three XbaI patterns were obtained (49 unique and four forming clusters). Cross-contamination between products and between the environment and products was confirmed in all abattoirs. While the proposed improvements reduced the risk of contamination, Good Hygiene Practices and Good Manufacturing Practices should be implemented in provincial abattoirs, stressing the importance of having a uniform national food safety standard.

Preliminary data on the antimicrobial effect of Cannabis sativa L. variety Futura 75 against food-borne pathogens in vitro as well as against naturally occurring microbial populations on minced meat during storage

In the present study, the antimicrobial effect of Cannabis sativa Futura 75 was evaluated both in vitro against foodborne bacterial pathogens, and on food against naturally occurring microbial groups of minced meat stored for 8 days at 4°C. Ethanol extraction was performed on the grind of the inflorescence. After extraction, ethanol was completely evaporated and substituted by water. Serial dilutions of the extract, the grind and cannabidiol 99% were added to Nutrient Agar and spotted with Listeria monocytogenes, Salmonella Typhimurium, Escherichia coli and Staphylococcus spp. Regarding the evaluation on food, 50 mL of extract, characterised by CBD at concentration of 322,70 μg/mL, were added to 2.5 kg of minced beef meat. Meat was divided into aliquots and stored for 8 days at 4°C. At 0, 1, 2, 3, 4, 7, and 8 days, aerobic bacteria, enterobacteria, coliforms and E. coli were enumerated. All tested products were efficient against Gram +. In particular, extract corresponding to CBD concentration of 0.017 and 0.3 mg/mL were effective against L. monocytogenes and Staphylococcus spp. respectively. After 8 days of storage at 4°C, treated minced meat showed a bright red colour in comparison to a brownish control meat. Moreover, Enterobacteriaceae and coliforms were significantly reduced of 2.3 log CFU/g and 1.6 log CFU/g respectively in treated meat in comparison to the control. Although preliminary, the present study suggests the antimicrobial properties of the extract of Cannabis sativa both in vitro and in minced meat.

The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country

Gradually, conventional methods for foodborne pathogen typing are replaced by whole genome sequencing (WGS). Despite studies describing the overall benefits, National Reference Laboratories of smaller countries often show slower uptake of WGS, mainly because of significant investments required to generate and analyze data of a limited amount of samples. To facilitate this process and incite policy makers to support its implementation, a Shiga toxin-producing Escherichia coli (STEC) O157:H7 (stx1+, stx2+, eae+) outbreak (2012) and a STEC O157:H7 (stx2+, eae+) outbreak (2013) were retrospectively analyzed using WGS and compared with their conventional investigations. The corresponding results were obtained, with WGS delivering even more information, e.g., on virulence and antimicrobial resistance genotypes. Besides a universal, all-in-one workflow with less hands-on-time (five versus seven actual working days for WGS versus conventional), WGS-based cgMLST-typing demonstrated increased resolution. This enabled an accurate cluster definition, which remained unsolved for the 2013 outbreak, partly due to scarce epidemiological linking with the suspect source. Moreover, it allowed detecting two and one earlier circulating STEC O157:H7 (stx1+, stx2+, eae+) and STEC O157:H7 (stx2+, eae+) strains as closely related to the 2012 and 2013 outbreaks, respectively, which might have further directed epidemiological investigation initially. Although some bottlenecks concerning centralized data-sharing, sampling strategies, and perceived costs should be considered, we delivered a proof-of-concept that even in smaller countries, WGS offers benefits for outbreak investigation, if a sufficient budget is available to ensure its implementation in surveillance. Indeed, applying a database with background isolates is critical in interpreting isolate relationships to outbreaks, and leveraging the true benefit of WGS in outbreak investigation and/or prevention.

An Overview of the Elusive Passenger in the Gastrointestinal Tract of Cattle: The Shiga Toxin Producing Escherichia coli

For approximately 10,000 years, cattle have been our major source of meat and dairy. However, cattle are also a major reservoir for dangerous foodborne pathogens that belong to the Shiga toxin-producing Escherichia coli (STEC) group. Even though STEC infections in humans are rare, they are often lethal, as treatment options are limited. In cattle, STEC infections are typically asymptomatic and STEC is able to survive and persist in the cattle GIT by escaping the immune defenses of the host. Interactions with members of the native gut microbiota can favor or inhibit its persistence in cattle, but research in this direction is still in its infancy. Diet, temperature and season but also industrialized animal husbandry practices have a profound effect on STEC prevalence and the native gut microbiota composition. Thus, exploring the native cattle gut microbiota in depth, its interactions with STEC and the factors that affect them could offer viable solutions against STEC carriage in cattle.

Genomic analysis of Shiga toxin-producing Escherichia coli from patients and asymptomatic food handlers in Japan

Shiga toxin-producing Escherichia coli (STEC) can cause severe gastrointestinal disease and colonization among food handlers. In Japan, STEC infection is a notifiable disease, and food handlers are required to undergo routine stool examination for STEC. However, the molecular epidemiology of STEC is not entirely known. We investigated the genomic characteristics of STEC from patients and asymptomatic food handlers in Miyagi Prefecture, Japan. Whole-genome sequencing (WGS) was performed on 65 STEC isolates obtained from 38 patients and 27 food handlers by public health surveillance in Miyagi Prefecture between April 2016 and March 2017. Isolates of O157:H7 ST11 and O26:H11 ST21 were predominant (n = 19, 29%, respectively). Non-O157 isolates accounted for 69% (n = 45) of all isolates. Among 48 isolates with serotypes found in the patients (serotype O157:H7 and 5 non-O157 serotypes, O26:H11, O103:H2, O103:H8, O121:H19 and O145:H28), adhesion genes eae, tir, and espB, and type III secretion system genes espA, espJ, nleA, nleB, and nleC were detected in 41 to 47 isolates (85–98%), whereas isolates with other serotypes found only in food handlers were negative for all of these genes. Non-O157 isolates were especially prevalent among patients younger than 5 years old. Shiga-toxin gene stx1a, adhesion gene efa1, secretion system genes espF and cif, and fimbrial gene lpfA were significantly more frequent among non-O157 isolates from patients than among O157 isolates from patients. The most prevalent resistance genes among our STEC isolates were aminoglycoside resistance genes, followed by sulfamethoxazole/trimethoprim resistance genes. WGS revealed that 20 isolates were divided into 9 indistinguishable core genomes (<5 SNPs), demonstrating clonal expansion of these STEC strains in our region, including an O26:H11 strain with stx1a+stx2a. Non-O157 STEC with multiple virulence genes were prevalent among both patients and food handlers in our region of Japan, highlighting the importance of monitoring the genomic characteristics of STEC.

Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance

Aim:

The present study was carried out to determine load of total bacteria, Escherichia coli and Salmonella spp. in dairy farm and its environmental components. In addition, the antibiogram profile of the isolated bacteria having public health impact was also determined along with identification of virulence and resistance genes by polymerase chain reaction (PCR) under a one-health approach.

Materials and Methods:

A total of 240 samples of six types (cow dung – 15, milk – 10, milkers’ hand wash – 10, soil – 10 water – 5, and vegetables – 10) were collected from four dairy farms. For enumeration, the samples were cultured onto plate count agar, eosin methylene blue, and xylose-lysine deoxycholate agar and the isolation and identification of the E. coli and Salmonella spp. were performed based on morphology, cultural, staining, and biochemical properties followed by PCR.The pathogenic strains of E. colistx1, stx2, and rfbO157 were also identified through PCR. The isolates were subjected to antimicrobial susceptibility test against 12 commonly used antibiotics by disk diffusion method. Detection of antibiotic resistance genes ereA, tetA, tetB, and SHV were performed by PCR.

Results:

The mean total bacterial count, E. coli and Salmonella spp. count in the samples ranged from 4.54±0.05 to 8.65±0.06, 3.62±0.07 to 7.04±0.48, and 2.52±0.08 to 5.87±0.05 log colony-forming unit/g or ml, respectively. Out of 240 samples, 180 (75%) isolates of E. coli and 136 (56.67%) isolates of Salmonella spp. were recovered through cultural and molecular tests. Among the 180 E. coli isolates, 47 (26.11%) were found positive for the presence of all the three virulent genes, of which stx1 was the most prevalent (13.33%). Only three isolates were identified as enterohemorrhagic E. coli. Antibiotic sensitivity test revealed that both E. coli and Salmonella spp. were found highly resistant to azithromycin, tetracycline, erythromycin, oxytetracycline, and ertapenem and susceptible to gentamycin, ciprofloxacin, and imipenem. Among the four antibiotic resistance genes, the most observable was tetA (80.51-84.74%) in E. coli and Salmonella spp. and SHV genes were the lowest one (22.06-25%).

Conclusion:

Dairy farm and their environmental components carry antibiotic-resistant pathogenic E. coli and Salmonella spp. that are potential threat for human health which requires a one-health approach to combat the threat.

Whole genome sequencing to characterize shiga toxin-producing Escherichia coli O26 in a public health setting

BACKGROUND

Shiga-toxin producing Escherichia coli (STEC) O26:H11 is the second most common cause of severe diarrhea and hemolytic uremic syndrome worldwide. The implementation of whole genome sequencing (WGS) enhances the detection and in-depth characterization of these non-O157 STEC strains. The aim of this study was to compare WGS to phenotypic serotyping and pulse field gel electrophoresis (PFGE) for characterization of STECO26 strains following a zoonotic outbreak from cattle to humans.

METHODS AND RESULTS

This study evaluated seven E. coli strains; two strains isolated from two children with gastrointestinal symptoms and five strains from five calves suspected as the source of infection. Six of these isolates were serotyped phenotypically and by WGS as E. coli O26:H11 while one bovine isolate could be serotyped only by WGS as E. coli O182:H25. Stx1 was detected in two human- and two bovine-isolates using PCR and WGS. Using WGS, all four STECO26 isolates belong to sequence type (ST) 21 while the two stx1 negative E. coli O26 were ST29. All four STECO26 isolates were indistinguishable by PFGE. However, the data generated by WGS linked the two human STECO26 isolates to only one bovine STECO26 strain by having identical high-quality single nucleotide polymorphisms (hqSNPs) and identical virulence factor profiles while the remaining bovine STECO26 isolate differed by 7 hqSNPs and lacked virulence factor toxB.

CONCLUSIONS

These data demonstrated that WGS provided significant information beyond traditional epidemiological tools allowing for comprehensive characterization of the STEC. Using this approach, WGS was able to identify the specific source of infection in this study.

Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7- loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silico using the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.

Dextran Sulfate Sodium Colitis Facilitates Colonization with Shiga Toxin-Producing Escherichia coli: a Novel Murine Model for the Study of Shiga Toxicosis

Shiga toxin-producing Escherichia coli (STEC) bacteria are globally important gastrointestinal pathogens causing hemorrhagic gastroenteritis with variable progression to potentially fatal Shiga toxicosis. Little is known about the potential effects of E. coli-derived Shiga-like toxins (STXs) on host gastrointestinal immune responses during infection, in part due to the lack of a reproducible immunocompetent-animal model of STEC infection without depleting the commensal microbiota. Here, we describe a novel and reproducible murine model utilizing dextran sulfate sodium (DSS) colitis to induce susceptibility to colonization with clinical-isolate STEC strains. After exposure to DSS and subsequent oral STEC challenge, all the mice were colonized, and 66% of STEC-infected mice required early euthanasia. Morbidity during STEC infection, but not infection with an isogenic STEC mutant with toxin deleted, was associated with increased renal transcripts of the injury markers KIM1 and NGAL, histological evidence of renal tubular injury, and increased renal interleukin 6 gene (IL-6) and CXCL1 inflammatory transcripts. Interestingly, the intestinal burden of STEC during infection was increased compared to its isogenic Shiga toxin deletion strain. Increased bacterial burdens during Shiga toxin production coincided with decreased induction of colonic IL-23 axis transcripts known to be critical for clearance of similar gastrointestinal pathogens in mice, suggesting a previously undescribed role for STEC Shiga toxins in suppressing host immune responses during STEC infection and survival. The DSS+STEC model establishes infection with clinical-isolate strains of STEC in immunocompetent mice without depleting the gastrointestinal microbiota, enabling characterization of the effects of STXs on the IL-23 axis and other gastrointestinal pathogen-host interactions.

Occurrence of Escherichia coli carrying Shiga toxin-producing genes in buffaloes on smallholdings in Bangladesh

Background and Aim:

Shiga toxin-producing Escherichia coli (STEC) has emerged as significant foodborne pathogens. Ruminants are the primary reservoir of the zoonotic STEC. In Bangladesh, previous studies reported the presence of STEC in cattle, goat, and sheep; however, there is little information about STEC carriage by buffaloes. This study aimed to determine the occurrence of STEC in healthy (absence of clinical signs and symptoms) buffaloes on smallholdings in Bangladesh and to assess the antimicrobial resistance pattern of identified STEC isolates.

Materials and Methods:

A total of 100 rectal swab samples were obtained from randomly selected buffaloes on 40 smallholdings in Chittagong Division, Bangladesh. Samples were subjected to bacteriological screening to identify E. coli. All E. coli isolates were examined for the presence of the Shiga toxin-producing genes - Shiga toxin 1 (stx1) and Shiga toxin 2 (stx2) using polymerase chain reaction. The antimicrobial susceptibility of identified STEC isolates was tested using the disk diffusion method.

Results:

Results show that 71 fecal samples were positive for E. coli in bacteriological screening. The proportion of buffaloes harboring STEC isolates was 11% (11/100) (95% confidence interval [CI] 6.1-18.8], of which 7% (7/100) (95% CI 3.2-13.9) and 4% (4/100) (95% CI 1.2-10.2) carried stx1 and stx2 genes, respectively. Antibiogram revealed that 91% (10/11), 73% (8/11), 55% (6/11), and 55% (6/11) STEC isolates were resistant to tetracycline, sulfamethoxazole-trimethoprim, erythromycin, and ampicillin, respectively. In contrast, 91% (10/11) STEC isolates were sensitive to ciprofloxacin, chloramphenicol, and gentamicin, whereas 73% (8/11) isolates were sensitive to ceftriaxone.

Conclusion:

This study highlights, for the first time, a significant proportion of fecal samples from healthy buffaloes on smallholdings in Bangladesh harboring antimicrobial-resistant STEC. Transmission of antimicrobial-resistant STEC from buffaloes to humans could pose an added risk to public health in rural Bangladesh.