Long-term survival of Shiga toxin-producing Escherichia coli in cattle effluents and environment: An updated review

Molecular detection and antibiogram of Shiga toxin-producing Escherichia coli (STEC) from raw milk in and around Bahir Dar town dairy farms, Ethiopia

Illnesses associated with consuming infected milk and milk products are a widespread problem in low and middle-income countries. Shiga toxin-producing Escherichia coli (STEC) is a bacterium commonly found in raw milk and causes foodborne diseases ranging from mild diarrhea to severe hemorrhagic colitis and hemolytic uremic syndrome. This study aimed to investigate the virulence gene and antimicrobial resistance profiles of Shiga toxin-producing E. coli strains isolated from raw milk in dairy farms in and around Bahir Dar town. Raw milk samples (n = 128) collected from December 2021 to July 2022 were cultured, and E. coli strains were isolated using standard methods. Shiga toxin-producing E. coli strains were identified genotypically by the presence of the virulence markers using a single-plex polymerase chain reaction. The antibiotic susceptibility testing of Shiga toxin-producing E. coli isolates was done by the agar disk diffusion method. In total, 32 E. coli isolates were recovered from milk samples from lactating animals. PCR screening of these isolates resulted in 19 (59.3%) positives for Shiga toxin-producing E. coli. The stx2 gene was detected in 53% of cases, followed by stx1 (31%) and eae (16%. The STEC isolates were highly sensitive to ciprofloxacin (94.7%) and kanamycin (89.5%), while exhibiting significant resistance to amoxicillin (89.5%) and streptomycin (73.7%). The present study points out the occurrence of virulent and antibiotic-resistant Shiga toxin-producing E. coli strains in raw milk that could pose a potential risk to public health. Further analysis by whole genome sequencing is necessary for an in-depth assessment and understanding of their virulence and resistance factors. Moreover, large-scale studies are needed to identify the prevalence and potential risk factors and to prevent the spread of antibiotic-resistant STEC strains in the milk production chain.

Spatially localised expression of the glutamate decarboxylase gadB in Escherichia coli O157:H7 microcolonies in hydrogel matrices

Functional diversity within isogenic spatially organised bacterial populations has been shown to trigger emergent community properties such as stress tolerance. Considering gadB gene encoding a key glutamate decarboxylase involved in E. coli tolerance to acidic conditions, we investigated its expression in hydrogels mimicking the texture of some structured food matrices (such as minced meat or soft cheese). Taking advantage of confocal laser scanning microscopy combined with a genetically-engineered dual fluorescent reporter system, it was possible to visualise the spatial patterns of bacterial gene expression from in-gel microcolonies. In E. coli O157:H7 microcolonies, gadB showed radically different expression patterns between neutral (pH 7) or acidic (pH 5) hydrogels. Differential spatial expression was determined in acidic hydrogels with a strong expression of gadB at the microcolony periphery. Strikingly, very similar spatial patterns of gadB expression were further observed for E. coli O157:H7 grown in the presence of L. lactis. Considering the ingestion of contaminated foodstuff, survival of E. coli O157:H7 to acidic stomachal stress (pH 2) was significantly increased for bacterial cells grown in microcolonies in acidic hydrogels compared to planktonic cells. These findings have significant implications for risk assessment and public health as they highlight inherent differences in bacterial physiology and virulence between liquid and structured food products. The contrasting characteristics observed underscore the need to consider the distinct challenges posed by these food types, thereby emphasising the importance of tailored risk mitigation strategies.

Risk factors associated with the prevalence of Shiga-toxin-producing Escherichia coli in manured soils on certified organic farms in four regions of the USA

Introduction

Biological soil amendments of animal origin (BSAAO), including untreated amendments are often used to improve soil fertility and are particularly important in organic agriculture. However, application of untreated manure on cropland can potentially introduce foodborne pathogens into the soil and onto produce. Certified organic farms follow the USDA National Organic Program (NOP) standards that stipulate a 90- or 120-day interval between application of untreated manure and crop harvest, depending on whether the edible portion of the crop directly contacts the soil. This time-interval metric is based on environmental factors and does not consider a multitude of factors that might affect the survival of the main pathogens of concern. The objective of this study was to assess predictors for the prevalence of Shiga-toxin-producing Escherichia coli (non-O157 STEC) in soils amended with untreated manure on USDA-NOP certified farms.

Methods

A longitudinal, multi-regional study was conducted on 19 farms in four USA regions for two growing seasons (2017–2018). Untreated manure (cattle, horse, and poultry), soil, and irrigation water samples were collected and enrichment cultured for non-O157 STEC. Mixed effects logistic regression models were used to analyze the predictors of non-O157 STEC in the soil up to 180 days post-manure application.

Results and discussion

Results show that farm management practices (previous use with livestock, presence of animal feces on the field, season of manure application) and soil characteristics (presence of generic E. coli in the soil, soil moisture, sodium) increased the odds of STEC-positive soil samples. Manure application method and snowfall decreased the odds of detecting STEC in the soil. Time-variant predictors (year and sampling day) affected the presence of STEC. This study shows that a single metric, such as the time interval between application of untreated manure and crop harvest, may not be sufficient to reduce the food safety risks from untreated manure, and additional environmental and farm-management practices should also be considered. These findings are of particular importance because they provide multi-regional baseline data relating to current NOP wait-time standards. They can therefore contribute to the development of strategies to reduce pathogen persistence that may contribute to contamination of fresh produce typically eaten raw from NOP-certified farms using untreated manure.

Differential Survival of Escherichia coli and Listeria spp. in Northeastern U.S. Soils Amended with Dairy Manure Compost, Poultry Litter Compost, and Heat-Treated Poultry Pellets and Fate in Raw Edible Radish Crops

ABSTRACT

Composted or heat-treated biological soil amendments of animal origin (BSAAOs) can be added to soils to provide nutrients for fresh produce. These products lower the risk of pathogen contamination of fresh produce compared with the use of untreated BSAAOs; however, meteorological conditions, geographic location, and soil properties can influence the presence of pathogenic bacteria or their indicators (e.g., generic Escherichia coli) and allow potential for produce contamination. Replicated field plots of loamy or sandy soils were tilled and amended with dairy manure compost (DMC), poultry litter compost (PLC), or no compost (NoC) over two field seasons and noncomposted heat-treated poultry pellets (HTPPs) during the second field season. Plots were inoculated with a three-strain cocktail of rifampin-resistant E. coli (rE. coli) at levels of 8.7 log CFU/m2. Direct plating and most-probable-number methods measured the persistence of rE. coli and Listeria spp. in plots through 104 days postinoculation. Greater survival of rE. coli was observed in PLC plots in comparison to DMC plots and NoC plots during year 1 (P < 0.05). Similar trends were observed for year 2, when rE. coli survival was also greater in HTPP-amended plots (P < 0.05). Survival of rE. coli depended on soil type, and water potential and temperature were significant covariables. Listeria spp. were found in NoC plots, but not in plots amended with HTPPs, PLC, or DMC. Radish data demonstrate that PLC treatment promoted the greatest level of rE. coli translocation compared with DMC and NoC treatments (P < 0.05). These results are consistent with findings from studies conducted in other regions of the United States, and they inform northeast produce growers that composted and noncomposted poultry-based BSAAOs support greater survival of rE. coli in field soils. This result has the potential to affect the food safety risk of edible produce grown in BSAAO-amended soils as a result of pathogen contamination.

HIGHLIGHTS

Nitrate enrichment does not affect enteropathogenic Escherichia coli in aquatic microcosms but may affect other strains present in aquatic habitats

Eutrophication of the planet's aquatic systems is increasing at an unprecedented rate. In freshwater systems, nitrate-one of the nutrients responsible for eutrophication-is linked to biodiversity losses and ecosystem degradation. One of the main sources of freshwater nitrate pollution in New Zealand is agriculture. New Zealand's pastoral farming system relies heavily on the application of chemical fertilisers. These fertilisers in combination with animal urine, also high in nitrogen, result in high rates of nitrogen leaching into adjacent aquatic systems. In addition to nitrogen, livestock waste commonly carries human and animal enteropathogenic bacteria, many of which can survive in freshwater environments. Two strains of enteropathogenic bacteria found in New Zealand cattle, are K99 and Shiga-toxin producing Escherichia coli (STEC). To better understand the effects of ambient nitrate concentrations in the water column on environmental enteropathogenic bacteria survival, a microcosm experiment with three nitrate-nitrogen concentrations (0, 1, and 3 mg NO₃-N /L), two enteropathogenic bacterial strains (STEC O26-human, and K99-animal), and two water types (sterile and containing natural microbiota) was run. Both STEC O26 and K99 reached 500 CFU/10 ml in both water types at all three nitrate concentrations within 24 hours and remained at those levels for the full 91 days of the experiment. Although enteropathogenic strains showed no response to water column nitrate concentrations, the survival of background Escherichia coli, imported as part of the in-stream microbiota did, surviving longer in 1 and 3 mg NO₃-N/Lconcentrations (P < 0.001). While further work is needed to fully understand how nitrate enrichment and in-stream microbiota may affect the viability of human and animal pathogens in freshwater systems, it is clear that these two New Zealand strains of STEC O26 and K99 can persist in river water for extended periods alongside some natural microbiota.

Spatiotemporal dynamics of Escherichia coli presence and magnitude across a national groundwater monitoring network, Republic of Ireland, 2011-2020

Groundwater is a vital drinking water resource and its protection from microbiological contamination is paramount to safeguard public health. The Republic of Ireland (RoI) is characterised by the highest incidence of verocytotoxigenic Escherichia coli (VTEC) enteritis in the European Union (EU), linked to high reliance on unregulated groundwater sources (~16% of the population). Yet, the spatio-temporal factors influencing the frequency and magnitude of microbial contamination remain largely unknown, with past studies typically constrained to spatio-temporally 'limited' sampling campaigns. Accordingly, the current investigation sought to analyse an extensive spatially distributed time-series (2011-2020) of groundwater monitoring data in the RoI. The dataset, compiled by the Environmental Protection Agency (EPA), showed 'high' contamination rates, with 66.7% (88/132) of supplies testing positive for E. coli, and 29.5% (39/132) exceeding concentrations of 10MPN/100 ml (i.e. gross contamination) at least once during the 10-year monitoring period. Seasonal decomposition analyses indicate that E. coli detection rates peak during late autumn/early winter, coinciding with increases in annual rainfall, while gross contamination peaks in spring (May) and late-summer (August), likely reflecting seasonal shifts in agricultural practices. Mixed effects logistic regression modelling indicates that monitoring sources located in karst limestone are statistically associated with E. coli presence (OR = 2.76, p = 0.03) and gross contamination (OR = 2.54, p = 0.037) when compared to poorly productive aquifers (i.e., transmissivity below 10m²/d). Moreover, 5-day and 30-day antecedent rainfall increased the likelihood of E. coli contamination (OR = 1.027, p < 0.001 and OR = 1.005, p = 0.016, respectively), with the former also being associated with gross contamination (OR = 1.042, p < 0.001). As such, it is inferred that preferential flow and direct ingress of surface runoff are the most likely ingress mechanisms associated with E. coli groundwater supply contamination. The results presented are expected to inform policy change around groundwater source protection and provide insight for the development of groundwater monitoring programmes in geologically heterogeneous regions.

Stimulatory effects of defective and effective 3-indoleacetic acid-producing bacterial strains on rice in an advanced stage of its vegetative cycle

The production of 3-indoleacetic acid (IAA) by plant growth-promoting bacteria (PGPR) stimulates root development and plant growth. In addition, morphological changes such as an increased root ramification and root hair production improves nutrient absorption and biomass accumulation. The objective of this work was to evaluate the effect of IAA-producing strains on rice in an advanced stage of its vegetative cycle. Rice was inoculated with Gluconacetobacter diazotrophicus PAL 5 and its lao- mutant, deficient in auxin production, Azospirillum baldaniorum Sp 245, and Escherichia coli DH10b. Both the mutant and wild-type G. diazotrophicus stimulated root elongation, area, volume, and diameter. However, the lao- mutant strain was the only one capable of increasing the number of roots. In turn, inoculation with A. baldaniorum had no significant effect on plant development. The inoculation with E. coli led to changes in root volume, area, and diameter, and a response that may be related to the stress caused by its presence. We conclude that the inoculation with G. diazotrophicus stimulates the root system's growth independently of their IAA production ability, suggesting that a metabolite other than IAA is responsible for this effect at advanced stages of the rice's vegetative cycle.

The Fate of Foodborne Pathogens in Manure Treated Soil

The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.

Differential Survival of Non-O157 Shiga Toxigenic Escherichia coli in Simulated Cattle Feedlot Runoff

Environmental survival time is important when evaluating adverse health outcomes from foodborne pathogens. Although outbreaks associated with manure-impacted irrigation or runoff water are relatively infrequent, their broad scope, regulatory importance, and severe health outcomes highlight the need to better understand the environmental survival of manure-borne pathogens. Shiga toxigenic Escherichia coli (STEC) are excreted in feces and persist in the environment until they die or recolonize a new host. Surface waters contaminated with manure-borne STEC can infect humans through drinking and recreational water use or irrigated crops that are minimally cooked. In this study, manure-impacted water microcosms mimicking beef cattle feedlot runoff were used to assess survival of STEC strains representing seven STEC serotypes (O26, O45, O103, O111, O121, O145, and O157) and persistence of target O antigen genes. Microcosms were sampled over the course of 1 year, and the entire experiment was repeated in a second year. Culture and polymerase chain reaction (PCR)-based techniques were used for detection and enumeration. Serotype-specific survival results were observed. Both STEC O26 and O45 declined slowly and remained culturable at 24 months. In contrast, STEC O121 and O145 decreased rapidly (-0.84 and -1.99 log10 abundance per month, respectively) and were unculturable by months 4 and 5, but detectable by PCR for a mean of 4.5 and 8.3 months, respectively. STEC O103, O111, and O157 remained culturable for a mean of 11.6, 5.5, and 15 months and detectable by PCR for a mean of 12, 13.8, and 18.6 months after inoculation, respectively. Results document that some STEC serotypes have the biological potential to survive in manure-impacted waters for extended periods of time when competing microflora are eliminated. Serotype-specific differences in survival of target bacteria and persistence of target genes were observed in this sample set, with STEC O26 and O45 strains appearing the most robust in these microcosm studies.

Shiga Toxin-Producing Escherichia coli in the Long-Term Survival Phase Exhibit Higher Chlorine Tolerance and Less Sublethal Injury Following Chlorine Treatment of Romaine Lettuce

The extent of chlorine inactivation and sublethal injury of stationary-phase (STAT) and long-term survival-phase (LTS) cells of Shiga toxin-producing Escherichia coli (STEC) in vitro and in a lettuce postharvest wash model was investigated. Four STEC strains were cultured in tryptic soy broth supplemented with 0.6% (w/v) yeast extract (TSBYE; 35°C) for 24 h and 21 d to obtain STAT and LTS cells, respectively. Minimum bactericidal concentration (MBC) and dose-response assays were performed to determine chlorine's antibacterial efficacy against STAT and LTS cells. Chlorine solutions (pH 6.5) and romaine lettuce were each inoculated with STAT and LTS cells to obtain initial populations of ∼7.8 log colony-forming units (CFU)/mL. Survivors in chlorine solutions were determined after 30 s. Inoculated lettuce samples were held at 22°C ± 1°C for 2 h or 20 h and then exposed to chlorine (10-40 ppm) for 60 s. Survivors were enumerated on nonselective and selective agar media following incubation (35°C, 48 h). The MBC for STAT and LTS cells was 0.04 and 0.08 ppm, respectively. Following exposure (30 s) to chlorine at 2.5, 5.0, and 10 ppm, STAT cells were reduced to <1.0 log CFU/mL, whereas LTS survivors were at 5.10 (2.5 ppm), 3.71 (5.0 ppm), and 2.55 (10 ppm) log CFU/mL. At 20 and 40 ppm chlorine, greater log CFU reductions of STAT cells (1.64 and 1.85) were observed compared with LTS cells (0.94 and 0.83) after 2 h of cell contact with lettuce (p < 0.05), but not after 20 h. Sublethal injury in STEC after chlorine (40 ppm) treatment was lower in LTS compared with STAT survivors (p < 0.05). Compared with STAT cells, LTS cells of STEC seem to have higher chlorine tolerance as planktonic cells and as attached cells depending on cell contact time on lettuce. In addition, a higher percentage of LTS cells, compared with STAT cells, survive in a noninjured state after chlorine (40 ppm) treatment of lettuce.

Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review

Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a "safe" drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.

Quantitative risk assessment of haemolytic uremic syndrome associated with beef consumption in Argentina

We developed a quantitative microbiological risk assessment (QMRA) of haemolytic uremic syndrome (HUS) associated with Shiga toxin-producing Escherichia coli (STEC)-contaminated beef (intact beef cuts, ground beef and commercial hamburgers) in children under 15 years of age from Argentina. The QMRA was used to characterize STEC prevalence and concentration levels in each product through the Argentinean beef supply chain, including cattle primary production, cattle transport, processing and storage in the abattoir, retail and home preparation, and consumption. Median HUS probability from beef cut, ground beef and commercial hamburger consumption was <10-15, 5.4x10-8 and 3.5x10-8, respectively. The expected average annual number of HUS cases was 0, 28 and 4, respectively. Risk of infection and HUS probability were sensitive to the type of abattoir, the application or not of Hazard Analysis and Critical Control Points (HACCP) for STEC (HACCP-STEC), stx prevalence in carcasses and trimmings, storage conditions from the abattoir to retailers and home, the joint consumption of salads and beef products, and cooking preference. The QMRA results showed that the probability of HUS was higher if beef cuts (1.7x) and ground beef (1.2x) were from carcasses provided by abattoirs not applying HACCP-STEC. Thus, the use of a single sanitary standard that included the application of HACCP-STEC in all Argentinean abattoirs would greatly reduce HUS incidence. The average number of annual HUS cases estimated by the QMRA (n = 32) would explain about 10.0% of cases in children under 15 years per year in Argentina. Since other routes of contamination can be involved, including those not related to food, further research on the beef production chain, other food chains, person-to-person transmission and outbreak studies should be conducted to reduce the impact of HUS on the child population of Argentina.

Escherichia coli O157 survival in liquid culture and artificial soil microcosms with variable pH, humic acid and clay content

AIMS

This research was performed to investigate the influence of clay and humic acid on Escherichia coli O157 survival in model soils. Additionally, the influence of pH and humic acid on E. coli O157 in liquid culture was investigated.

METHODS AND RESULTS

Artificial soil microcosms were prepared with sand, kaolinite, bentonite and humic acid. Artificial soil microcosms pH was adjusted (6·0-7·0) with aluminium sulphate before E. coli O157 inoculation. After 56 days of incubation at 30°C, significant differences in E. coli O157 log CFU per gram were observed between 0 and 1000 ppm (P < 0·0001) and 0 and 5000 ppm (P < 0·0001) humic acid in 1·5% clay soils, but not in 7·5 or 15% clay soils. Significant differences (P < 0·05) in E. coli O157 log CFU per ml were observed in liquid culture influenced by humic acid concentrations after 8 h at 37°C.

CONCLUSIONS

The developed model soils support E. coli O157 populations over 28 days, and higher clay soils may aid in E. coli O157 survival.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results provide insights into physicochemical properties of soil that may influence E. coli O157 in the environment and help explain E. coli O157 survival in various soils and geographical regions.

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.

Plant variety and soil type influence Escherichia coli O104:H4 strain C227/11ϕcu adherence to and internalization into the roots of lettuce plants

Human disease outbreaks caused by pathogenic Escherichia coli are increasingly associated with the consumption of contaminated fresh produce. Internalization of enteroaggregative/enterohemorrhagic E. coli (EAEC/EHEC) strains into plant tissues may present a serious threat to public health. In the current study, the ability of the fluorescing Shiga toxin-negative E. coli O104:H4 strain C227/11ϕcu/pKEC2 to adhere to and to internalize into the roots of Lactuca sativa and Valerianella locusta grown in diluvial sand (DS) and alluvial loam (AL) was investigated. In parallel, the soil microbiota was analyzed by partial 16S rRNA gene sequencing. The experiments were performed in a safety level 3 greenhouse to simulate agricultural practice. The adherence of C227/11ϕcu/pKEC2 to the roots of both plant varieties was increased by at least a factor three after incubation in DS compared to AL. Compared to V. locusta, internalization into the roots of L. sativa was increased 12-fold in DS and 108-fold in AL. This demonstrates that the plant variety had an impact on the internalization ability, whereas for a given plant variety the soil type also affected bacterial internalization. In addition, microbiota analysis detected the inoculated strain and showed large differences in the bacterial composition between the soil types.

Shiga Toxin-Producing Escherichia coli Contamination of Raw Beef and Beef-Based Ready-to-Eat Products at Retail Outlets in Pretoria, South Africa

ABSTRACT

A cross-sectional study was conducted to determine the prevalence of and factors associated with Shiga toxin-producing Escherichia coli (STEC) in raw beef and ready-to-eat (RTE) beef products sold in 31 retail outlets in Pretoria, South Africa, and nearby areas. A total of 463 beef and RTE samples were screened for four STEC virulence genes (stx1, stx2, eaeA, and hlyA) and seven O-serogroups (O113, O157, O26, O91, O145, O111, and O103) with a multiplex PCR assay. The total aerobic plate count (TAPC) per gram was also determined. A total of 38 STEC isolates were recovered and characterized by conventional PCR assay and serotyping. The overall prevalence of STEC in the beef and RTE samples tested was 16.4% (76 of 463 samples; 95% confidence interval, 13 to 20%). The prevalence of STEC differed significantly by product type (P < 0.0001), with the highest prevalence (35%) detected in boerewors (spicy sausage). The STEC prevalences in minced beef, brisket, RTE cold beef, and biltong were 18, 13, 9, and 5%, respectively. The most frequently detected stx gene was stx2 (13%), and STEC serogroups from recovered isolates were detected at the following prevalences: O2, 15%; O8, 12%; O13, 15%; O20, 8%; O24, 3%; O39, 3%; O41, 8%; O71, 3%; O76, 3%; O150, 12%; and O174, 3%. A high proportion (77%) of the samples had TAPCs that exceeded the South African microbiological standards for meat export (5.0 log CFU/g). The prevalence of O157 STEC (16%) and the diversity of non-O157 STEC serogroups found in five common beef-based products from retail outlets in South Africa suggest exposure of raw beef and beef products to multiple contamination sources during carcass processing and/or cutting and handling at retail outlets. These data provide direct estimates of the potential health risk to consumers from undercooked contaminated products and indicate the need to improve sanitary practices during slaughter and processing of beef and beef-based RTE products. A risk-based surveillance system for STEC may be needed.

HIGHLIGHTS

Evaluating the risks associated with Shiga-toxin-producing Escherichia coli (STEC) in private well waters in Canada

Shiga-toxin-producing Escherichia coli (STEC) represent a major concern for waterborne disease outbreaks associated with consumption of contaminated groundwater. Over 4 million people rely on private groundwater systems as their primary drinking water source in Canada; many of these systems do not meet current standards for water quality. This manuscript provides a scoping overview of studies examining STEC prevalence and occurrence in groundwater, and it includes a synopsis of the environmental variables affecting survival, transport, persistence, and overall occurrence of these important pathogenic microbes in private groundwater wells used for drinking purposes.

Investigating behavioral drivers of seasonal Shiga-Toxigenic Escherichia Coli (STEC) patterns in grazing cattle using an agent-based model

The causes of seasonal variability in pathogen transmission are not well understood, and have not been comprehensively investigated. In an example for enteric pathogens, incidence of Escherichia coli O157 (STEC) colonization in cattle is consistently higher during warmer months compared to cooler months in various cattle production systems. However, actual mechanisms for this seasonality remain elusive. In addition, the influence of host (cattle) behavior on this pattern has not been thoroughly considered. To that end, we constructed a spatially explicit agent-based model that accounted for the effect of temperature fluctuations on cattle behavior (direct contact among cattle and indirect between cattle and environment), as well as its effect on pathogen survival in the environment. We then simulated the model in a factorial approach to evaluate the hypothesis that temperature fluctuations can lead to seasonal STEC transmission dynamics by influencing cattle aggregation, grazing, and drinking behaviors. Simulation results showed that higher temperatures increased the frequency at which cattle aggregated under shade in pasture, resulting in increased direct contact and transmission of STEC between individual cattle, and hence higher incidence over model simulations in the warm season. In contrast, increased drinking behavior during warm season was not an important transmission pathway. Although sensitivity analyses suggested that the relative importance of direct vs. indirect (environmental) pathways depend to upon model parameterization, model simulations indicated that factors influencing cattle aggregation, such as temperature, were likely strong drivers of transmission dynamics of enteric pathogens.

Use of an improved high-throughput absolute abundance quantification method to characterize soil bacterial community and dynamics

High-throughput sequencing has dramatically expanded our understanding of bacterial communities based on the information of the species types and their relative abundances. Recently, researchers have also become aware of a deficiency in not considering the absolute abundance in this technique. Combining two or more different methods has typically been used to achieve absolute quantification of microbial communities. However, making a combination of different methods not only is time-consuming but also involves potential uncertainty due to variations in the experimental conditions. To simplify the experimental procedure and improve the high-throughput absolute abundance quantification (HAAQ) of a soil bacterial community, we propose an HAAQ method that uses an internal standard strain (ISS) HAAQ-GFP to simultaneously obtain both the relative and absolute abundances in the soil bacterial community. The results showed that a soil bacterial community and its dynamics can be better characterized by the HAAQ method when the optimal concentrations of ISS HAAQ-GFP (10⁵ to 10⁷cellsg^-1) were used, and a 16S rRNA gene copy number adjustment was applied. Based on the HAAQ method, we first found that soil bacterial absolute abundances at the genus level fitted well to the partial log-normal distribution function, and most genera concentrations were in the range of 10^3.5 to 10^6.5cellsg^-1 in the test soils. Our case studies also indicated that more comprehensive descriptions of soil bacterial communities and their dynamics can be achieved by both the relative and absolute abundances than by the relative abundance alone. The improved HAAQ method can be potentially applied to other microbial ecological studies and to stimulating the development of quantitative bacterial ecology studies.

Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH

Escherichia coli is deposited into soil with feces and exhibits subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process, and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics, and soil chemistry influence the prevalence of cultivable E. coli in surface soil. Soils from forests and pasture lands had equally high prevalences of E. coli Edge interactions were also observed among land cover types, with proximity to forests and pastures affecting the likelihood of E. coli isolation from surrounding soils. E. coli is thought to be more prevalent in sediments with high moisture, but this was observed only in grass- or crop-dominated lands in this study. Because differing E. coli phylogroups are thought to have differing ecology profiles, isolates were also typed using a novel single-nucleotide polymorphism (SNP) genotyping assay. Phylogroup B1 was the dominant group isolated from soil, as has been reported in all other surveys of environmental E. coli Although differences were small, isolates belonging to phylogroups B2 and D were associated with wooded areas, slightly more acidic soils, and soil sampling after rainfall events. In contrast, isolates from phylogroups B1 and E were associated with pasture lands.IMPORTANCE The consensus is that complex niches or life cycles should select for complex genomes in organisms. There is much unexplained biodiversity in E. coli, and its cycling through complex extrahost environments may be a cause. In order to understand the evolutionary processes that lead to adaptation for survival and growth in soil, an isolate collection that associates soil conditions and isolate genome sequences is required. An equally important question is whether traits selected in soil or other extrahost habitats can be transmitted to E. coli residing in hosts via gene flow. The new findings about the distribution of E. coli in soil at the landscape scale (i) enhance our capability to study how extrahost environments influence the evolution of E. coli and other bacteria, (ii) advance our knowledge of the environmental biology of this microbe, and (iii) further affirm the emerging scientific consensus that E. coli in waterways originates from nonpoint sources not associated with human activity or livestock farming.

Characterization of Escherichia coli strains isolated from raw vegetables

Vegetables are an important part of the human diet. Sometimes, contamination by pathogenic Escherichia coli can be underestimated; moreover there is a risk of antibiotic resistance spreading via the food chain. The purpose of this study was to examine the prevalence of Escherichia coli in fresh vegetables sold in retail market in the Czech Republic and to evaluate the risk to human health. Antibiotic resistance against 12 antibiotics, the presence of 12 virulence and 15 resistance genes were determined among 15 isolated strains. Most of tested strains belonged to B1 phylogenetic group, less frequently represented was B2 and D phylogroup. These results indicate that most strains are probably of human origin. All E. coli strains were resistant to at least one of twelve tested antibiotics. A multidrug resistance was observed in four strains. In this study, the presence of virulence factors Einv and papC and also genes encoding toxins (CNF1, CNF2) was detected. Nevertheless, none strain can be considered as STEC or EHEC. The widespread appearance of a growing trend associated with the prevalence of antibiotic resistance among enterobacterial isolates is undeniable and the possibility of transfer to humans cannot be ignored. Nevertheless, these results indicate that raw vegetables sold in the retail market can constitute a potential health risk for consumers.

Shiga Toxin-Producing Escherichia coli O157 Shedding Dynamics in an Australian Beef Herd

Shiga toxin-producing Escherichia coli (STEC) O157 is an important foodborne pathogen that can be transmitted to humans both directly and indirectly from the feces of beef cattle, its primary reservoir. Numerous studies have investigated the shedding dynamics of E. coli O157 by beef cattle; however, the spatiotemporal trends of shedding are still not well understood. Molecular tools can increase the resolution through the use of strain typing to explore transmission dynamics within and between herds and identify strain-specific characteristics that may influence pathogenicity and spread. Previously, the shedding dynamics and molecular diversity, through the use of multilocus variable number of tandem repeat analysis (MLVA) of STEC O157, were separately investigated in an Australian beef herd over a 9-month study period. Variation in shedding was observed over time, and 33 MLVA types were identified. The study presented here combines the two datasets previously published with an aim to clarify the relationship between epidemiological variables and strain types. Three major genetic clusters (GCs) were identified that were significantly associated with the location of the cattle in different paddocks. No significant association between GCs and individual cow was observed. Results from this molecular epidemiological study provide evidence for herd-level clonal replacement over time that may have been triggered by movement to a new paddock. In conclusion, this study has provided further insight into STEC O157 shedding dynamics and pathogen transmission. Knowledge gaps remain regarding the relationship of strain types and the shedding dynamics of STEC O157 by beef cattle that could be further clarified through the use of whole-genome sequencing.

A comparison of extended spectrum β-lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location

Extended spectrum β-lactamase producing Escherichia coli (ESBL-EC) are excreted via effluents and sewage into the environment where they can re-contaminate humans and animals. The aim of this observational study was to detect and quantify ESBL-EC in recreational water and wastewater, and perform a genetic and phenotypic comparative analysis of the environmental strains with geographically associated human urinary ESBL-EC. Recreational fresh- and saltwater samples from four different beaches and wastewater samples from a nearby sewage plant were filtered and cultured on differential and ESBL-selective media. After antimicrobial susceptibility testing and multi-locus variable number of tandem repeats assay (MLVA), selected ESBL-EC strains from recreational water were characterized by whole genome sequencing (WGS) and compared to wastewater and human urine isolates from people living in the same area. We detected ESBL-EC in recreational water samples on 8/20 occasions (40%), representing all sites. The ratio of ESBL-EC to total number of E. coli colony forming units varied from 0 to 3.8%. ESBL-EC were present in all wastewater samples in ratios of 0.56-0.75%. ST131 was most prevalent in urine and wastewater samples, while ST10 dominated in water samples. Eight STs and identical ESBL-EC MLVA-types were detected in all compartments. Clinical ESBL-EC isolates were more likely to be multidrug-resistant (p<0.001). This study confirms that ESBL-EC, including those that are capable of causing human infection, are present in recreational waters where there is a potential for human exposure and subsequent gut colonisation and infection in bathers. Multidrug-resistant E. coli strains are present in urban aquatic environments even in countries where antibiotic consumption in both humans and animals is highly restricted.

Characterization of Diarrheagenic Escherichia coli Isolated in Organic Waste Products (Cattle Fecal Matter, Manure and, Slurry) from Cattle's Markets in Ouagadougou, Burkina Faso

Cattle farming can promote diarrheal disease transmission through waste, effluents or cattle fecal matter. The study aims to characterize the diarrheagenic Escherichia coli (DEC) isolated from cattle feces, manure in the composting process and slurry, collected from four cattle markets in Ouagadougou. A total of 585 samples (340 cattle feces, 200 slurries and 45 manures in the composting process) were collected from the four cattle markets between May 2015 and May 2016. A multiplex Polymerase Chain Reaction (PCR), namely 16-plex PCR, was used to screen simultaneously the virulence genes specific for shiga toxin-producing E. coli (STEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC) and enteroaggregative E. coli (EAEC). DEC was detected in 10.76% of samples. ETEC was the most prevalent (9.91%). STEC and EAEC have been observed with the same rate (0.51%). ETEC were detected in 12.64% of cattle feces, in 6.66% of manure in the composting process and in 5% of slurry. STEC were detected in 0.58% of cattle feces and in 2.22% of manure in the composting process. EAEC was detected only in 1% of slurry and in 2.22% of manure in the composting process. ETEC strains were identified based on estIa gene and/or estIb gene and/or elt gene amplification. Of the 58 ETEC, 10.34% contained astA, 17.24% contained elt, 3.44% contained estIa and 79.31% contained estIb. The two positive EAEC strains contained only the aggR gene, and the third was positive only for the pic gene. The results show that effluent from cattle markets could contribute to the spreading of DEC in the environment in Burkina Faso.

Prevalence of Escherichia coli O157:H7 From House Flies (Diptera: Muscidae) and Dairy Samples in North Central Florida1

La detección de Escherichia coli O157:H7 en las lecherías es importante para mejorar la seguridad de los productos lácteos, y se ha llevado a cabo principalmente mediante el aislamiento de las bacterias a partir de las muestras de estiércol. Sin embargo, los componentes biliares presentes en el estiércol complica la identificación genética utilizando la técnica del PCR, y el aislamiento microbiológico se dificulta por la presencia de bacterias competidoras que comparten características microbiológicas similares. El aislamiento de E. coli O157:H7 a partir de la mosca doméstica evita las dificultades asociadas con el estiércol del ganado. El aislamiento de patógenos a partir de las moscas domésticas proporciona información adicional sobre el potencial impacto epidemiológico de la dispersión de la mosca doméstica en la distribución de patógenos, ya que las moscas domésticas se dispersan desde las lecherías donde la E. coli O157:H7 existe en forma endémica en el ganado. En este estudio, se encontró que las moscas domésticas son 2,6 veces más sensibles para la detección de E. coli O157:H7 en las lecherías. Las moscas son más fáciles de capturar y manejar que el estiércol, y deberían ser utilizadas en cualquier ensayo para detectar E. coli O157:H7 en las lecherías y otros establecimientos.

Prevalence, virulence potential, and pulsed-field gel electrophoresis profiling of Shiga toxin-producing Escherichia coli strains from cattle

BACKGROUND

As a primary source of Shiga-toxin-producing Escherichia coli (STEC) infection, cattle are often targeted to develop strategies for reducing STEC contamination. Monitoring the virulence potentials of STEC isolates from cattle is important for tracing contamination sources, managing outbreaks or sporadic cases, and reducing the risks for human infection. This study aimed to investigate the prevalence of STEC in cattle farm samples in South Korea and to assess their virulence potentials.

RESULTS

In total, 63 STEC were isolated from 496 cattle farm samples, and temperature and rainfall affected STEC prevalence (p < 0.001). The O157 serogroup was most prevalent, followed by O108, O8, O84, O15, and O119. In the stx variant test, high prevalence of stx2a and stx2c (known to be associated with high STEC virulence) were observed, and stx2g, a bovine STEC variant, was detected in STEC O15 and O109. Additionally, stx1c was detected in eae-positive STEC, suggesting genetic dynamics among the virulence genes in the STEC isolates. STEC non-O157 strains were resistant to tetracycline (17.9%), ampicillin (14.3%), and cefotaxime (3.6%), while STEC O157 was susceptible to all tested antimicrobials, except cefotaxime. The antimicrobial resistance genes, bla_TEM (17.5%), tetB (6.3%), and tetC (4.8%), were only detected in STEC non-O157, whereas tetE (54.0%) was detected in STEC O157. AmpC was detected in all STEC isolates. Clustering was performed based on the virulence gene profiles, which grouped STEC O84, O108, O111, and O157 together as potentially pathogenic STEC strains. Finally, PFGE suggested the presence of a prototype STEC that continues to evolve by genetic mutation and causes within- and between-farm transmission within the Gyeonggi province.

CONCLUSIONS

Considerable numbers of STEC non-O157 were isolated from cattle farms, and the virulence and antimicrobial resistance features were different between the STEC O157 and non-O157 strains. STEC from cattle with virulence or antimicrobial resistance genes might represent a threat to public health and therefore, continual surveillance of both STEC O157 and non-O157 would be beneficial for controlling and preventing STEC-related illness.

The fate of verocytotoxigenic Escherichia coli C600φ3538(Δvtx2 ::cat) and its vtx2 prophage during grass silage preparation

AIMS

Silage is grass, preserved by fermentation and used as winter feed for cattle. The impact of a range of current grass silage preparation practices on the survival of Escherichia coli C600φ3538(Δvtx₂ ::cat) and on the induction, release and infectivity of free phage were investigated.

METHODS AND RESULTS

Wilted and fresh grass samples, from plots with and without slurry application, were ensiled with or without formic acid. Each treatment combination was inoculated with approximately 6 log₁₀ CFU per g E. coli C600φ3538(Δvtx₂ ::cat) (donor strain) and E. coli C600::kanamycin^R (recipient strain) in test-tube model silos and incubated in the dark at 15°C. The physico-chemical (pH, ammonia, ethanol, lactic acid and volatile fatty acids) and microbiological (total viable counts, TVC, total Enterobacteriaceae counts, TEC, E. coli counts, ECC and lactic acid bacteria, LAB) properties of each fermentation were monitored throughout the experiment as were the concentrations of E. coli C600φ3538(Δvtx₂ ::cat), E. coli C600::kanamycin^R , free phage and transductants, using culture and PCR-based methods. Over the course of the experiment the pH of the grass samples typically decreased by 2 pH units. TVC, TEC and ECC decreased by up to 2·3, 6·4 and 6·2 log₁₀ CFU per g, respectively, while the LAB counts remained relatively stable at 5·2-7·1 log₁₀ CFU per g. Both donor and recipient strains decreased by approximately 5 log₁₀ CFU per g. Free phages were detected in all treatments and transductants were detected and confirmed by PCR in the silo containing wilted grass, pretreated with slurry and ensiled without formic acid.

CONCLUSIONS

Verocytotoxigenic E. coli may survive the ensiling process and the conditions encountered are sufficient to induce vtx₂ bacteriophage leading to low levels of phage-mediated vtx₂ gene transfer.

SIGNIFICANCE AND IMPACT OF THE STUDY

These studies suggest that the ensiling of grass may create an environment which facilitates the emergence of new verocytotoxigenic E. coli.

Potential for transfer of Escherichia coli O157:H7, Listeria monocytogenes and Salmonella Senftenberg from contaminated food waste derived compost and anaerobic digestate liquid to lettuce plants

The diversion of food wastes from landfill to sustainable disposal methods, such as composting and anaerobic digestion, has led to an increase in the soil amendment products that are now commercially available and which are derived from both of these processes. The use of such products as soil amendments during the production of ready-to-eat (RTE) crops is increasing worldwide. The aim of this study was to investigate the potential of three well-recognised bacterial pathogens of importance to public health, namely Escherichia coli O157:H7, Salmonella Senftenberg and Listeria monocytogenes, to become internalised in lettuce plants from peat growing media amended with contaminated food waste derived compost and anaerobic digestion liquid. The results demonstrated both S. Senftenberg and E. coli O157:H7 are capable of internalisation at lower inoculation levels, compared to previous studies. The internalisation was visualised through confocal microscopy. Internalisation of L. monocytogenes did not occur, however significant levels of L. monocytogenes contamination occurred on the non-sterilised plant surface. Assessing the internalisation potential for each of these pathogens, through the compost and anaerobic digestate matrices, allows for better risk assessment of the use of these products in a horticultural setting.

Prevalence of Escherichia Coli O157:H7 and Enterobacteriaceae on Hands of Workers in Halal Cattle Abattoirs in Peninsular Malaysia

BACKGROUND

Several occupational diseases of multiple origins are encountered among abattoir workers. Presence of indicator microorganisms (coliforms) on hands of workers can be used a gauge for hygienic practices.

METHODS

A cross-sectional study was performed to assess the prevalence of E.coli and enterobacteriaceae among Halal abattoir workers in some government halal abattoirs of Malaysia. A total of one hundred and sixty-five hand swab samples were collected from workers of Halal abattoirs in Malaysia. The samples were subjected to microbiological analysis for characterisation and serotyping.

RESULTS

The results have shown that no Escherichia coli O157:H7 was isolated on the hands of abattoir workers before and after work. However, a total prevalence of 9.7% was recorded for all samples during work. For non-O157:H7, total prevalence of 33.3% during work and 13% after work were obtained. High prevalence was recorded in sample taken during work from Tampin, Jasin and Kemaman (100% each) while low prevalence where observed in Shah Alam, Banting and Ipoh (20% each).

CONCLUSIONS

Based on the findings the hygienic practices of hand washing among the workers in few locations was found to be low especially after work.

Strategies for recovering of planktonic and sessile cells of Escherichia coli O157:H7 from freshwater environment

The experiments were performed with Escherichia coli O157:H7 EDL 933 in freshwater microcosms at 12 °C. At 35, 45, and 70 days, samples were taken and filtered through 0.45 μm membrane filters. The following alternatives were tested to evaluate the recovery percentage of injured cells: (1) selective media CHROMagar(™)O157 and chromID(™)O157:H7 agar, at 37 °C for 24 h; (2) tryptic soy agar supplemented with yeast extract (TSAE), incubated at 25 °C for 2 or 4 h, then transferred to CHROMagar(™)O157 or chromID(™)O157:H7 agar at 37 °C (TSAE2h-CHROM, TSAE4h-CHROM and TSAE2h-ID, TSAE4h-ID); (3) thin agar layer (TAL) method, TSAE was overlaid on CHROMagar(™)O157 or chromID(™)O157:H7 agar (TALCHROM and TALID, respectively) and incubated at 37 °C for 24 h; and (4) TALCHROM at 25 °C for 4 h, then continued up to complete 24 h at 37 °C (TALCHROM4h). Furthermore, the recovery of E. coli O157:H7 cells adhering to glass coverslips were evaluated to mimic biofilm conditions. The recovery percentages obtained from each alternative were calculated relative to TSAE counts. After 70 days, TSAE4h-CHROM and TALCHROM4h showed the highest recovery percentage (>90 %) from water microcosms. Despite the improved recovery of cell adhering to glass surfaces, the percentages obtained with TSAE4h-CHROM were low. Further studies for the recovery of biofilm-forming E. coli O157:H7 are required. Pre-incubation on TSAE at 25 °C for 4 h, combined with CHROMagar(™)O157, or by thin agar layer method (TALCHROM) enhanced significantly the recovery of viable cells of E. coli O157:H7 after prolonged stay in water microcosms.

Long-term survival of the Shiga toxin-producing Escherichia coli O104:H4 outbreak strain on fenugreek seeds

A major outbreak of Shiga toxin-producing Escherichia coli (STEC) O104:H4 occurred in Germany in 2011. The epidemiological investigation revealed that a contaminated batch of fenugreek seeds (Trigonella foenum-graecum) was the most probable source of the pathogen. It was suggested that the most probable point of contamination was prior to leaving the importer, meaning that the seed contamination with STEC O104:H4 should have happened more than one year before the seeds were used for sprout production. Here, we investigated the capacity of STEC O104:H4 and closely related pathogenic as well as non-pathogenic Escherichia coli strains for long-term survival on dry fenugreek seeds. We did not observe a superior survival capacity of STEC O104:H4 on dry seeds. For none of the strains tested cultivatable cells were found without enrichment on contaminated seeds after more than 24 weeks of storage. Our findings suggest that contamination previous to the distribution from the importer may be less likely than previously assumed. We show that seeds contaminated with E. coli in extremely high numbers can be completely sterilized by a short treatment with bleach. This simple and cheap procedure does not affect the germination capacity of the seeds and could significantly improve safety in sprout production.

Rapid Detection of Escherichia coli O157 and Shiga Toxins by Lateral Flow Immunoassays

Shiga toxin-producing Escherichia coli O157:H7 (STEC) cause food-borne illness that may be fatal. STEC strains enumerate two types of potent Shiga toxins (Stx1 and Stx2) that are responsible for causing diseases. It is important to detect the E. coli O157 and Shiga toxins in food to prevent outbreak of diseases. We describe the development of two multi-analyte antibody-based lateral flow immunoassays (LFIA); one for the detection of Stx1 and Stx2 and one for the detection of E. coli O157 that may be used simultaneously to detect pathogenic E. coli O157:H7. The LFIA strips were developed by conjugating nano colloidal gold particles with monoclonal antibodies against Stx1 and Stx2 and anti-lipid A antibodies to capture Shiga toxins and O157 antigen, respectively. Our results indicate that the LFIA for Stx is highly specific and detected Stx1 and Stx2 within three hours of induction of STEC with ciprofloxacin at 37 °C. The limit of detection for E. coli O157 LFIA was found to be 10⁵ CFU/mL in ground beef spiked with the pathogen. The LFIAs are rapid, accurate and easy to use and do not require sophisticated equipment or trained personnel. Following the assay, colored bands on the membrane develop for end-point detection. The LFIAs may be used for screening STEC in food and the environment.

Assessing the impacts of temperature and storage on Escherichia coli, Salmonella, and L. monocytogenes decay in dairy manure

Elevated levels of animal waste-borne pathogen in ambient water is a serious human health issue. Mitigating influx of pathogens from animal waste such as dairy manure to soil and water requires improving our existing knowledge of pathogen reductions in dairy manure treatment methods. This study was conducted to enhance the  understanding of human pathogen decay in liquid dairy manure in anaerobic (AN) and limited aerobic (LA) storage conditions. The decay of three pathogens (Escherichia coli, Salmonella spp., and Listeria monocytogenes) was assessed in bench-scale batch reactors fed with liquid slurry. A series of temperatures (30, 35, 42, and 50 °C) conditions were tested to determine the impacts of temperature on Escherichia coli, Salmonella, and L. monocytogenes decay in AN and LA conditions. Results showed prolonged survival of E. coli compared to Salmonella and L. monocytogenes in both LA and AN environments. Variations in survival among pathogens with temperature and environmental conditions (i.e., LA and AN) indicated the necessity of developing improved dairy manure waste treatment methods for controlling animal waste-borne pathogens. The results of this study will help in improving the current understanding of human pathogen decay in dairy manure for making informed decisions of animal manure treatment by stakeholders.

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.

Detection of Shiga Toxin-Producing Escherichia coli from Nonhuman Sources and Strain Typing

Shiga toxin-producing Escherichia coli (STEC) strains are commonly found in the intestine of ruminant species of wild and domestic animals. Excretion of STEC with animal feces results in a broad contamination of food and the environment. Humans get infected with STEC through ingestion of contaminated food, by contact with the environment, and from STEC-excreting animals and humans. STEC strains can behave as human pathogens, and some of them, called enterohemorrhagic E. coli (EHEC), may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Because of the diversity of STEC types, detection strategies for STEC and EHEC are based on the identification of Shiga toxins or the underlying genes. Cultural enrichment of STEC from test samples is needed for identification, and different protocols were developed for this purpose. Multiplex real-time PCR protocols (ISO/CEN TS13136 and USDA/FSIS MLG5B.01) have been developed to specifically identify EHEC by targeting the LEE (locus of enterocyte effacement)-encoded eae gene and genes for EHEC-associated O groups. The employment of more genetic markers (nle and CRISPR) is a future challenge for better identification of EHEC from any kinds of samples. The isolation of STEC or EHEC from a sample is required for confirmation, and different cultivation protocols and media for this purpose have been developed. Most STEC strains present in food, animals, and the environment are eae negative, but some of these strains can cause HC and HUS in humans as well. Phenotypic assays and molecular tools for typing EHEC and STEC strains are used to detect and characterize human pathogenic strains among members of the STEC group.

A New Immunoassay for Detecting All Subtypes of Shiga Toxins Produced by Shiga Toxin-Producing E. coli in Ground Beef

BACKGROUND

Shiga toxin (Stx) is a common virulence factor of all Shiga toxin producing E. coli (STEC) that cause a wide spectrum of disease, including hemorrhagic colitis and hemolytic uremic syndrome (HUS). Although several commercial kits are available for detection of Stx produced by STEC, none of them are capable of recognizing all subtypes of Stxs, which include three subtypes of Stx1 and seven subtypes of Stx2.

METHODS AND FINDINGS

New monoclonal and polyclonal antibodies against Stx1 and Stx2 were developed. A universal sandwich ELISA capable of detecting all known subtypes of Stx1 and Stx2 was established using a pool of newly developed antibodies. To precisely monitor the sensitivity of the assay for each subtype of Stxs, recombinant toxoids were created and used as standards in ELISAs. Because of the high affinity of the antibodies incorporated, the ELISA assay is highly sensitive with a limit of detection for the different subtypes of Stx1a and Stx2a between 10 and 50 pg/mL in phosphate buffered saline (PBS). The assay was also able to identify STEC based on the production of Stxs using the supernatants of culture fluids or even single colonies on agar plates without lengthy enrichment in liquid medium. When applied to ground beef samples, this newly developed ELISA was capable of distinguishing beef samples spiked with a single bacterial cell.

CONCLUSIONS

A highly sensitive and universal assay for all subtypes of Stx1 and Stx2 was developed. It has significantly improved upon the current technologies by avoiding false negative results due to the narrow detection range of the assay. The assay developed in this study can be useful for prompt detection of new and emerging serotypes and screening ground beef samples for contamination of STEC at an early stage in the food supply chain, thus avoiding the need for possible recall.

An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits

Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antimicrobial resistance profiles of environmental O145 strains recovered from a major produce production region in California. Multilocus sequence typing analyses revealed that sequence type 78 (ST-78), a common ST in clinical strains, was the predominant genotype among the environmental strains. Similarly, all California environmental strains belonged to H28, a common H serotype in clinical strains. Although most environmental strains carried an intact fliC gene, only one strain retained swimming motility. Diverse stx subtypes were identified, including stx1a, stx2a, stx2c, and stx2e. Although no correlation was detected between the stx genotype and Stx1 production, high Stx2 production was detected mainly in strains carrying stx2a only and was correlated positively with the cytotoxicity of Shiga toxin. All environmental strains were capable of producing enterohemolysin, whereas only 10 strains were positive for anaerobic hemolytic activity. Multidrug resistance appeared to be common, as nearly half of the tested O145 strains displayed resistance to at least two different classes of antibiotics. The core virulence determinants of enterohemorrhagic E. coli were conserved in the environmental STEC O145 strains; however, there was large variation in the expression of virulence traits among the strains that were highly related genotypically, implying a trend of clonal divergence. Several cattle isolates exhibited key virulence traits comparable to those of the STEC O145 outbreak strains, emphasizing the emergence of hypervirulent strains in agricultural environments.

Fate of Escherichia coli O157: H7 in agricultural soils amended with different organic fertilizers

Five organic fertilizers (vermicompost, pig manure, chicken manure, peat and oil residue) were applied to agricultural soils to study their effects on the survival of Escherichia coli O157:H7 (E. coli O157:H7). Results showed that E. coli O157:H7 survival changed greatly after organic fertilizers application, with shorter td values (survival time needed to reach the detection limit of 100 CFU g(-1)) (12.57±6.57 days) in soils amended with chicken manure and the longest (25.65±7.12 days) in soils amended with pig manure. Soil pH, EC and free Fe/Al (hydro) oxides were significant explanatory factors for E. coli O157:H7 survival in the original soils. Soil constituents (minerals and organic matter) and changes in their surface charges with pH increased the effect of soil pH on E. coli O157:H7 survival. However, electrical conductivity played a more important role in regulating E. coli O157:H7 survival in fertilizer-amended soils. This study highlighted the importance of choosing appropriate organic fertilizers in the preharvest environment to reduce food-borne bacterial contamination.

Longitudinal observational study over 38 months of verotoxigenic Escherichia coli O157:H7 status in 126 cattle herds

Verotoxigenic Escherichia coli O157:H7 (VTEC O157:H7) is an important zoonotic pathogen capable of causing infections in humans, sometimes with severe symptoms such as hemorrhagic colitis and hemolytic uremic syndrome (HUS). It has been reported that a subgroup of VTEC O157:H7, referred to as clade 8, is overrepresented among HUS cases. Cattle are considered to be the main reservoir of VTEC O157:H7 and infected animals shed the bacteria in feces without showing clinical signs of disease. The aims of the present study were: (1) to better understand how the presence of VTEC O157:H7 in the farm environment changes over an extended period of time, (2) to investigate potential risk factors for the presence of the bacteria, and (3) describe the distribution of MLVA types and specifically the occurrence of the hypervirulent strains (clade 8 strains) of VTEC O157:H7. The farm environment of 126 cattle herds in Sweden were sampled from October 2009 to December 2012 (38 months) using pooled pat and overshoe sampling. Each herd was sampled, on average, on 17 occasions (range=1-20; median=19), at intervals of 64 days (range=7-205; median=58). Verotoxigenic E. coli O157:H7 were detected on one or more occasions in 53% of the herds (n=67). In these herds, the percentage of positive sampling occasions ranged from 6% to 72% (mean=19%; median=17%). Multi-locus variable number tandem repeat analysis (MLVA) typing was performed on isolates from infected herds to identify hypervirulent strains (clade 8). Clustering of MLVA profiles yielded 35 clusters and hypervirulent strains were found in 18 herds; the same cluster was often identified on consecutive samplings and in nearby farms. Using generalized estimating equations, an association was found between the probability of detecting VTEC O157:H7 and status at the preceding sampling, season, herd size, infected neighboring farms and recent introduction of animals. This study showed that the bacteria VTEC O157:H7 were spontaneously cleared from the farm environment in most infected herds over time, and key factors were identified to prevent the spread of VTEC O157:H7 between cattle herds.

Dynamics of Escherichia coli Virulence Factors in Dairy Herds and Farm Environments in a Longitudinal Study in the United States

Pathogenic Escherichia coli or its associated virulence factors have been frequently detected in dairy cow manure, milk, and dairy farm environments. However, it is unclear what the long-term dynamics of E. coli virulence factors are and which farm compartments act as reservoirs. This study assessed the occurrence and dynamics of four E. coli virulence factors (eae, stx1, stx2, and the gamma allele of the tir gene [γ-tir]) on three U.S. dairy farms. Fecal, manure, water, feed, milk, and milk filter samples were collected from 2004 to 2012. Virulence factors were measured by postenrichment quantitative PCR (qPCR). All factors were detected in most compartments on all farms. Fecal and manure samples showed the highest prevalence, up to 53% for stx and 21% for γ-tir in fecal samples and up to 84% for stx and 44% for γ-tir in manure. Prevalence was low in milk (up to 1.9% for stx and 0.7% for γ-tir). However, 35% of milk filters were positive for stx and 20% were positive for γ-tir. All factors were detected in feed and water. Factor prevalence and levels, expressed as qPCR cycle threshold categories, fluctuated significantly over time, with no clear seasonal signal independent from year-to-year variability. Levels were correlated between fecal and manure samples, and in some cases autocorrelated, but not between manure and milk filters. Shiga toxins were nearly ubiquitous, and 10 to 18% of the lactating cows were potential shedders of E. coli O157 at least once during their time in the herds. E. coli virulence factors appear to persist in many areas of the farms and therefore contribute to transmission dynamics.

Persistence of Pathogenic and Non-Pathogenic Escherichia coli Strains in Various Tropical Agricultural Soils of India

The persistence of Shiga-like toxin producing E. coli (STEC) strains in the agricultural soil creates serious threat to human health through fresh vegetables growing on them. However, the survival of STEC strains in Indian tropical soils is not yet understood thoroughly. Additionally how the survival of STEC strain in soil diverges with non-pathogenic and genetically modified E. coli strains is also not yet assessed. Hence in the present study, the survival pattern of STEC strain (O157-TNAU) was compared with non-pathogenic (MTCC433) and genetically modified (DH5α) strains on different tropical agricultural soils and on a vegetable growing medium, cocopeat under controlled condition. The survival pattern clearly discriminated DH5α from MTCC433 and O157-TNAU, which had shorter life (40 days) than those compared (60 days). Similarly, among the soils assessed, the red laterite and tropical latosol supported longer survival of O157-TNAU and MTCC433 as compared to wetland and black cotton soils. In cocopeat, O157 recorded significantly longer survival than other two strains. The survival data were successfully analyzed using Double-Weibull model and the modeling parameters were correlated with soil physico-chemical and biological properties using principal component analysis (PCA). The PCA of all the three strains revealed that pH, microbial biomass carbon, dehydrogenase activity and available N and P contents of the soil decided the survival of E. coli strains in those soils and cocopeat. The present research work suggests that the survival of O157 differs in tropical Indian soils due to varied physico-chemical and biological properties and the survival is much shorter than those reported in temperate soils. As the survival pattern of non-pathogenic strain, MTCC433 is similar to O157-TNAU in tropical soils, the former can be used as safe model organism for open field studies.