Surveillance of Dairy Production Holdings Supplying Raw Milk to the Farmhouse Cheese Sector for Escherichia coli O157, O26 and O111

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States.

Methods

In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed.

Results

We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated.

Discussion

This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.

DIARRHEAGENIC Escherichia coli IN RAW MILK, WATER, AND CATTLE FECES IN NON-TECHNIFIED DAIRY FARMS

Abstract This study focused on detecting diarrheagenic Escherichia coli, enteropathogenic E. coli (EPEC), Shiga-toxin-producing E. coli (STEC), enterohemorrhagic E. coli (EHEC or STEC:EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC) in raw milk, water, and cattle feces sampled from non-technified dairy farms located in the northeastern São Paulo State, Brazil. Thirty-six water samples were collected at different points, namely, water wells (8 samples), water intended for human consumption (8 samples), water from milking parlor (8 samples), and water intended for animal consumption (7 samples), headwaters (1 sample), rivers (3 samples), and reservoirs (1 sample). Three raw milk samples were taken directly from bulk tanks in each farm, totalizing 24 samples. Feces samples were collected using rectal swabs from 160 bovines (20 animals per farm). E. coli was detected in 128 feces samples (80%), 16 raw milk samples (66.67%), and 20 water samples (55.56%). STEC (26 samples, 16.25%), EPEC (10 samples, 6.25%), STEC: EPEC (5 samples, 3.13%), and STEC: ETEC (1 sample, 0.63%) were the most prevalent strains detected in samples from cattle feces. EPEC, STEC, and STEC: EPEC strains were detected in 4.17% (1 sample), 16.67% (4 samples), and 4.17% (1 sample) of raw milk samples, respectively. STEC strains were detected in water used in the milking parlor, while no EAEC strain was detected. As a conclusion, cattle feces are important contamination sources of pathogenic E. coli in non-technified dairy farms and, consequently, cross-contamination among feces, water, and/or raw milk can occur. The use of quality water and hygienic practices during milking are recommended to avoid contamination since pathogens can be transmitted to humans via raw milk or raw milk cheese ingestion.

An assessment of Irish farmers’ knowledge of the risk of spread of infection from animals to humans and their transmission prevention practices

The aim of this study was to ascertain farmers’ knowledge of the risk of spread of infection from animals to humans, and their transmission prevention practices. This was a survey of farmers who submitted material to Ireland's Regional Veterinary Laboratories in 2015. There was an 84% response rate (1044 farmers). Ninety per cent of farmers were not aware that infection can be acquired from apparently healthy animals. Over half were not aware that disease could be contracted from sick poultry or pets. Conversely, the knowledge of the risk to pregnant women of infection from birthing animals was high (88%). Four-fifths of farmers sourced drinking water from a private well, and of these, 62% tested their water less frequently than once a year. Of dairy farmers, 39% drank unpasteurised milk once a week or more frequently. Veterinarians were the most commonly cited information source for diseases on farms. The survey findings indicate that the level of farmers’ knowledge and awareness of the spread of infection from animals to humans is a concern. Further education of the farming community is needed to increase awareness of both the potential biohazards present on farms and the practical measures that can be taken to mitigate the risk of zoonoses.

Survival capabilities of Escherichia coli O26 isolated from cattle and clinical sources in Australia to disinfectants, acids and antimicrobials

Background

After E. coli O157, E. coli O26 is the second most prevalent enterohaemorrhagic E. coli (EHEC) serotype identified in cases of foodborne illness in Australia and throughout the world. E. coli O26 associated foodborne outbreaks have drawn attention to the survival capabilities of this organism in a range of environments. The aim of the present study was to assess the ability of E. coli O26 to survive the effects of disinfectants, acids and antimicrobials and investigate the possible influence of virulence genes in survival and persistence of E. coli O26 from human and cattle sources from Australia.

Results

Initial characterization indicated that E. coli O26 are a genetically diverse group that were shown to belong to a number of pathotypes. Overall, 86.4% of isolates were susceptible to all antimicrobials tested with no significant differences in resistance observed between pathotypes. A representative subset of isolates (n = 40) were selected to determine their ability to survive disinfectants at proposed industry working concentrations and acid stress. Profoam, Kwiksan 22, and Topactive DES. were able to inhibit the growth of 100% of isolates. The remaining three disinfectants (Dairy Chlor 12.5%, Envirosan and Maxifoam) were not effective against the subset of 40 E. coli O26. Finally, elevated MICs (1,024 to 4,096 μg/ml) of acetic, propionic, lactic, and citric acids were determined for the majority of the isolates (85%).

Conclusions

Australian E. coli O26 isolates belong to a range of pathotypes that harbor differing virulence markers. Despite this, their response to antimicrobials, disinfectants and acids is similar confirming that stress response appears unrelated to the presence of EHEC virulence markers. Notwithstanding, the tolerance to disinfectants and the elevated acid MICs for EHEC and the other E. coli O26 pathotypes examined in this study may contribute to bacterial colonization on food contact surfaces and subsequent foodborne illness caused by this pathogen.

Longitudinal Study of Two Irish Dairy Herds: Low Numbers of Shiga Toxin-Producing Escherichia coli O157 and O26 Super-Shedders Identified

A 12-month longitudinal study was undertaken on two dairy herds to ascertain the Shiga-toxin producing Escherichia coli (STEC) O157 and O26 shedding status of the animals and its impact (if any) on raw milk. Cattle are a recognized reservoir for these organisms with associated public health and environmental implications. Animals shedding E. coli O157 at >10,000 CFU/g of feces have been deemed super-shedders. There is a gap in the knowledge regarding super-shedding of other STEC serogroups. A cohort of 40 lactating cows from herds previously identified as positive for STEC in a national surveillance project were sampled every second month between August, 2013 and July, 2014. Metadata on any potential super-shedders was documented including, e.g., age of the animal, number of lactations and days in lactation, nutritional condition, somatic cell count and content of protein in milk to assess if any were associated with risk factors for super-shedding. Recto-anal mucosal swabs (RAMS), raw milk, milk filters, and water samples were procured for each herd. The swabs were examined for E. coli O157 and O26 using a quantitative real time PCR method. Counts (CFU swab-1) were obtained from a standard calibration curve that related real-time PCR cycle threshold (Ct) values against the initial concentration of O157 or O26 in the samples. Results from Farm A: 305 animals were analyzed; 15 E. coli O157 (5%) were recovered, 13 were denoted STEC encoding either stx1 and/or stx2 virulence genes and 5 (2%) STEC O26 were recovered. One super-shedder was identified shedding STEC O26 (stx1&2). Farm B: 224 animals were analyzed; eight E. coli O157 (3.5%) were recovered (seven were STEC) and 9 (4%) STEC O26 were recovered. Three super-shedders were identified, one was shedding STEC O157 (stx2) and two STEC O26 (stx2). Three encoded the adhering and effacement gene (eae) and one isolate additionally encoded the haemolysin gene (hlyA). All four super-shedders were only super-shedding once during the 1-year sampling period. The results of this study show, low numbers of super-shedders in the herds examined, with high numbers of low and medium shedding. Although four super-shedding animals were identified, no STEC O157 or O26 were recovered from any of the raw milk, milk filter, or water samples. The authors conclude that this study highlights the need for further surveillance to assess the potential for environmental contamination and food chain security.

CapE (capture, amplify, extract): A rapid method for detection of low level contamination of water with Verocytotoxigenic Escherichia coli (VTEC)

Verocytotoxigenic Escherichia coli (VTEC) is associated with a wide spectrum of disease from mild self-limiting diarrhoea to haemolytic uremic syndrome. Contaminated drinking water is accepted as an important route of transmission in Ireland as elsewhere however established methods for detection of VTEC in drinking water have limitations. We describe a sensitive and rapid method for detection of VTEC from large volumes (20 to 30L) of drinking water based on filtration, enrichment culture of filters and real-time PCR detection of VTEC virulence and O antigen determinants from enrichments. The method has potential applications for other waterborne pathogens.

Status of Laboratory Biosafety and Biosecurity in Veterinary Research Facilities in Nigeria

Background

This study determined current status of laboratory biosafety in Nigerian veterinary research facilities.

Methods

A questionnaire was developed to obtain information from researchers across Nigeria from July 2014 to July 2015. Information regarding demographics, knowledge of laboratory biosafety, availability and proper use of personal protective equipment (PPE), any priority pathogens researched, attitude on and use of standard laboratory practices, and biosafety awareness was obtained using a numeric scoring system. Data were analyzed with descriptive statistics, and univariate and multivariate logistic regression.

Results

A total of 74 participants from 19 facilities completed the questionnaire. General knowledge scores ranged from 3 to 28 (out of 28 possible points), with 94.6% of respondents receiving low scores (scores < mean + 1 standard deviation). Very few (17.6%) reported availability or use PPE. Many participants (63.5%) reported no access to biosafety level (BSL)-1–3 facilities. None reported availability of a BSL-4 facility. Knowledge scores pertaining to biosafety management practices ranged from 0 to 14 (out of 14 possible points) with 47.3% of respondents receiving good scores (scores > mean + 1 standard deviation). Only 16.2% of respondents (from four facilities) reported having biosafety officers. Rabies virus was the most researched pathogen (31.1% of respondents). The majority (71.6%) were unaware of laws guiding biosafety. Researchers [odds ratio (OR) = 18.0; 95% confidence interval (CI): 1.63, 198.5; p = 0.023], especially in BSL-2 (OR = 258.5; 95% CI: 12.71, 5256; p < 0.001) facility of research institute (OR = 25.0; 95% CI: 5.18, 120.6; p < 0.001), are more likely to have adequate access to and properly utilize biosafety devices and PPE.

Conclusions

Current knowledge of laboratory biosafety is limited except among a few researchers.

Veterinary Public Health Approach to Managing Pathogenic Verocytotoxigenic Escherichia coli in the Agri-Food Chain

Verocytoxigenic Escherichia coli (VTEC) comprises many diverse serogroups, but seven serogroups, O157, O26, O103, O145, O111, O21, and O45, have been most commonly linked to severe human infections, though illness has also been reported from a range of other VTEC serogroups. This poses challenges in assessing the risk to humans from the diverse range of VTEC strains that may be recovered from animals, the environment, or food. For routine assessment of risk posed by VTEC recovered from the agri-food chain, the concept of seropathotype can be used to rank the human risk potential from a particular VTEC serogroup on the basis of both serotype (top seven serogroups) and the presence of particular virulence genes (vt in combination with eae, or aaiC plus aggR). But for other VTEC serogroups or virulence gene combinations, it is not currently possible to fully assess the risk posed. VTEC is shed in animal feces and can persist in the farm environment for extended periods ranging from several weeks to many months, posing an ongoing reservoir of contamination for grazing animals, water courses, and fresh produce and for people using farmland for recreational purposes. Appropriate handling and treatment of stored animal waste (slurries and manures) will reduce risk from VTEC in the farm environment. Foods of animal origin such as milk and dairy products and meat may be contaminated with VTEC during production and processing, and the pathogen may survive or grow during processing operations, highlighting the need for well-designed and validated Hazard Analysis Critical Control Point management systems. This article focuses on a veterinary public health approach to managing VTEC, highlighting the various routes in the agri-food chain for transmission of human pathogenic VTEC and general approaches to managing the risk.

PCR and ELISA (VIDAS ECO O157(®)) Escherichia coli O157:H7 identification in Minas Frescal cheese commercialized in Goiânia, GO

Escherichia coli O157:H7 has been incriminated in food poisoning outbreaks and sporadic cases of hemorrhagic colitis and hemolytic uremic syndrome in many countries. Considering the high susceptibility of Minas Frescal cheese to contamination by E. coli O157:H7, the aim of this study was to determine the occurrence of this pathogen through PCR (Polymerase Chain Reaction) and ELISA (VIDAS ECO O157^®, bioMérieux, Lyon, France) test. Thirty cheese samples manufactured by artisan farmhouse producers were collected from open-air markets in Goiânia and thirty from industries under Federal Inspection located in Goiás State which trade their products in supermarkets in Goiânia. E. coli O157:H7 was detected in 6.67% samples collected in open air markets using ELISA, and 23,33% with PCR. The pathogen was not detected in samples from industries under Federal Inspection.

Foodborne pathogens in in-line milk filters and associated on-farm risk factors in dairy farms authorized to produce and sell raw milk in northern Italy

All dairy farms authorized to produce and sell raw milk in a province of Northern Italy were investigated to determine the presence of Campylobacter spp., verocytotoxin-producing Escherichia coli (VTEC), Listeria monocytogenes, and Salmonella spp. in in-line milk filters and to assess their association with suspected risk factors on farms. A logistic regression model was used to analyze data collected describing the characteristics and management practices of 27 farms and the microbiological status of 378 in-line milk filters by both culture-based and molecular methods. Thermotolerant Campylobacter, VTEC, and L. monocytogenes were detected in 24 (6.45%), 32 (8.4%), and 2 (0.5%) samples, respectively. No Salmonella spp. were detected. For risk analysis, data of L. monocytogenes and Salmonella spp. were not included in the model because of the low prevalence or absence of these organisms. The univariate analysis disclosed that the presence of VTEC and/or Campylobacter spp. in milk filters was associated with lack of cleanliness of bedding, water trough, and feed trough; nonevaluation of water hardness; lack of cleanliness of milk tank; and nonapplication of forestripping. After multivariate analysis, an association was observed with inadequate cleanliness of bedding and milk tank and the nonapplication of forestripping. PCR analysis of milk filters was a rapid and sensitive method for the microbiological evaluation of herd contamination status and should be included among the registration requirements for the authorization to produce and sell raw milk. Specific control actions must be incorporated into the farmer's daily practices to ensure the low-risk production of raw milk.

Surveillance of verocytotoxigenic Escherichia coli in Irish bovine dairy herds

Verocytotoxigenic Escherichia coli (VTEC) are highly significant zoonotic threats to public health, and have been the causative agent implicated in numerous high-profile outbreaks affecting large numbers of people. Serovar O157 is most frequently linked with human illness; however, other serovars, such as O26, O103, O111 and O145, have also been implicated. This study aimed to characterize the prevalence and virulence determinants of these five serovars in Irish dairy farm herds, and their milk. Using real-time PCR (RTi-PCR), bovine rectal faecal swabs and raw milk samples, along with milk filters, were screened for the presence of vt genes. Positive samples were then screened for the five serovars using sero-specific PCR. Serovar-positive samples were subjected to immunomagnetic separation, to isolate viable VTEC strains. These isolates were subsequently screened for four virulence factors: vt1, vt2, eaeA and hlyA. Three hundred and eighty six of the 600 rectal faecal swabs, 85 of the 117 milk-filters and 43 of the 120 bulk-tank milk samples, were positive for vt genes. From these 514 total vt-positive samples, 58 O26, 162 O103, 1 O111, 324 O145 and 26 O157 positives were detected by sero-specific RTi-PCR. Immunomagnetic separation yielded 12 O26, 26 O103, 0 O111, 19 O145 and 10 O157 isolates. Ten of these isolates contained at least one of the four virulence determinants screened for (i.e. vt1, vt2, eaeA and hlyA). Of these 10 isolates, pulsed-field gel electrophoresis showed that two of the O26 isolates from different farms were indistinguishable. Two O157 isolates were also indistinguishable. This study found serovars O103 and O145 to be the most prevalent in samples tested. Apart from the occurrence of VTEC in dairy herds, this study shows a high occurrence of vt genes in the environment, creating the possibility of horizontal gene transfer and emergence of new VTEC strains.