Shiga toxin-producing Escherichia coli O103:H2 outbreak in Germany after school trip to Austria due to raw cow milk, 2017 - The important role of international collaboration for outbreak investigations

Antibiotic Resistance and Genomic Analysis of Shiga Toxin-Producing Escherichia coli from Dairy Cattle, Raw Milk, and Farm Environment in Shaanxi Province, China

To investigate the epidemiology of Shiga toxin-producing Escherichia coli (STEC) in dairy cattle, 975 samples (185 feces, 34 silage, 36 cattle drinking water, 360 raw milk, and 360 teat skin swabs) were collected from two dairy farms in Baoji and Yangling, Shaanxi Province, China, and were screened for STEC. Whole-genome sequencing was used to analyze the genomic characteristics and potential transmission of STEC isolates. A total of 32 samples were contaminated with STEC, including 4.0% (19/479) in Farm A and 2.6% (13/496) in Farm B. Compared with adult cows (4.5%), nonadult cows had a higher rate (21.3%) of STEC colonization. A total of 14 serotypes and 11 multilocus sequence typing were identified in 32 STEC isolates, among which O55:H12 (25.0%) and ST101 (31.3%) were the most predominant, respectively. Six stx subtypes/combinations were identified, including stx1a (53.1%), stx2g (15.6%), stx2d, stx2a+stx2d, stx1a+stx2a (6.3%, for each), and stx2a (3.1%). Of 32 STEC isolates, 159 virulence genes and 27 antibiotic resistance genes were detected. Overall, STEC isolates showed low levels of resistance to the 16 antibiotics tested (0-40.6%), with most common resistance to ampicillin (40.6%). The phylogenetic analysis confirmed that STEC in the gut of cattle can be transmitted through feces. The results of this study help to improve our understanding of the epidemiological aspects of STEC in dairy cattle and provide early warning and control of the prevalence and spread of the bacterium.

Effects of PEF on Cell and Transcriptomic of Escherichia coli

Pulsed electric field (PEF) is an up-to-date non-thermal processing technology with a wide range of applications in the food industry. The inactivation effect of PEF on Escherichia coli was different under different conditions. The E. coli inactivated number was 1.13 ± 0.01 lg CFU/mL when PEF was treated for 60 min and treated with 0.24 kV/cm. The treatment times were found to be positively correlated with the inactivation effect of PEF, and the number of E. coli was reduced by 3.09 ± 0.01 lg CFU/mL after 100 min of treatment. The inactivation assays showed that E. coli was inactivated at electrical intensity (0.24 kV/cm) within 100 min, providing an effective inactivating outcome for Gram-negative bacteria. The purpose of this work was to investigate the cellular level (morphological destruction, intracellular macromolecule damage, intracellular enzyme inactivation) as well as the molecular level via transcriptome analysis. Field Emission Scanning Electron Microscopy (TFESEM) and Transmission Electron Microscope (TEM) results demonstrated that cell permeability was disrupted after PEF treatment. Entocytes, including proteins and DNA, were markedly reduced after PEF treatment. In addition, the activities of Pyruvate Kinase (PK), Succinate Dehydrogenase (SDH), and Adenosine Triphosphatase (ATPase) were inhibited remarkably for PEF-treated samples. Transcriptome sequencing results showed that differentially expressed genes (DEGs) related to the biosynthesis of the cell membrane, DNA replication and repair, energy metabolism, and mobility were significantly affected. In conclusion, membrane damage, energy metabolism disruption, and other pathways are important mechanisms of PEF's inhibitory effect on E. coli.

Genomic surveillance of STEC/EHEC infections in Germany 2020 to 2022 permits insight into virulence gene profiles and novel O-antigen gene clusters

Shiga toxin-producing E. coli (STEC), including the subgroup of enterohemorrhagic E. coli (EHEC), are important bacterial pathogens which cause diarrhea and the severe clinical manifestation hemolytic uremic syndrome (HUS). Genomic surveillance of STEC/EHEC is a state-of-the-art tool to identify infection clusters and to extract markers of circulating clinical strains, such as their virulence and resistance profile for risk assessment and implementation of infection prevention measures. The aim of the study was characterization of the clinical STEC population in Germany for establishment of a reference data set. To that end, from 2020 to 2022 1257 STEC isolates, including 39 of known HUS association, were analyzed and lead to a classification of 30.4 % into 129 infection clusters. Major serogroups in all clinical STEC analyzed were O26, O146, O91, O157, O103, and O145; and in HUS-associated strains were O26, O145, O157, O111, and O80. stx1 was less frequently and stx2 or a combination of stx, eaeA and ehxA were more frequently found in HUS-associated strains. Predominant stx gene subtypes in all STEC strains were stx1a (24 %) and stx2a (21 %) and in HUS-associated strains were mainly stx2a (69 %) and the combination of stx1a and stx2a (12.8 %). Furthermore, two novel O-antigen gene clusters (RKI6 and RKI7) and strains of serovars O45:H2 and O80:H2 showing multidrug resistance were detected. In conclusion, the implemented surveillance tools now allow to comprehensively define the population of clinical STEC strains including those associated with the severe disease manifestation HUS reaching a new surveillance level in Germany.

Prevalence, antibiotic resistance, and virulence gene profile of Escherichia coli strains shared between food and other sources in Africa: A systematic review

Background and Aim

Foodborne diseases caused by Escherichia coli are prevalent globally. Treatment is challenging due to antibiotic resistance in bacteria, except for foodborne infections due to Shiga toxin-producing E. coli, for which treatment is symptomatic. Several studies have been conducted in Africa on antibiotic resistance of E. coli isolated from several sources. The prevalence and distribution of resistant pathogenic E. coli isolated from food, human, and animal sources and environmental samples and their virulence gene profiles were systematically reviewed.

Materials and Methods

Bibliographic searches were performed using four databases. Research articles published between 2000 and 2022 on antibiotic susceptibility and virulence gene profile of E. coli isolated from food and other sources were selected.

Results

In total, 64 articles were selected from 14 African countries: 45% of the studies were conducted on food, 34% on animal samples, 21% on human disease surveillance, and 13% on environmental samples. According to these studies, E. coli is resistant to ~50 antimicrobial agents, multidrug-resistant, and can transmit at least 37 types of virulence genes. Polymerase chain reaction was used to characterize E. coli and determine virulence genes.

Conclusion

A significant variation in epidemiological data was noticed within countries, authors, and sources (settings). These results can be used as an updated database for monitoring E. coli resistance in Africa. More studies using state-of-the-art equipment are needed to determine all resistance and virulence genes in pathogenic E. coli isolated in Africa.

Milk-borne diseases through the lens of one health

Reviewing “zoonotic diseases” classically brings to mind human infections contracted in close association with animals, where outdoor occupations and afforested lands usually play a key role in the epidemiological triad. However, there is a very common, yet overlooked route of infection where humans may not come in direct contact with animals or implicated environments. Milk-borne diseases are a unique set of infections affecting all age groups and occupational categories of humans, causing 4% of all the foodborne diseases in the world. The infection reservoir may lie with milch animals and associated enzootic cycles, and the infectious agent is freely secreted into the animal’s milk. Commercial pooling and processing of milk create unique environmental challenges, where lapses in quality control could introduce infective agents during downstream processing and distribution. The infectious agent is finally brought to the doorstep of both rural and urban households through such animal products. The domestic hygiene of the household finally determines human infections. One health approach can target preventive measures like immunization in animals, pasteurization and stringent quality control during the commercial processing of milk, and finally, hygienic practices at the level of the consumer, to reduce the burden of milk-borne diseases. This review hopes to draw the attention of policymakers to this unique route of infection, because it can be easily regulated with cost-effective interventions, to ensure the safety of this precious food product, permeating the life and livelihood of humans from all walks of life.

A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics

Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml^-1. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.

The "Big Six": Hidden Emerging Foodborne Bacterial Pathogens

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging serogroups that often result in diseases ranging from diarrhea to severe hemorrhagic colitis in humans. The most common non-O157 STEC are O26, O45, O103, O111, O121, and O145. These serogroups are known by the name "big six" because they cause severe illness and death in humans and the United States Department of Agriculture declared these serogroups as food contaminants. The lack of fast and efficient diagnostic methods exacerbates the public impact of the disease caused by these serogroups. Numerous outbreaks have been reported globally and most of these outbreaks were caused by ingestion of contaminated food or water as well as direct contact with reservoirs. Livestock harbor a variety of non-O157 STEC serovars that can contaminate meat and dairy products, or water sources when used for irrigation. Hence, effective control and prevention approaches are required to safeguard the public from infections. This review addresses the disease characteristics, reservoirs, the source of infections, the transmission of the disease, and major outbreaks associated with the six serogroups ("big six") of non-O157 STEC encountered all over the globe.

Childcare and School Acute Gastroenteritis Outbreaks: 2009-2020

OBJECTIVES

Acute gastroenteritis (AGE) outbreaks commonly occur in congregate settings, including schools and childcare facilities. These outbreaks disrupt institutions, causing absences and temporary facility closures. This study analyzed the epidemiology of school and childcare AGE outbreaks in the United States.

METHODS

We analyzed AGE outbreaks occurring in kindergarten to grade 12 schools and childcare facilities reported via the National Outbreak Reporting System in the United States from 2009 to 2019 and compared this information to 2020 data. Outbreak and case characteristics were compared using the Kruskal-Wallis rank sum test, χ2 goodness-of-fit test, and Fisher exact test.

RESULTS

From 2009 to 2019, there were 2623 school, 1972 childcare, and 38 school and childcare outbreaks. School outbreaks were larger (median, 29 cases) than childcare outbreaks (median, 10 cases). Childcare outbreaks were longer (median, 15 days) than school outbreaks (median, 9 days). Norovirus (2383 outbreaks; 110 190 illnesses) and Shigella spp. (756 outbreaks; 9123 illnesses) were the most reported etiologies. Norovirus was the leading etiology in schools; norovirus and Shigella spp. were dominant etiologies in childcare centers. Most (85.7%) outbreaks were spread via person-to-person contact. In 2020, 123 outbreaks were reported, 85% in the first quarter.

CONCLUSIONS

Schools and childcare centers are common AGE outbreak settings in the United States. Most outbreaks were caused by norovirus and Shigella spp. and spread via person-to-person transmission. Fewer outbreaks were reported in 2020 from the COVID-19 pandemic. Prevention and control efforts should focus on interrupting transmission, including environmental disinfection, proper handwashing, safe diapering, and exclusion of ill persons.

Characterization of Antibiotic Resistant Coliform Bacteria and Resistance Genes Isolated from Samples of Smoothie Drinks and Raw Milk

Raw foodstuffs have been marked as a healthier alternative in the context of nutrient content and are becoming more popular with consumers. Thermally untreated foods may represent a microbiological risk connected with the possible presence of antimicrobial resistance. The aim of this study was to prove that popular raw food beverages such as smoothies and raw milk may be a source of antibiotic-resistant coliform bacteria and resistant genes. The majority of antibiotic-resistant isolates (110) were identified as Enterobacter spp., Escherichia coli, and species of Klebsiella spp., predominantly β-lactam and chloramphenicol resistant. Multidrug resistance has been registered in one-third of resistants. Overproduction of efflux pumps was clarified in 8 different bacteria. The majority of resistant isolates were strong biofilm producers. Antibiotic resistance gene blaOXA was detected in 25% of isolates, especially in E. coli. Resistance genes blaTEM and blaSHV were detected in 19% and 14%, respectively. This is the first study to point out that popular raw drinks such as smoothies or raw milk, besides their nutrient benefits, could represent a reservoir of antibiotic-resistant bacteria as well as antibiotic resistance genes. According to this, raw drinks could contribute to the dissemination of antibiotic resistance in the human gastrointestinal tract and environment.

Occurrence and D-Tryptophan Application for Controlling the Growth of Multidrug-Resistant Non-O157 Shiga Toxin-Producing Escherichia coli in Dairy Products

The objectives of the current study were first to determine the prevalence of non O157:H7E. coli, especially Shiga toxin-producing Escherichia coli (STEC) in retailed milk and dairy products in Egypt. Second, the antimicrobial resistance profiling and virulence genes of the isolated E. coli strains were screened. Third, evaluation of the inhibitory effects of D-tryptophan against E. coli O26:H11 was further performed. The results revealed that 20% (30/150) of the samples were STEC positive, with 64 isolates harboring some virulent genes, such as Stx1, Stx2, eaeA, and hylA. Serological identification revealed four different pathotypes belonging to EPEC, ETEC, EHEC, and EIEC. Antimicrobial susceptibility testing revealed that 100%, 98.44%, 92.19%, 71.87%, 65.63% and 64.06% of the isolates had a resistance against tetracycline, oxacillin, erythromycin, nalidixic acid, sulphamethoxazol, and ampicillin, respectively. D-tryptophan addition (40 mM) to E. coli O26:H11-inoculated soft cheese and ice cream revealed a significant reduction (p < 0.05) in bacterial growth, especially when accompanied with other food stressors. D-Tryptophan is considered as an effective food preservative and as a promising alternative candidate in the dairy industry.

Escherichia coli O103 outbreak associated with minced celery among hospitalized individuals in Victoria, British Columbia, 2021

BACKGROUND

In April 2021, a Shiga toxin-producing Escherichia coli (E. coli) (STEC) O103 outbreak was identified among patients at two hospitals in Victoria, British Columbia (BC). The objective of this study is to describe this outbreak investigation and identify issues of food safety for high-risk products prepared for vulnerable populations.

METHODS

Confirmed cases of E. coli O103 were reported to the Island Health communicable disease unit. The provincial public health laboratory conducted whole genome sequencing on confirmed case isolates, as per routine practice for STEC in BC. Exposure information was obtained through case interviews and review of hospital menus. Federal and local public health authorities conducted an inspection of the processing plant for the suspect source.

RESULTS

Six confirmed cases of E. coli O103 were identified, all related by whole genome sequencing. The majority of cases were female (67%) and the median age was 61 years (range 24-87 years). All confirmed cases were inpatients or outpatients at two hospitals and were exposed to raw minced celery within prepared sandwiches provided by hospital food services. A local processor supplied the minced celery exclusively to the two hospitals. Testing of product at the processor was infrequent, and chlorine rinse occurred before mincing. The spread of residual E. coli contamination through the mincing process, in addition to temperature abuse at the hospitals, are thought to have contributed to this outbreak.

CONCLUSION

Raw vegetables, such as celery, are a potential source of STEC and present a risk to vulnerable populations. Recommendations from this outbreak include more frequent testing at the processor, a review of the chlorination and mincing process and a review of hospital food services practices to mitigate temperature abuse.

Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm

Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103.

Genetic diversity and pathogenic potential of Shiga toxin-producing Escherichia coli (STEC) derived from German flour

Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the potential of plant based food as transmission routes for STEC. In Germany STEC has been isolated from flour, but no cases of illness have been linked to flour. In this study, we characterized 123 STEC strains isolated from flour and flour products collected between 2015 and 2019 across Germany. In addition to determination of serotype and Shiga toxin subtype, whole genome sequencing (WGS) was used for isolates collected in 2018 to determine phylogenetic relationships, sequence type (ST), and virulence-associated genes (VAGs). We found a high diversity of serotypes including those frequently associated with human illness and outbreaks, such as O157:H7 (stx2c/d, eae), O145:H28 (stx2a, eae), O146:H28 (stx2b), and O103:H2 (stx1a, eae). Serotypes O187:H28 (ST200, stx2g) and O154:H31 (ST1892, stx1d) were most prevalent, but are rarely linked to human cases. However, WGS analysis revealed that these strains, as well as, O156:H25 (ST300, stx1a) harbour high numbers of VAGs, including eae, nleB and est1a/sta1. Although STEC-contaminated flour products have yet not been epidemiologically linked to human clinical cases in Germany, this study revealed that flour can serve as a vector for STEC strains with a high pathogenic potential. Further investigation is needed to determine the sources of STEC contamination in flour and flour products particularly in regards to these rare serotypes.

Characterization of Non-O157 Shiga Toxin-Producing Escherichia coli Cultured from Cattle Farms in Xinjiang Uygur Autonomous Region, China, During 2016-2017

Most outbreaks of Shiga toxin-producing Escherichia coli (STEC) are attributed to consumption of contaminated foodstuffs including beef and dairy products. In this study, we evaluated the prevalence of non-O157 STEC cultured from beef and dairy cattle and collected in Xinjiang Uygur Autonomous Region in China. Results identified 67 non-O157 STEC recovered from the 793 samples including beef cattle (10.28%, 43/418) and dairy cattle (6.40%, 24/375). A total of 67 non-O157 STEC was sequenced allowing for in silico analyses of their serotypes, virulence genes, and identification of the corresponding multilocus sequence types (STs). Twenty-one O serogroups and nine H serotypes were identified and the dominant serotype identified was O22:H8. One stx1 subtype (stx1a) and four stx2 subtypes (2a, 2b, 2c, and 2d) were found in the 67 non-O157 STEC isolates. The results revealed that stx1a+stx2a-positive STEC isolates were predominant (32.83%, 22/67), followed by stx1a+stx2d (29.85%, 20/67) and stx2a alone (17.91%, 12/67). Non-O157 STEC isolates carried virulence genes ehxA (98.51%), subA (53.73%), and cdtB (17.91%). Of the four adherence-associated genes tested, eaeA was absent, whereas lpfA and iha were present in 67 and 55 non-O157 STEC isolates, respectively. The STEC isolates were divided into 48 pulsed-field gel electrophoresis patterns and 10 STs, and ST446 (O22:H8) was the dominant clone (22.38%). Our results revealed that there was a high genetic diversity among non-O157 STEC isolated from beef and dairy cattle, some of which have potential to cause human diseases.

Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) of Listeria monocytogenes and Listeria innocua

Nucleotide sequence-based methods focusing on the single-nucleotide polymorphisms (SNPs) of Listeria monocytogenes and L. innocua housekeeping genes (multilocus sequence typing) and in the core genome (core genome MLST) facilitate the rapid and interlaboratory comparison in open accessible databases as provided by Institute Pasteur ( https://bigsdb.web.pasteur.fr/listeria/listeria.html ). Strains can be compared on a global level and help to track forward and trace backward pathogen contamination events in food processing facilities and in outbreak scenarios.

Potential of N2 Gas Flushing to Hinder Dairy-Associated Biofilm Formation and Extension

Worldwide, the dairy sector remains of vital importance for food production despite severe environmental constraints. The production and handling conditions of milk, a rich medium, promote inevitably the entrance of microbial contaminants, with notable impact on the quality and safety of raw milk and dairy products. Moreover, the persistence of high concentrations of microorganisms (especially bacteria and bacterial spores) in biofilms (BFs) present on dairy equipment or environments constitutes an additional major source of milk contamination from pre- to post-processing stages: in dairies, BFs represent a major concern regarding the risks of disease outbreaks and are often associated with significant economic losses. One consumption trend toward "raw or low-processed foods" combined with current trends in food production systems, which tend to have more automation and longer processing runs with simultaneously more stringent microbiological requirements, necessitate the implementation of new and obligatory sustainable strategies to respond to new challenges regarding food safety. Here, in light of studies, performed mainly with raw milk, that considered dominant "planktonic" conditions, we reexamine the changes triggered by cold storage alone or combined with nitrogen gas (N2) flushing on bacterial populations and discuss how the observed benefits of the treatment could also contribute to limiting BF formation in dairies.

Applications of Electrolyzed Water as a Sanitizer in the Food and Animal-By Products Industry

Food demand is increasing every year and, usually animal-derived products are generated far from consumer-places. New technologies are being developed to preserve quality characteristics during processing and transportation. One of them is electrolyzed water (EW) that helps to avoid or decrease the development of foodborne pathogens, or losses by related bacteria. Initially, EW was used in ready-to-eat foods such as spinach, lettuce, strawberries, among others; however, its application in other products is under study. Every product has unique characteristics that require an optimized application of EW. Different sanitizers have been developed; unfortunately, they could have undesirable effects like deterioration of quality or alterations in sensory properties. Therefore, EW is gaining popularity in the food industry due to its characteristics: easy application and storage, no corrosion of work surfaces, absence of mucosal membrane irritation in workers handling food, and it is considered environmentally friendly. This review highlights the advantages of using EW in animal products like chicken, pork, beef, eggs and fish to preserve their safety and quality.

Prevalence and antimicrobial resistance of Shiga toxin-producing Escherichia coli in milk and dairy products in Egypt

Food contaminated with Shiga toxin-producing Escherichia coli (STEC) represents a hazardous public health problem worldwide. Therefore, the present study was performed to elucidate the virulent and antimicrobial resistance characteristics of STEC isolated from milk and dairy products marketed in Egypt. A total of 125 samples (raw market milk, bulk tank milk, Kareish cheese, white soft cheese, and small scale-produced ice cream, 25 each) were collected for determination the prevalence and antimicrobial resistance profiling of STEC. Thirty-six STEC isolates were recovered from milk and dairy products. Serological analysis illustrated that three isolates were E. coli O157:H7 and 33 isolates belonged to different serotypes. Molecular examination indicated that all isolates harboured stx1 and/or stx2 genes, 14 isolates expressed eaeA gene and 3 isolates possessed rfbE gene. Antimicrobial resistance profiling of the isolates was both phenotypically and genetically examined. Interestingly, 31 out of 36 (86.11%) isolates were multidrug-resistant and harboured the extended-spectrum β-lactamase encoding genes, namely, bla_CTX-M-15, bla_SHV-12 and bla_CTX-M-14. Moreover, 12 isolates (33.33%) harboured plasmid-mediated quinolone resistant gene, qnrS. The overall conclusion of the current investigation indicated insufficient hygienic measures adopted during milking, handling, and processing leading to development of pathogenic and multidrug-resistant STEC.

Comparative Analysis of Tools and Approaches for Source Tracking Listeria monocytogenes in a Food Facility Using Whole-Genome Sequence Data

As WGS is increasingly used by food industry to characterize pathogen isolates, users are challenged by the variety of analysis approaches available, ranging from methods that require extensive bioinformatics expertise to commercial software packages. This study aimed to assess the impact of analysis pipelines (i.e., different hqSNP pipelines, a cg/wgMLST pipeline) and the reference genome selection on analysis results (i.e., hqSNP and allelic differences as well as tree topologies) and conclusion drawn. For these comparisons, whole genome sequences were obtained for 40 Listeria monocytogenes isolates collected over 18 years from a cold-smoked salmon facility and 2 other isolates obtained from different facilities as part of academic research activities; WGS data were analyzed with three hqSNP pipelines and two MLST pipelines. After initial clustering using a k-mer based approach, hqSNP pipelines were run using two types of reference genomes: (i) closely related closed genomes (“closed references”) and (ii) high-quality de novo assemblies of the dataset isolates (“draft references”). All hqSNP pipelines identified similar hqSNP difference ranges among isolates in a given cluster; use of different reference genomes showed minimal impacts on hqSNP differences identified between isolate pairs. Allelic differences obtained by wgMLST showed similar ranges as hqSNP differences among isolates in a given cluster; cgMLST consistently showed fewer differences than wgMLST. However, phylogenetic trees and dendrograms, obtained based on hqSNP and cg/wgMLST data, did show some incongruences, typically linked to clades supported by low bootstrap values in the trees. When a hqSNP cutoff was used to classify isolates as “related” or “unrelated,” use of different pipelines yielded a considerable number of discordances; this finding supports that cut-off values are valuable to provide a starting point for an investigation, but supporting and epidemiological evidence should be used to interpret WGS data. Overall, our data suggest that cgMLST-based data analyses provide for appropriate subtype differentiation and can be used without the need for preliminary data analyses (e.g., k-mer based clustering) or external closed reference genomes, simplifying data analyses needs. hqSNP or wgMLST analyses can be performed on the isolate clusters identified by cgMLST to increase the precision on determining the genomic similarity between isolates.

Practical applications of DNA genotyping in diagnostic pathology

INTRODUCTION

Among various human tissue identity testing platforms, short tandem repeat (STR) genotyping has emerged as the most powerful and cost-effective method. Beyond forensic applications, tissue identity testing has become increasingly important in modern medical practice, in areas such as diagnostic pathology. Areas covered: A brief overview of various molecular/genetic techniques for identity testing is provided. This includes restriction fragment length polymorphism, single nucleotide polymorphism array and STR genotyping by multiplex PCR. Diagnostic applications of STR genotyping are covered in greater details: genotyping diagnosis of gestational trophoblastic disease, resolving tissue specimen mislabeling or histologic contaminant or 'floaters', bone marrow engraftment/chimerism analysis and interrogation of the primary source of malignancy in patients receiving organ donation. Four clinical cases are then presented to further illustrate these important clinical applications along with discussion of the interpretation, limitations, and pitfalls of STR genotyping. Expert commentary: STR genotyping is currently the most applicable method of identity testing and has extended its role well into the practice of diagnostic pathology with novel and powerful applications beyond forensics.

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.

The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2017

This report of the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring activities carried out in 2017 in 37 European countries (28 Member States (MS) and nine non-MS). Campylobacteriosis was the commonest reported zoonosis and its EU trend for confirmed human cases increasing since 2008 stabilised during 2013-2017. The decreasing EU trend for confirmed human salmonellosis cases since 2008 ended during 2013-2017, and the proportion of human Salmonella Enteritidis cases increased, mostly due to one MS starting to report serotype data. Sixteen MS met all Salmonella reduction targets for poultry, whereas 12 MS failed meeting at least one. The EU flock prevalence of target Salmonella serovars in breeding hens, laying hens, broilers and fattening turkeys decreased or remained stable compared to 2016, and slightly increased in breeding turkeys. Salmonella results on pig carcases and target Salmonella serovar results for poultry from competent authorities tended to be generally higher compared to those from food business operators. The notification rate of human listeriosis further increased in 2017, despite Listeria seldom exceeding the EU food safety limit in ready-to-eat food. The decreasing EU trend for confirmed yersiniosis cases since 2008 stabilised during 2013-2017. The number of confirmed shiga toxin-producing Escherichia coli (STEC) infections in humans was stable. A total of 5,079 food-borne (including waterborne) outbreaks were reported. Salmonella was the commonest detected agent with S. Enteritidis causing one out of seven outbreaks, followed by other bacteria, bacterial toxins and viruses. The agent was unknown in 37.6% of all outbreaks. Salmonella in eggs and Salmonella in meat and meat products were the highest risk agent/food pairs. The report further summarises trends and sources for bovine tuberculosis, Brucella, Trichinella, Echinococcus, Toxoplasma, rabies, Coxiella burnetii (Q fever), West Nile virus and tularaemia.

Genomic Epidemiology of Campylobacter jejuni Transmission in Israel

Objectives: Campylobacter jejuni is responsible for 80% of Campylobacter infections in Israel, a country with a high incidence reaching 91/100,000 population. We studied the phylogeny, diversity and prevalence of virulence factors using whole genome sequencing (WGS) of a national sample of C. jejuni clinical, food, and animal isolates collected over a 10-year period (2003-2012). Methods: C. jejuni isolates (n = 263) were subject to WGS using Illumina sequencing (PE 250bpx2). Raw reads and de novo assemblies were analyzed with the BioNumerics whole genome MLST (wgMLST) pipeline. Reads were screened for 71 virulence genes by the SRST2 script. Allelic profiles were analyzed to create minimum spanning trees and allelic core distances were investigated to determine a reliable cutoff for strain determination. Results: wgMLST analysis of 263 C. jejuni isolates indicated significant diversity among the prevalent clonal complexes (CCs) with CC-21 and CC-353 being the most diverse, and CC-574 the most clonal. Within CC-21, sequence type (ST)-1359 created a separate clade. Human, poultry and bovine isolates clustered together across the different STs. Forty four percent of studied isolates were assigned to 29 genetic clusters. Temporal and geographical relatedness were found among the minority of clusters, while most phylogenetically associated cases appeared diffuse and unassociated epidemiologically. The majority of virulence factors were highly prevalent across the dataset and not associated with genotype, source of isolation or invasiveness. Conversely, all 13 genes associated with type VI secretion system (T6SS) were lineage-related and identified in only 18% of the isolates. T6SS was detected in 95.2% of ST-1359, a common type in Israel. Conclusions: wgMLST supported the assessment that poultry and cattle are likely food sources of infection in Israel. Substantial genetic clustering among C. jejuni isolates suggested multiple point source and diffuse outbreaks that were previously unreported in Israel. The high prevalence of T6SS among ST-1359 isolates is unique to Israel, and requires further investigation. This study exemplifies the importance of studying foodborne pathogens using advanced genomic approaches across the entire spectrum of One Health.