Phenotypic Antimicrobial Resistance Profiles of Human Campylobacter Species Isolated in Northwest Italy, 2020-2023.

The spread of antimicrobial resistant Campylobacter strains, linked to antimicrobials use and abuse in humans and food animals, has become a global public health problem. In this study, we determine the prevalence of antimicrobial resistance (AMR) in human Campylobacter isolates (n = 820) collected in Piedmont, Italy, from March 2020 to July 2023. The strains underwent susceptibility testing to determine the minimal inhibitory concentration for erythromycin, ciprofloxacin, gentamicin, streptomycin, and tetracycline: 80.1% of the strains showed resistance to at least one antibiotic. The highest prevalence of AMR was noted for ciprofloxacin and tetracycline (72.1% and 52.9%, respectively) and the lowest for erythromycin and aminoglycosides (streptomycin/gentamicin) (3.2% and 5.4%, respectively). The prevalence of co-resistance against fluoroquinolones and tetracyclines was 41.1%. The prevalence of multidrug resistant strains was 5.7%. Our data support evidence that AMR in human Campylobacter strains is common, particularly against ciprofloxacin and tetracycline, two medically important antimicrobials for humans.

Performance Evaluation of a Commercial Real-Time PCR Method for the Detection of Lupin Traces in Food.

In accordance with U.S. FDA Foods Program Regulatory Science Steering Committee guidelines, with this study, we optimized and validated a commercial real-time PCR method for the detection of low amounts of lupin in four classes of food matrices: chocolate cookies, ragù, Olivier salad, and barley and rice flour. DNA extracted from blank (true negative) samples artificially contaminated with lupin (Lupinus albus) flour at 1000 ppm underwent dilutions with the DNA extracted from the true negative samples up to 0.5 ppm. The limit of detection for real-time PCR was 0.5 ppm in the complex matrices (range, Ct 26-34), making this a specific, robust, and rapid method for lupin allergen detection and labeling. Our validation data support the suitability of this commercially available real-time PCR method for this purpose.

Detection and Characterization of Zoonotic Pathogens in Game Meat Hunted in Northwestern Italy.

Wildlife can represent a reservoir of zoonotic pathogens and a public health problem. In the present study, we investigated the spread of zoonotic pathogens (Salmonella spp., Yersinia enterocolitica, Listeria monocytogenes, Shiga-toxin-producing Escherichia coli (STEC), and hepatitis E virus (HEV)) considering the presence of virulence and antibiotic resistance genes in game meat from animals hunted in northwest Italy. During two hunting seasons (2020 to 2022), samples of liver and/or muscle tissue were collected from chamois (n = 48), roe deer (n = 26), deer (n = 39), and wild boar (n = 35). Conventional microbiology and biomolecular methods were used for the detection, isolation, and characterization of the investigated pathogens. Two L. monocytogenes serotype IIa strains were isolated from wild boar liver; both presented fosfomycin resistance gene and a total of 22 virulence genes were detected and specified in the text. Eight Y. enterocolitica biotype 1A strains were isolated from chamois (2), wild boar (5), and deer (1) liver samples; all showed streptogramin and beta-lactam resistance genes; the virulence genes found were myfA (8/8 strains), ymoA (8/8), invA (8/8), ystB (8/8), and ail (4/8). Our data underscore the potential role of wildlife as a carrier of zoonotic and antibiotic-resistant pathogens in northwest Italy and a food safety risk for game meat consumers.

In Vivo Evaluation of the Potential of Thyme and Lemon Hydrolates as Processing Aids to Reduce Norovirus Concentration during Oyster Depuration.

In this study, we evaluated the use of hydrolates, co-products of essential oil distillation, as processing aids to improve the depuration process of Pacific oysters (Crassostrea gigas) as a post-harvest method aimed at reducing the norovirus (NoV) viral load. Live oysters were kept in water to which hydrolates of Thymus serpyllum and Citrus limon at 1% were added for 24 h. The concentration of NoV was quantified using the ISO 15216-1 quantitative real-time RT-PCR method in the oyster digestive tissue both before and after the treatment. The results showed a significant reduction of 0.2 log in the NoV GII concentration after 24 h of treatment with 1% C. limon hydrolate. Conversely, treatment with T. serpyllum did not appear to reduce the concentration of NoV compared to the control. Additionally, a sensory analysis was conducted through a blind survey comparing untreated and treated oysters. No changes in the sensory and physical characteristics of the oysters were observed, except for a decrease in the marine flavour intensity, which was positively perceived by consumers. These results indicate that the addition of hydrolates of C. limon at 1% during depuration might represent a promising processing aid for enhancing both the safety and acceptability of live oysters.

First Report of Food Poisoning Due to Staphylococcal Enterotoxin Type B in Döner Kebab (Italy).

Staphylococcal food poisoning results from the consumption of food contaminated by staphylococcal enterotoxins. In July 2022, the Turin local health board was notified of a suspected foodborne outbreak involving six children who had consumed döner kebab purchased from a takeaway restaurant. The symptoms (vomiting and nausea) were observed 2-3 h later. A microbiological analysis of the food samples revealed high levels (1.5 × 107 CFU/g) of coagulase-positive staphylococci (CPS). The immunoassay detected a contamination with staphylococcal enterotoxins type B (SEB). The whole genome sequencing of isolates from the food matrix confirmed the staphylococcal enterotoxin genes encoding for type B, which was in line with the SEB detected in the food. This toxin is rarely reported in staphylococcal food poisoning, however, because there is no specific commercial method of detection. The involvement of enterotoxin type P (SEP) was not confirmed, though the corresponding gene (sep) was detected in the isolates. Nasal swabs from the restaurant food handlers tested positive for CPS, linking them to the likely source of the food contamination.

Food Safety Monitoring of Salmonella spp. in Northern Italy 2019-2021.

Salmonella is the second most frequent bacterial pathogen involved in human gastrointestinal outbreaks in the European Union; it can enter the food-production chain from animal or environmental sources or from asymptomatic food operators. European food legislation has established microbiological criteria to ensure consumer protection. Salmonella is listed under both process hygiene criteria and food safety criteria. Each EU member state designates an agency to organize or perform controls and other official activities. This paper describes the official control plans performed by competent authorities in Northern Italy in the three-year period 2019-2021. A total of 4413 food samples were delivered to the IZS Food Safety laboratories for Salmonella detection, of which 36 (0.8%) tested positive. Salmonella was most frequently detected in poultry meat samples (25/36 positive samples) followed by other meat products and pork products. The official controls for the protection of consumer health apply the EU's farm-to-fork approach: the samples were collected during production (food production plants), from products on the market, and from collective catering (restaurants, cafeterias, canteens). This manuscript will provide information about the presence of Salmonella in foodstuffs that can help competent authorities to set control plans based on risk assessments.

Soy, Rice and Oat Drinks: Investigating Chemical and Biological Safety in Plant-Based Milk Alternatives.

During the last decades, plant-based milk has become very appreciated by consumers, becoming a staple ingredient, especially for alternative breakfasts. Milk contains lactose, which is a sugar hydrolysed by the lactase enzyme. Lactose intolerance and lactose malabsorption are very common food intolerances among individuals. However, a lot of consumers consider themselves as lactose intolerant on the basis of self-reported intolerance and start to avoid dairy products, ignoring that plant-based milk alternatives are not nutritionally comparable to animal milk, especially in terms of protein intake. The aim of this study is to grow folder knowledge of the security of plant-based drinks, helping competent authorities to issue a risk assessment and to apply national plans about consumer safety. Results show that proper sanitary practices, such as pasteurization, are necessary in plant-based milk alternatives as well as in dairy milk. Chemical analysis has highlighted that there are no pesticide risks for consumers.

Influence of Season and Food Type on Bacterial and Entero-Toxigenic Prevalence of Staphylococcus aureus.

Staphylococcus (S.) aureus is a coagulase-positive pathogen of interest for human health and food safety in particular. It can survive in a wide environmental temperature range (7-48 °C, optimum 37 °C). Its enterotoxins are thermostable, which increases the risk of potential contamination in a variety of food products. Here we investigated the influence of seasonality and food type on bacterial count and presence of S. aureus enterotoxins. To do this, we analyzed 3604 food samples collected over a 5-year period (2016-2020). Ordinal logistic regression showed an influence of both seasonality and food type on the bacterial count. Regarding bacterial counts, winter was found to be the season with the highest risk, while with regards to enterotoxin production, the highest risk was found in autumn, specifically in October. The risk of contamination with S. aureus was greatest for dairy products. Our findings may inform food epidemiologists about foodborne illness prevention and risk to human health.

Biofilm formation and genomic features of Listeria monocytogenes strains isolated from meat and dairy industries located in Piedmont (Italy).

Listeria monocytogenes is considered a major challenge for the food industry as it can persist for long periods in food processing plants by forming biofilms. The aims of this study were: i) to assess the biofilm producing ability of 57 Listeria monocytogenes isolates previously subjected to whole-genome sequencing (WGS); ii) to compare the levels of biofilm formation with the presence or absence of biofilm associated genes. To determine the presence or absence of a known set of biofilm associated genes, a comparative genomic analysis was performed on each strain. Among Listeria monocytogenes isolates, 58 %, 38.5 % and 3.5 % exhibited weak, moderate or strong biofilm production, respectively. No difference in biofilm production was observed between food and environmental isolates. The percentage of Listeria monocytogenes strains isolated from meat products (57 %) classified as moderate or strong biofilm producers was higher than the percentage obtained for strains isolated from dairy products (28 %). The presence of the Stress Survival Islet 1, the arsD stress gene and the truncated inlA protein was significantly associated with increased levels of biofilm. Combining biofilm phenotype with molecular and genotyping data may provide the opportunity to better understand the relationship between genes linked to biofilm formation in Listeria monocytogenes.

Detection of Peanut Traces in Food by an Official Food Safety Laboratory.

Food safety laboratories rely on validated methods that detect hidden allergens in food to ensure the safety and health of allergic consumers. Here we present test results for the validation and accreditation of a real-time PCR assay for the detection of peanut traces in food products. The method was tested on five classes of food matrices: bakery and pastry products, meats, ready-to-eat and dairy products, and grains and milling products. Blank samples were spiked starting with the peanut samples (Arachis hypogaea) at a concentration of 1000 ppm. Serial dilutions were then prepared with the DNA extracted from the blank samples to a final concentration of 0.5 ppm. The limit of detection in grains and milling products, ready-to-eat, meats, bakery and pastry products was 0.5 ppm (range, Ct 27-34) and 2.5 ppm in dairy products (range, Ct 25-34). In order to determine the exclusivity parameter of the method, the ragù matrix was contaminated with Prunus dulcis (almonds), Glycine max (soy), Sinapis alba (mustard), Apium graveolens (celery), Allium cepa (onion), Pisum sativum (peas), Daucus carota (carrots), and Theobroma cacao (cocoa); no cross-reactions were observed. The method was rated satisfactory for sensitivity (98%), specificity (100%), robustness, and repeatability and it was fully validated and accredited.

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service.

BACKGROUND: Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of "on-demand" Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server's initial configuration and deployment. RESULTS: "Laniakea@ReCaS", the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. CONCLUSIONS: During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers' work.

Comparison of Clostridioides difficile strains from animals and humans: First results after introduction of C. difficile molecular typing and characterization at the Istituto Zooprofilattico Sperimentale of Piemonte, Liguria e Valle d'Aosta, Italy.

PCR ribotypes (RTs027 and 078) are known causes of Clostridioides difficile infection (CDI) in humans. Molecular typing and characterization of 39 C. difficile strains isolated from samples from humas and animals in 2016-2018 indicated an overlap of RTs between community-acquired patients (CA-CDI) and domestic animals from the same geographical area; 14 RTs were identified: 12 RTs were positive for toxins A/B; RT078, RT080 and RT126 were also positive for binary toxin (CDT). Most of the RTs from the animals (RTs020, 078, 106, 126) were also detected in the samples from humans. Strains grouped into three clusters: cluster I included prevalently human strains, mainly RT 018; clusters II and III included strains from humans and animals, mainly RT078 and RT020. The CA-CDI strains suggested animals as a reservoir of C. difficile isolated together with other microorganisms from animals, highlighting the association of enteric pathogens as a cause of infection and death.

Genetic Characterization of a Listeria monocytogenes Serotype IVb Variant 1 Strain Isolated from Vegetal Matrix in Italy.

We report the chromosome and plasmid sequences of a strain of Listeria monocytogenes IVb variant 1, a recently emerging serotype, isolated in Italy from ready-to-eat vegetables.

An Italian survey of undeclared allergens in food over the years 2014-2018.

Large population studies estimated that the frequency of food allergies is increasing worldwide. In the last two decades, a 'second wave' of the allergy epidemic has emerged as a growing public health problem. EU regulation strengthened information to consumers about allergens in pre-packed food, since December 2014 it has been extended to non-prepacked foods by the Regulation (EU) No 1169/2011 of the European Commission. The present work aims to present a five-year survey on the presence of nine types of allergen in several foods, including food of animal origin and baby food. The concentration found for each irregular allergen is generally low, but some samples with no gluten indication contained a concentration above 10 mg kg-1 with the highest value of 138.5 mg kg-1 in a dietetic food, during the screening in 2017. These data underline the importance and the necessity of a complete food labelling to protect the majority of allergic individuals.

Arcobacter spp. in raw milk from vending machines in Piedmont and occurrence of virulence genes in isolates.

Arcobacter spp. has been recognized as an emerging foodborne pathogen and a hazard to human health. In the dairy chain, it has been isolated from different sources, nevertheless data on Arcobacter occurrence in raw milk provided by vending machines are few. This study aimed to identify potentially pathogenic Arcobacter spp. in raw milk intended for human consumption sold through vending machines located in Piedmont. In an 8-month period, 37 raw milk samples were collected from 24 dairy farms: 12 (32,4%) were collected directly in farm from bulk tank milk and 25 (67,6%) from vending machines. Eight (21,6%) out of the 37 milk samples and 7 (29,2%) out of the 24 dairy farms were positive for Arcobacter spp. by culture examination. Four (16%) out of the 25 samples from vending machines and 4 (33,3%) out of the 12 samples from bulk tank milk were positive. All 8 isolates were identified as A. butzleri both by MALDI-TOF MS and multiplex end-point PCR. According to the detection of virulence genes, a total of four Patho-types were highlighted: 5 isolates in P-type 1 and only one isolate for each of the P-types 2-3-4. A. butzleri isolates carrying encoding virulence factors genes were isolated from raw milk intended for human consumption: these findings strengthen the compulsory consumption after boiling as required by current legislation and suggest the need of enlarging the analytical investigations to other microorganisms not yet included in the food safety criteria.

Evaluation of the efficacy of a training course in food safety addressed to food charity volunteers.

In Italy, the Banco Alimentare Onlus manages a network of 8,000 charitable organizations that distribute 67,000 tons of foodstuffs to 1.6 million needy persons. To provide their volunteers with the required food safety knowledge, the Banco Alimentare del Piemonte Onlus commissioned the Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta to hold training courses in food safety. Before and after each session, the participants completed a questionnaire to evaluate their knowledge on the topic of food safety. The responses were entered in a dedicated database and analyzed using STATA ver. 15.1. Comparison of the scores for each participant before and after training revealed a considerable discordance [ICC 0.06, 95% confidence interval (CI) 0.00-0.18]. Analysis of the post-training questionnaires showed that the number of questions left unanswered decreased and the number of correct answers increased. The difference between the percentage of correct and incorrect responses before and after the training course was statistically significant (P<0.001). Comparison of responses to the pre- and post-training questionnaires provided the data for statistical evaluation of the efficacy of the training course.

Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses.

Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins' genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.

Analysis of Gluten Content in Gluten-Free Pizza from Certified Take-Away Pizza Restaurants.

Currently, a strict gluten-free diet is the only treatment for celiac disease. In Italy, food service establishments and restaurants can be certified for providing gluten-free foods, including pizza restaurants that make both gluten-free pizza and traditional wheat-based pizza. With this study we analyzed the gluten content in samples of gluten-free pizza prepared and purchased at certified restaurants in the Turin metropolitan area. All samples, from 28 pizzas and 28 cooked dough bases, produced results below the test limit of detection, except for one sample of cooked dough, that tested positive for gluten but still below the warning level for celiac consumers (<20 ppm). Gluten-free pizza, as advertised in the restaurants surveyed, can be considered a safe option for gluten-free consumption. Attention to and compliance with good manufacturing practices, a requisite for obtaining gluten-free certification for restaurants, were noted to have a positive effect on the final product.

Microbiological Parameters in the Primary Production of Berries: A Pilot Study.

The primary production of fresh soft fruits was considered to be a suspected critical point for the contamination of frozen berries that were responsible for the large 2013⁻2014 Hepatitis A virus (HAV) outbreak in Europe. In this study, an Italian berries’ production area was studied for its agro-technical characteristics, and the fresh fruits were analyzed for the presence of enteric viruses (HAV and Norovirus (NoV) genogroup I and genogroup II (GGI and GGII)), the enumeration of hygienic quality parameters, and the prevalence of bacterial pathogens. A total of 50 producers were sampled, who specialized in the exclusive or shared cultivation of berries. Escherichia coli was detected in two blackberry samples, whereas HAV and Norovirus were not detected. The samples were negative for Salmonella spp., Listeria monocytogenes, and Shiga toxin-producing Escherichia coli (STEC). The farms’ attributes were not associated with positive samples, apart from the presence of E. coli and the aerobic mesophilic bacteria for blackberry that were statistically correlated. In blueberries, the high aerobic mesophilic count could likely be associated with the resistance of the outer layer to handling. However, the two pathogens (Salmonella spp. and STEC) and the targeted viruses (HAV, NoV GGI and GGII) were not detected, highlighting the low risk of foodborne pathogens and viral contamination at the primary production stage of the berry food chain in the area considered in this pilot study.

Outbreak of febrile gastroenteritis caused by Listeria monocytogenes 1/2a in sliced cold beef ham, Italy, May 2016.

In May 2016, two separate clusters of febrile gastroenteritis caused by Listeria monocytogenes were detected by the local health authority in Piedmont, in northern Italy. We carried out epidemiological, microbiological and traceback investigations to identify the source. The people affected were students and staff members from two different schools in two different villages located in the Province of Turin; five of them were hospitalised. The epidemiological investigation identified a cooked beef ham served at the school canteens as the source of the food-borne outbreak. L. monocytogenes was isolated from the food, the stools of the hospitalised pupils and the environment of the factory producing the cooked beef ham. All isolates except one were serotype 1/2a, shared an indistinguishable PFGE pattern and were 100% identical by whole genome sequencing (WGS). By combining a classical epidemiological approach with both molecular subtyping and WGS techniques, we were able to identify and confirm a Listeria gastroenteritis outbreak associated with consumption of sliced cold beef ham.