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Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94-96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences.

The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916 -carrying tetM gene and plasmid-encoded ermB . Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.

A commercial olive leaf extract (OL), effective against Salmonella enterica , Escherichia coli , Listeria monocytogenes , and Staphylococcus aureus , was added to three different coating formulations (methylcellulose, MC; chitosan, CT; and alginate, ALG) to produce active polylactic acid (PLA) coated films. Evaluation of these coated PLA films revealed significant inhibition of S. aureus growth, particularly with the MC and CT formulations exhibiting the highest inhibition rates (99.7%). The coated films were then tested for food contact compatibility with three food simulants (A: 10% ethanol; B: 3% acetic acid; D2: olive oil), selected to assess their suitability for pre-cut hams and ready-to-eat vegetables in relation to overall migration. However, coated films with active functions exhibited migration values in simulants A and B above legal limits, while promising results were obtained for simulant D2, highlighting the need to deeply investigate these coatings' impact on a real food system. Untargeted metabolomics revealed that the type of coating influenced the selective release of certain phenolic classes based on the food simulant tested. The Oxitest analysis of simulant D2 demonstrated that the MC and ALG-coated PLA films slightly slowed down the oxidation of this food simulant, which is an edible vegetable oil.

Companilactobacillus alimentarius is a facultatively heterofermentative lactic acid bacterium (LAB) that is a significant constituent within the microbiota of various traditional fermented foods exerting several functions in fermentative or ripening processes. This species has been isolated from Spanish fermented sausages, where its frequency of isolation was comparable to those of Latilactobacillus sakei and Latilactobacillus curvatus. Despite to its presence in several niches, ecological information on this species is still scarce and only few publications report information about its safety features (i.e. antibiotic resistance). Since studies on C. alimentarius concern the analysis of a few individual traits regarding this species, a more extensive work on a larger number of isolates from the same matrix have been performed to allow a clearer interpretation of their phenotypic and technological characteristics. Specifically, 14 strains of C. alimentarius isolated from Mediterranean spontaneously fermented sausages, have been screened for their safety and technological characteristics (such as antibiotic resistance, biogenic amine production, inhibiting potential, growth at different temperatures and NaCl concentrations) and with phenotype microarrays with the aim to elucidate their potential role and contribution to sausage fermentation and ripening. In general, a wide variability was observed in relation to the parameters considered. Several of the tested strains were able to produce histamine, tyramine and putrescine while the antibiotic resistance greatly varied according to the strains, with the exception of vancomycin. In addition, C. alimentarius strains showed a relevant potential to grow in conditions of salt and temperature mimicking those found in fermented foods. In particular, the growth at 10 °C and in the presence of salt can explain the presence of C. alimentarius in sausages and its adaptation to fermented meat environment in which low temperature can be applied during ripening. The differentiation of the phenotypic profile reflected the environmental conditions that influenced the isolation source, including those derived by the raw materials. Given the species frequent association with spontaneous fermentations or the ripening microbiota of various products, despite not being intentionally used as starter cultures, the data presented in this study contribute to a deeper comprehension of their role, both advantageous and detrimental, in numerous significant fermented foods., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Paratuberculosis is an enteric disease caused by Mycobacterium avium subs. Paratuberculosis (MAP). Quantifying the load of MAP in faeces samples offers the advantage of determining the stage of infection and planning control measures. Currently, detection of MAP in faecal specimens relies on cultural assays and quantitative PCR (qPCR), but both methods have limitations such as prolonged isolation times for cultural assay and the absence of nucleic acid standards for qPCR. Digital PCR (dPCR) represents an advancement over qPCR as it allows direct quantification of nucleic acid in a sample without the need for a standard curve. The present paper reports about the validation process, following ISO 20395:2019 guidelines, of a F57 digital PCR assay for quantifying MAP cells in faecal samples. Based on our validation, the Limit Of Detection (LOD) corresponds to 7.85 10 4 MAP cells/g, and the Limit Of Quantification (LOQ) to 7.85 10 5 MAP cells, with an efficiency of recovery at LOQ estimated about 4.5%. To assess precision, we evaluated the same faecal sample extracted by two different operators at different times. The standard deviation under repeatability conditions (S Repeatability) and intersession variability conditions (S Intermediate) were calculated, resulting in values of 0.43 and 0.26, respectively. Trueness was determined at LOQ and a value ten times higher, yielding percentages of 3.35% and 5.16%, respectively. Linearity showed a R 2 value of 0.998, indicating strong linear correlation. Measurement uncertainty was 26% in absolute value and 3% on a logarithmic base 10 scale. Overall, the assay exhibits good specificity and robustness. Our validation underlines the good performance of the quantification method and allow the laboratory to provide quantitative results of MAP/cells on faecal samples., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The past decade witnessed the emergence in Shiga toxin-producing Escherichia coli (STEC) infections linked to the consumption of unpasteurized milk and raw milk cheese. The virulence of STEC is primarily attributed to the presence of Shiga toxin genes ( stx1 and stx2 ) carried by Stx-converting bacteriophages, along with the intimin gene eae . Most of the available information pertains to the "Top 7" serotypes associated with STEC infections. The objectives of this study were to characterize and investigate the pathogenicity potential of E. coli UC4224, a STEC O174:H2 strain isolated from semi-hard raw milk cheese and to develop surrogate strains with reduced virulence for use in food-related studies. Complete genome sequence analysis of E. coli UC4224 unveiled the presence of a Stx1a bacteriophage, a Stx2a bacteriophage, the Locus of Adhesion and Autoaggregation (LAA) pathogenicity island, plasmid-encoded virulence genes, and other colonization facilitators. In the Galleria mellonella animal model, E. coli UC4224 demonstrated high pathogenicity potential with an LD 50 of 6 CFU/10 μL. Upon engineering E. coli UC4224 to generate single and double mutant derivatives by inactivating stx1a and/or stx2a genes, the LD 50 increased by approximately 1 Log-dose in the single mutants and 2 Log-doses in the double mutants. However, infectivity was not completely abolished, suggesting the involvement of other virulence factors contributing to the pathogenicity of STEC O174:H2. Considering the possibility of raw milk cheese serving as a reservoir for STEC, cheesemaking model was developed to evaluate the survival of UC4224 and the adequacy of the respective mutants as reduced-virulence surrogates. All tested strains exhibited the ability to survive the curd cooking step at 48°C and multiplied (3.4 Log CFU) in cheese within the subsequent 24 h. These findings indicate that genomic engineering did not exert any unintended effect on the double stx1 - stx2 mutant behaviour, making it as a suitable less-virulent surrogate for conducting studies during food processing., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Milani, Belloso Daza, Cortimiglia, Bassi and Cocconcelli.)

Raw milk and dairy products are usually considered the major sources of Mycobacterium avium subsp. paratuberculosis (MAP) exposure for humans. During the production process of mozzarella cheese, as well as of other pasta-filata cheeses made with pasteurized or raw milk, curd is heated and stretched by addition of hot or boiling water. This step is the critical point for the inactivation of MAP during the production process, but, to our knowledge, no studies have been published about the thermal death time values of MAP in curd. The aim of this study was to determine the inactivation kinetics of MAP in curd used to produce pasta-filata cheese in six independent experiments. The milk was inoculated with a mix of MAP strains (field and registered strains) and, with the aim to simulate the thermal treatment of the curd during the stretching step, samples of 10 g of contaminated curd were vacuum packed and treated separately at six different temperatures from 60°C to 75°C in a water bath. MAP survival was then evaluated by plate count method and inactivation parameters were estimated for determining the thermal resistance of the pathogen directly in the curd. D-values increased from 0.15 min (D 75 -value) to 4.22 min (D 60 -value) and the calculated z-value was 10.2°C. These data aid: (i) to design food thermal process treatments defining acceptance limits of critical control points to ensure safety against MAP; (ii) to predict the time/temperature combinations needed to obtain a certain MAP log reduction during the curd stretching step; (iii) to optimize or validate pasta-filata cheese process., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Barsi, Dalzini, Russo, Cosciani-Cunico, Monastero, Arrigoni, Garbarino, Cortimiglia, Losio and Ricchi.)

The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn 916 -carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn 916 -carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Belloso Daza, Milani, Cortimiglia, Pietta, Bassi and Cocconcelli.)

Antimicrobial resistance (AMR) represents an increasing issue worldwide, spreading not only in humans and farmed animals but also in wildlife. One of the most relevant problems is represented by Extended-Spectrum Beta-Lactamases (ESβLs) producing Escherichia coli because they are the cause of important infections in human. Wild boars ( Sus scrofa ) as a source of ESβLs attracted attention due to their increasing density and their habits that lead them to be at the human-livestock-wildlife interface. The aim of this study was to increase the knowledge about the ESβLs E. coli strains carried by wild boars living in a particularly high-density area of Northern Italy. The analysis of 60 animals allowed to isolate 16 ESβL-producing E. coli strains (prevalence 23.3%), which were characterised from a phenotypical and molecular point of view. The overall analysis revealed that the 16 isolates were all not only ESβL producers but also multidrug resistant and carried different types of plasmid replicons. The genome analysis performed on a subset of isolates confirmed the heterogeneity observed with pulsed-field gel electrophoresis (PFGE) and highlighted the presence of two pandemic sequence types, ST131 and ST10, with different collections of virulence factors. The genomic context of ESβL genes further evidenced that all of them were surrounded by transposons and insertion sequences, suggesting the possibility to exchange AMR genes. Overall, this study shows the worrying dissemination of ESβL-producing E. coli in wild boars in Northern Italy, suggesting the role of these animals as a spreader of AMR and their inclusion in surveillance programmes, to shed light on the "One Health" complex interactions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Mercato, Cortimiglia, Abualsha’ar, Piazza, Marchesini, Milani, Bonardi, Cocconcelli and Migliavacca.)

The thermal stability of four different commercial citrus peel extracts was tested and improved by an encapsulation process with β-cyclodextrins in a spray-dryer. All extracts after the encapsulation process maintained a good antioxidant capacity, with an apparent loss in total phenolic compounds of around 20-25%. In addition, all samples showed good antimicrobial activity (MIC 5-0.625 mg/mL) against Staphylococcus aureus , which was maintained after the encapsulation process (MIC 5-1.25 mg/mL). Based on the antioxidant and antimicrobial activity results, the best-encapsulated citrus extract was selected for incorporation into a polylactic acid/polyhydroxy butyrate (PLA/PHB) film. The latter was then produced on an industrial scale by cast extrusion and was found to be suitable for food contact as it showed overall migration values in different food simulants lower than the legislative limit of 10 mg of non-volatile substances per 1 dm 2 of surface area. The UHPLC-HRMS analysis, performed to evaluate the migration of the active compounds, revealed about 13.41% release in food simulant A and 11.02% in food simulant B. Antimicrobial analysis conducted directly on the film showed a growth inhibition activity towards Escherichia coli and Staphylococcus aureus equal to 30 and 60%, respectively.

Clostridium tyrobutyricum represents the main spoiling agent responsible for late blowing defects (LBD) in hard and semi-hard cheeses. Its spores are resistant to manufacturing procedures and can germinate during the long ripening process, causing the burst of the cheese paste with a consequent undesirable taste. The lower quality of blown cheeses leads to considerable financial losses for the producers. The early identification of spore contaminations in raw milk samples thus assumes a pivotal role in industrial quality control. Herein, we developed a point of care (POC) testing method for the sensitive detection of C. tyrobutyricum in milk samples, combining fast DNA extraction (with no purification steps) with a robust colorimetric loop-mediated isothermal amplification (LAMP) technique. Our approach allows for the sensitive and specific detection of C. tyrobutyricum spores (limit of detection, LoD: ~2 spores/mL), with the advantage of a clear naked-eye visualization of the results and a potential semi-quantitative discrimination of the contamination level. In addition, we demonstrated the feasibility of this strategy using a portable battery-operated device that allowed both DNA extraction and amplification steps, proving its potential for on-site quality control applications without the requirement of sophisticated instrumentation and trained personnel.

Enterococcus lactis and the heterotypic synonym Enterococcus xinjiangensis from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. Enterococcus faecium type strain NCTC 7171 T was used as the reference genome for determining E. lactis and E. faecium to be separate species. However, this taxonomic classification did not consider the diverse lineages of E. faecium , and the double nature of hospital-associated (clade A) and community-associated (clade B) isolates. Here, we investigated the taxonomic relationship among isolates of E. faecium of different origins and E. lactis , using a genome-based approach. Additional to 16S rRNA gene sequence analysis, we estimated the relatedness among strains and species using phylogenomics based on the core pangenome, multilocus sequence typing, the average nucleotide identity and digital DNA-DNA hybridization. Moreover, following the available safety assessment schemes, we evaluated the virulence profile and the ampicillin resistance of E. lactis and E. faecium clade B strains. Our results confirmed the genetic and evolutionary differences between clade A and the intertwined clade B and E. lactis group. We also confirmed the absence in these strains of virulence gene markers IS16, hylEfm and esp and the lack of the PBP5 allelic profile associated with ampicillin resistance. Taken together, our findings support the reassignment of the strains of E. faecium clade B as E. lactis .

Shiga-toxin-producing Escherichia coli (STEC) represents a significant cause of foodborne disease. In the last years, an increasing number of STEC infections associated with the consumption of raw and pasteurized milk cheese have been reported, contributing to raise the public awareness. The aim of this study is to evaluate the main genomic features of STEC strains isolated from a semi-hard raw milk cheese, focusing on their pathogenic potential. The analysis of 75 cheese samples collected during the period between April 2019 and January 2020 led to the isolation of seven strains from four stx -positive enrichment. The genome investigation evidenced the persistence of two serotypes, O174:H2 and O116:H48. All strains carried at least one stx gene and were negative for eae gene. The virulence gene pattern was homogeneous among the serogroup/ST and included adherence factors ( lpfA , iha , ompT , papC , saa , sab , hra , and hes ), enterohemolysin ( ehxA ), serum resistance ( iss , tra ), cytotoxin-encoding genes like epeA and espP , and the Locus of Adhesion and Autoaggregation Pathogenicity Islands (LAA PAIs) typically found in Locus of Enterocyte Effacement (LEE)-negative STEC. Genome plasticity indicators, namely, prophagic sequences carrying stx genes and plasmid replicons, were detected, leading to the possibility to share virulence determinants with other strains. Overall, our work adds new knowledge on STEC monitoring in raw milk dairy products, underlining the fundamental role of whole genome sequencing (WGS) for typing these unknown isolates. Since, up to now, some details about STEC pathogenesis mechanism is lacking, the continuous monitoring in order to protect human health and increase knowledge about STEC genetic features becomes essential., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Cortimiglia, Borney, Bassi and Cocconcelli.)

Lactobacillus helveticus is a thermophilic lactic acid bacterium that is widely employed as a starter culture for manufacturing several Swiss and Italian hard-cooked cheeses. The sequencing of L. helveticus Lh 23, which consists of 2,100,230 bp with a GC content of 36.5%, reveals industrially useful traits and interesting metabolic pathways., (Copyright © 2020 Bertani et al.)

Staphylococcus aureus is one of the major pathogens responsible for intramammary infections in small ruminants, causing severe economic losses in dairy farms. In addition, S. aureus can contaminate milk and dairy products and produce staphylococcal enterotoxins, being responsible for staphylococcal food poisoning. Currently, data on the population structure and the virulence gene patterns of S. aureus strains isolated from goat milk is limited. Therefore, this study aimed at defining Ribosomal Spacer PCR (RS-PCR) genotypes, clonal complexes (CC), spa types, and virulence gene profiles of S. aureus isolated from goat milk samples from Lombardy region of Italy. A total of 295 S. aureus isolates from 65 goat bulk tank milk samples were genotyped by RS-PCR. spa typing and virulence gene patterns of a subgroup of 88 isolates were determined, and MLST was performed on a further subgroup of 39 isolates, representing all the spa types identified during the analysis. This study revealed 7 major genotypic clusters (CLR, CLAA, CLZ, CLAW, CLBW, CLS, and CLI), of which S. aureus CLR (19.8%) was the most common. A total of 26 different spa types were detected, the most prevalent types were t1773 (24%), t5428 (22.7%), and t2678 (12.5%). Overall, 44.3% of all isolates harbored at least one enterotoxin gene. The most prevalent was the combination of sec - sel genes (35.2%). Based on their MLST, isolates were assigned to 14 different CC, with majority grouped as CC133 (24%), CC130 (19.6%), and CC522 (19.6%). The caprine S. aureus population was depicted with a minimum spanning tree and an evolutionary analysis based on spa typing and MLST, respectively. Then, the variability of such strains was compared to that of bovine strains isolated in the same space-time span. Our results confirmed that S. aureus isolates from goats have wide genetic variability and differ from the bovine strains, supporting the idea that S. aureus from small ruminants may constitute a distinct population., (Copyright © 2020 Romanò, Gazzola, Bianchini, Cortimiglia, Maisano, Cremonesi, Graber, Vezzoli and Luini.)

Dairy products can harbor various microorganisms (e.g., Campylobacter spp., Salmonella spp., Listeria monocytogenes , verocytotoxin-producing Escherichia coli ) arising from animal reservoirs, and which can become important sources of foodborne illness. Therefore, early detection of food pathogens is crucial to prevent diseases. We wished to develop an accurate quantitative protocol based on a droplet digital polymerase chain reaction (ddPCR) involving eight individual TaqMan™ reactions to detect simultaneously, without selective enrichment, Listeria spp., L. monocytogenes, Salmonella spp., verocytotoxin-producing E. coli and Campylobacter spp. in cheese. ddPCR (a "third-generation PCR") provides absolute quantification of target DNAs without requirement of a standard curve, which simplifies experimentation and data comparability. The accuracy, specificity and sensitivity of the developed ddPCR system were assessed using purified DNA from 50 reference pathogenic and non-pathogenic strains from international or Italian collections and analyzing soft cheese samples artificially contaminated with serial dilutions (from 4 × 10 6 to 4 × 10 1 CFU/g) of pure cultures from the American Type Culture Collection. Finally, the performance of our ddPCR system was compared by parallel testing with quantitative PCR: it gave higher sensitivity (10 2 CFU/g for the Listeria spp. assay) without the necessity of a standard curve. In conclusion, this is the first ddPCR system developed for simultaneous detection of common foodborne pathogens in cheese using a single set of amplification conditions. As such, it could become a useful strategy for high-throughput screening of microorganisms to evaluate the quality and safety of food products.