Globally, large quantities of animal waste and human sewage sludge are generated annually. Their application as soil amendments can enhance soil quality and support a circular economy. However, these wastes may harbour pathogenic bacteria, posing contamination risks to soil and water and potential transmission to animals and humans. This study investigated the survival of five bacterial pathogens during six months of storage in five types of organic waste and following their subsequent application to soil. During storage, T90 values ranged as follows: Salmonella Typhimurium (2.3-17.7 days), Campylobacter jejuni (0 to 23.9 days), Escherichia coli O157:H7 (4.3 to 57.8 days), and Listeria monocytogenes (1.9 to 170.4 days). In soil, T90 values were S. Typhimurium (4.2 to 17.4 days), C. jejuni (4.8 to 26.8 days), E. coli O157:H7 (4.3 to 52.9 days), and L. monocytogenes (2 to 83.7 days). Clostridium sporogenes remained stable throughout both experiments, preventing T90 calculation. Contrary to our initial hypothesis that soil microbiota would accelerate pathogen decline, T90 values were higher during storage in 11 cases and higher in soil in nine scenarios. These findings highlight the need for pre-treatment strategies for animal waste and biosolids before land spreading to consistently mitigate risks of pathogen transmission and environmental contamination.

This study identified and investigated the relative abundance of bacterial and fungal (predominantly yeast) species in the milk kefir grains, during a typical fermentation (25°C for 48 h) and subsequent chilled storage (4°C for up to 30d) using Nanopore sequencing (16S and ITS amplicon). Challenge studies were also undertaken to examine the behaviour of Listeria monocytogenes, Salmonella Senftenberg, Escherichia coli O157:H7, Staphylococcus aureus as well as non-toxigenic mesophilic and psychrophilic Clostridium spp. (Clostridium sporogenes and Clostridium gasigenes, respectively). Lactobacillus and Lactococcus were the predominant bacterial genera with relative abundance of 91% and 2% in milk kefir grains, 32% and 63.7% after 24 h of the fermentation, 87% and 2% after 48 h, respectively. Other bacteria detected included Lentilactobacillus, Leuconostoc, Acetobacter, Asaia and Entomobacter. The most abundant fungal genus in the milk kefir grains was the yeast, Brettanomyces (90%), consisting solely of the species Brettanomyces anomalus, which remained dominant at 24 h (80.7%), 14d (71.7%) and 21d (75.6%). Zygotorulaspora florentina was most abundant immediately after adding the grains to the milk (42.8%) and after 7d (33.9%). Other significant yeast genera detected included Kazachstania (mainly K. unispora) and Grigorovia (mainly G. humatica). In the challenge studies, the L. monocytogenes population increased by 1.3 log10 cfu ml−1 after 8 h, remained static until 32 h, decreased by 2.9 log10 cfu ml−1 (48 h) with the residual population of approximately 0.6 log10 cfu ml−1 being maintained during chilled storage. S. Senftenberg and E. coli O157:H7 also increased by approximately 1.3 and 2.8 log10 cfu ml−1 after 8 h and 24 h, respectively. The former were not detectable after 48 h while the E. coli O157:H7 population had decreased by approximately 3 log10 cfu ml−1 leaving a sub-population of approximately 0.5 log10 cfu ml−1 that was still detectable up to 14 days. In contrast, S. aureus growth was limited and these bacteria were not detected at 48 h, while C. sporogenes and C. gasigenes populations were stable at 1.8–2.1 log10 cfu ml−1 and 1.6–2.4 log10 cfu ml−1, respectively, throughout the kefir fermentation and during chilled storage. It was concluded that the dominant bacterial and fungal species in the milk kefir grains and product were Lactobacillus kefiranofaciens and Brettanomyces anomalus, respectively, although other bacteria and yeasts were also present. Despite the production of lactic acid with rapid acidification, bacterial pathogens survived suggesting the safety of these products is reliant on pasteurisation of the milk, good hygiene practices throughout the process and efficient chilled storage of the final product.

This study investigated the potential growth of Clostridioides difficile RT078 and RT126 in brain heart infusion (BHI) broth (without supplements) and in beef, chicken, cottage cheese and spinach incubated at 25°C and 37°C. Cells were enumerated on BHI agar with selective C. difficile supplements including cefoxitin, d-cycloserine and sodium taurocholate (BHIST). Growth was obtained for all ribotype-temperature combinations in BHI. Significantly higher counts, as compared to the initial concentration, were also obtained in chicken for both ribotypes at 37°C but not at 25°C. The counts achieved were 6.0 log10 cfu g-1 for RT078 and 5.8 log10 cfu g-1 for RT126, both after 4 days. Growth was not observed in beef, cottage cheese, or spinach. To the best of our knowledge this is the first time growth of C. difficile has been reported on chicken meat.

Clostridioides difficile (C. difficile), once considered a predominantly nosocomial pathogen, is increasingly implicated in community-acquired infections (CA-CDIs). This study investigates the prevalence, ribotypes, and antimicrobial susceptibility of C. difficile in Irish pork products and abattoirs, with a focus on the potential public health implications. A total of 180 retail pork products and 150 pig carcase swabs from three abattoirs were examined, alongside 30 environmental lairage samples. The C. difficile isolates were characterised through ribotyping and tested in terms of antimicrobial susceptibility. No C. difficile was isolated from the retail pork, while the carcase swabs yielded a low recovery rate (0.66%). However, the lairage areas were contaminated with C. difficile (33%), and six different ribotypes were identified, including the clinically relevant RT078. The ribotypes exhibited susceptibility to the antibiotics used to treat C. difficile infection (CDI) (fidaxomicin, vancomycin, and metronidazole) but showed resistance to tetracycline (9%) and ciprofloxacin (100%). These findings align with the international findings on antimicrobial resistance in C. difficile and suggest that strict EU food safety standards could mitigate retail pork contamination risks. Nevertheless, the environmental exposure during slaughtering and handling processes presents potential transmission risks for workers.

Kefir is an increasingly popular dairy- or sugar-based fermented food product. The aim of our study was to investigate the bacterial and fungal communities in 28 retail kefirs including 21 milk kefirs, 3 thick kefir yogurts, and 4 water kefir products. Full-length amplicon nanopore sequencing of both 16S rRNA genes (for bacteria) and intergenic spacer genes (for fungi) was undertaken. The diversity within and between groups was analyzed (α- and β-diversity) and linear discriminant analysis effect size analysis was undertaken to identify biomarkers that differentially characterize the microbial communities associated with different kefir types. The pH, lactic acid concentration, total viable counts (TVC), lactic acid bacteria (LAB), total coliform counts (TCC), and yeast counts were also investigated. The main bacterial genera (and species) were Lactococcus (cremoris) and Streptococcus (thermophilus), and other bacteria such as Lactobacillus (delbrueckii) and Lentilactobacillus (kefiri) were also detected. The fungal populations were mainly composed of Brettanomyces (anomalus), Zygotorulaspora (florentina) and Kazachstania (unispora), but with many different fungal genera/species detected. The pH ranged from 3.1 to 4.7 with a mean of 4.2 ± 0.07 and the lactic acid content ranged from 0.1 to 9 g/L with a mean of 5.6 ± 0.53 g/L. In milk kefirs the TVC, LAB, TCC, and yeast counts ranged from 3.1 to 9.1, 3.4 to 9.0, not detected (ND) to 2 and ND to 6.5 log10 cfu/mL or cfu/g, respectively. The corresponding counts in water kefirs were 4.1 to 7.3 (TVC), 4.1 to 7.0 (LAB), ND to 1.1 (TCC), and 3.9 to 7.0 (yeast) log10 cfu/mL or cfu/g, respectively. It was concluded that, although the 28 retail kefirs analyzed had a rich diversity of bacteria and fungi, the bacteriome was dominated by bacteria belonging to the Lactococcus and Streptococcus genera and the main bacterial species were Lactococcus cremoris, Streptococcus thermophiles, Streptococcus suis, Lactobacillus delbrueckii, and Streptococcus sp. HSISS1. The fungal microbiome was dominated by Zygotorulaspora, and the most abundant fungal species included Zygotorulaspora florentina, Brettanomyces anomalus, and Kazachstania unispora. To the best of our knowledge, this is the first study in Ireland to use full-length nanopore sequencing to characterize both bacterial and fungal communities in retail kefirs.

Aim This study aimed to investigate the bacteriology of cold smoked salmon (CSS), specifically changes in the bacterial quality (total viable count and total Enterobacteriaceae count), the concentration of spoilage bacteria (lactic acid bacteria, hydrogen sulphide producing bacteria and Pseudomonas spp.) and Listeria monocytogenes during salting, washing, smoking, maturation, packaging and chilled storage. Methods and results In-plant and laboratory based studies were undertaken. The salt concentration, pH and aw of the commercial product were 3.8% (w/w), 5.9% and 0.95%, respectively while those of the laboratory prepared CSS were 1.1%, 6.2%, and 0.94%. Although the CSS preparation process enhanced microbial quality, as determined by significant (P < 0.05) reductions in indicator and spoilage bacterial counts, L. monocytogenes was unaffected and all bacteria showed significant (P < 0.05) growth during chilled storage of the final product. Conclusions The microbial quality and safety of CSS is reliant on using uncontaminated fillets, good hygiene practices and ensuring that the shelf life does not afford L. monocytogenes sufficient time to exceed the 100 cfu g(-1) maximum allowed in current EU legislation (EC 2073/2005).

Modern requirements for ‘green label’ meat products have led to the design of novel antimicrobial innovations which prioritise quality, safety and longevity. Plasma-functionalised water (PFW), ultraviolet light and natural antimicrobial compositions have been investigated and optimised for control of foodborne pathogens like Campylobacter jejuni and Salmonella enterica serovar Typhimurium. However, given the adaptive mechanisms present in bacteria under external stresses, it is imperative to understand the effect that sublethal treatment may have on the bacterial transcriptome. In this study, Salmonella Typhimurium and C. jejuni were treated with sublethal doses of ultraviolet light, a citrus juice/essential oil marinade, and ‘spark’ or ‘glow’ cold plasma generation system-produced PFW. Immediately after treatment, cells were lysed and RNA was extracted and purified. mRNA was converted to cDNA by reverse transcription-PCR and sequenced by an Illumina MiSeq® system. Sequences were filtered and analysed using the Tuxedo workflow. Sublethal treatment of Campylobacter jejuni and Salmonella Typhimurium led to increased immediate cellular and metabolic activity, as well as diversification in protein and metabolic functioning. There was further expression of pathogenesis and virulence-associated traits associated with spark PFW and marinade treatment of Salmonella Typhimurium . However, similar concerns were not raised with glow PFW or UV-treated samples. This study provides science-based evidence of the efficacy of multi-hurdle antimicrobial system using green-label marinades and PFW or UV to inactivate pathogens without upregulating virulence traits in surviving cells. This study will inform policymakers and food industry stakeholders and reinforces the need to incorporate in-line novel technologies to ensure consumer safety. Key points • Salmonella and C. jejuni showed increased cell activity in immediate response to stress. • Virulence genes showed increased expression when treated with natural antimicrobials and sPFW. • Reduced immediate transcriptomic response to gPFW and UV treatment indicates lower risk.

This study investigated the combined effect of Ultraviolet (UV) light-emitting diode (LED) technology treatment with refrigerated storage of chicken breast meat over 7 days on Campylobacter jejuni, Salmonella enterica serovar Typhimurium, total viable counts (TVC) and total Enterobacteriaceae counts (TEC). An optimised UV-LED treatment at 280 nm for 6 min decreased inoculated S. Typhimurium and C. jejuni populations by 0.6-0.64 log CFU/g, and TVC and TEC population by 1-1.2 log CFU/g in chicken samples. During a 7-day storage at 4 °C, a 0.73 log reduction in C. jejuni was achieved compared with non-treated samples. Moreover, the UV-LED effectiveness to reduce TVC and TEC during refrigerated storage was compared with a conventional UV lamp and a similar efficiency was observed. The impact of UV-LED and UV lamp devices on the microbial community composition of chicken meat during storage was further examined using 16 S rRNA gene amplicon sequencing. Although similar bacterial reductions were observed for both technologies, the microbial communities were impacted differently. Treatment with the UV conventional lamp increased the proportion of Brochothrix spp. In meat samples, whilst Photobacterium spp. Levels were reduced.

The increased detection of clinical cases of Clostridioides difficile coupled with the persistence of clostridial spores at various stages along the food chain suggest that this pathogen may be foodborne. This study examined C. difficile (ribotypes 078 and 126) spore viability in chicken breast, beef steak, spinach leaves and cottage cheese during refrigerated (4 °C) and frozen (-20 °C) storage with and without a subsequent sous vide mild cooking (60 °C, 1 h). Spore inactivation at 80 °C in phosphate buffer solution, beef and chicken were also investigated to provide D80°C values and determine if PBS was a suitable model system for real food matrices. There was no decrease in spore concentration after chilled or frozen storage and/or sous vide cooking at 60 °C. Non-log-linear thermal inactivation was observed for both C. difficile ribotypes at 80 °C in phosphate buffer solution (PBS), beef and chicken. The predicted PBS D80°C values of 5.72±[2.90, 8.55] min and 7.50±[6.61, 8.39] min for RT078 and RT126, respectively, were in agreement with the food matrices D80°C values of 5.65 min (95% CI range from 4.29 to 8.89 min) for RT078 and 7.35 min (95% CI range from 6.81 to 7.01 min) for RT126. It was concluded that C. difficile spores survive chilled and frozen storage and mild cooking at 60 °C but may be inactivated at 80 °C. Moreover thermal inactivation in PBS was representative of that observed in real food matrices (beef and chicken).

Clostridioides difficile is a human pathogen that is ubiquitous in soil. Despite increasing infection rates and evidence of foodborne transmission, there is limited data on prevalence in soil or which factors influence persistence. The aim of this study was to investigate the prevalence of these bacteria in soil from three different spinach fields and to examine the chemical composition (carbon, organic carbon, nitrogen, organic matter, minerals and pH) and microbiota to gain insight into the factors that may promote/inhibit C. difficile. The overall C. difficile prevalence (10%) was lower than expected (based on international studies) and a significantly (P < 0.05) higher prevalence was obtained in Field 3 (20%) as compared to Fields 1 and 2 (5% each). Analysis of the soil suggested that the pH as well as organic matter, calcium and phosphorus content directly and indirectly (via the microbiota) influenced the prevalence of C. difficile in adjacent fields, where other factors (eg. climate) are similar. Although further studies are required to validate our findings, the data provides the first step in developing potential soil based control strategies.

Introduction: The presence of meat-borne pathogens entering the home remains a concern for consumers, despite advances made in improving antimicrobial interventions and systems within the processing line. Naturally antibacterial food ingredients including citrus juice and essential oils have been proven to inhibit the proliferation of microbial growth with varying success.Aims: This study aims to investigate the antimicrobial and sensory effects of mixtures of essential oils, fruit juices and herbs at established Minimum Inhibitory Concentrations (MICs) for their biopreservative effect on general microbiota of chicken and against chicken challenged with selected pathogenic/surrogate microorganisms.Materials and methods: Three marinade compositions were designed for use on chicken meat; lemon juice, thyme oil and black pepper (M1), lime juice, lemongrass oil and chilli paste (M2), and olive oil, oregano oil, basil oil and garlic paste (M3). These marinades were assessed for antibacterial effects against Salmonella enterica, Campylobacter jejuni and Listeria innocua on marinaded chicken drumsticks stored in aerobic conditions at 4 degrees C. Consumer tasting sessions were also conducted with a small focus group using selected final marinades.Results: M1 and M2 were effective at significantly reducing initial pathogen carriage from 6 Log CFU/g to 2 Log CFU/g on refrigerated chicken meat as well as increasing the shelf-life of the product during cold-storage from 2 days to 7 days. However, consumer studies indicate that the flavours these marinades impart to treated products can be strong.Conclusion: These findings indicate that these designed marinades have shown excellent potential to improve food safety as well as shelf-life for the consumer, particularly in settings where food safety is often compromised such as barbecuing or in care settings. However, further recipe optimisation is required to make these marinades acceptable to consumers.

The bactericidal properties of chemically patterned lithium niobate substrates under a super-bandgap UV light source is established. UV irradiation of lithium niobate surfaces inoculated with bacteria leads to antimicrobial activity compared to a glass substrate under similar conditions, as determined by surface enhanced Raman spectroscopy and corroborated with a fluorescence-based live/dead assay. This finding may expand the possible biomedical applications of lithium niobate.

Meat processing facilities play a vital role in the establishment of the end-product microbiota, from control steps implemented to control pathogens to adulterant exposure to the establishment of the product spoilage microbiota. Incidents of contamination can involve exposure to the nascent microbiome of the processing environment with possible consequences for product safety and quality. This study sought to assess the fluctuations in selected pre- and postchill sites during the processing day in one small- and one large-scale Irish poultry processor using culture-based and 16S rRNA gene amplicon sequencing. Culture-based studies show that bacterial abundance did not significantly change within bacterial groups on sampled sites during the processing day in either the small or large poultry processor. This was reinforced by 16S sequence analysis of samples, which showed variation in the microbiome by the processing site, but no significant (P = 0.05) time-based alterations were consistently observed within processors. However, spoilage-related microbes did show variations in abundance, particularly in postchill sites. Pathogenic taxa tended to be present at very low concentrations in both processors, with findings raising concerns over the consistent presence of ESKAPE taxa, Listeria monocytogenes, and Escherichia coli in many locations within processing sites in both processors, particularly after the primary antimicrobial steps of washing and chilling. These findings demonstrate the influence of processing on the quality and safety of meat products and underpin the need for further antibacterial steps within modern poultry processing.

The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic (T) (20 mg trimethoprim and 100 mg sulfamethoxazole per ml in the drinking water for 3 days) and the other was left untreated (UT). The GIT contents of 51 treated and untreated birds were aseptically removed from the upper (U), middle (M) and lower (L) sections. These were pooled in triplicate (n = 17 per section per flock), the DNA extracted and purified, 16S amplicon metagenomic sequencing performed and the resultant data analysed using a range of bioinformatics software. There were significant differences in the microbiota of the upper, middle and lower GIT, and treatment with the antibiotic significantly affected the microbiota in each of these sections. This study provides new data on broiler GIT microbiota and suggests that GIT location is a more important determinant of the constituent bacterial flora rather than the use or otherwise of antimicrobial treatments, at least when applied early in the production cycle.

The present study compared the impact of two UV light devices: conventional UV lamp and UV-LED on the colour, pH, lipid and protein oxidation of fresh chicken breast meat aerobically stored at 4 °C for 10 days. Lipid oxidation was the most impacted quality attribute in UV lamp treated meat, unlike UV-LED that showed no effect compared to non-treated meat. Slight changes were observed in colour, pH and protein oxidation of chicken samples subjected to UV lamp and UV-LED. To evaluate these changes from a consumer perspective, the different treatment samples were stored at 4 °C for 3 days and colour likeness, odour likeness and overall appearance were assessed by consumer sensory analysis. However, alterations in quality parameters of chicken meat caused by UV light did not decrease overall acceptance in the sensory analysis. UV-LED was the preferred chicken meat by the participants, even compared to non-treated meat.

The aim of this study was to characterize C. difficile isolates from the farm, abattoir, and retail outlets in Ireland in terms of ribotype and antibiotic resistance (vancomycin, erythromycin, metronidazole, moxifloxacin, clindamycin, and rifampicin) using PCR and E-test methods, respectively. The most common ribotype in all stages of the food chain (including retail foods) was 078 and a variant (RT078/4). Less commonly reported (014/0, 002/1, 049, and 205) and novel (RT530, 547, and 683) ribotypes were also detected, but at lower frequencies. Approximately 72% (26/36 tested) of the isolates tested were resistant to at least one antibiotic, with the majority of these (65%; 17/26) displaying a multi-drug (three to five antibiotics) resistant phenotype. It was concluded that ribotype 078, a hypervirulent strain commonly associated with C. difficile infection (CDI) in Ireland, was the most frequent ribotype along the food chain, resistance to clinically important antibiotics was common in C. difficile food chain isolates, and there was no relationship between ribotype and antibiotic resistance profile.

Campylobacter jejuni remains a high priority in public health worldwide. Ultraviolet light emitting-diode technology (UV-LED) is currently being explored to reduce Campylobacter levels in foods. However, challenges such as differences in species and strain susceptibilities, effects of repeated UV-treatments on the bacterial genome and the potential to promote antimicrobial cross-protection or induce biofilm formation have arisen. We investigated the susceptibility of eight C. jejuni clinical and farm isolates to UV-LED exposure. UV light at 280 nm induced different inactivation kinetics among strains, of which three showed reductions greater than 1.62 log CFU/mL, while one strain was particularly resistant to UV light with a maximum reduction of 0.39 log CFU/mL. However, inactivation was reduced by 0.46-1.03 log CFU/mL in these three strains and increased to 1.20 log CFU/mL in the resistant isolate after two repeated-UV cycles. Genomic changes related to UV light exposure were analysed using WGS. C. jejuni strains with altered phenotypic responses following UV exposure were also found to have changes in biofilm formation and susceptibility to ethanol and surface cleaners.

Background: Different strategies have been developed over the years to improve the safety of foods without compromising on their quality. Ultraviolet (UV) light has shown potential to meet these expectations. However, due to environmental and safety concerns regarding the use of UV mercury lamps, UV-light emitting diode (LED) devices have emerged more recently, which may be more suited to applications in the food industry. Thus, further evaluation of UV-LED technology is required.Scope and approach: In this review, challenges involving the application of UV-LED technology as a disinfection strategy in the food chain are described. Stress-related mechanisms induced by UV light exposure in microorganisms and their potential consequences are reviewed. Moreover, other future challenges associated with the inactivation of foodborne pathogens and spoilage microorganisms are considered, together with the impact of the application of UV-LED technology on the quality of food.Key findings and conclusions: UV-LEDs have been shown to inactivate a wide range of foodborne pathogens and spoilage microorganisms. However, there are limited studies assessing the effectiveness of UV-LED on products to enhance food safety. Additionally, further studies are required to explore the impact of sublethal exposure to UV LEDs and the potential consequences of UV-LED exposure in different microorganisms at various wavelengths. Furthermore, UV-LEDs can negatively affect some physicochemical attributes of food. Thus, more attention should be paid to the underlying mechanism of quality changes induced by UV-LEDs.

Chicken meat is the most popularly consumed meat worldwide, with free-range and ethically produced meat a growing market among consumers. However, poultry is frequently contaminated with spoilage microbes and zoonotic pathogens which impact the shelf-life and safety of the raw product, constituting a health risk to consumers. The free-range broiler microbiota is subject to various influences during rearing such as direct exposure to the external environment and wildlife which are not experienced during conventional rearing practices. Using culture-based microbiology approaches, this study aimed to determine whether there is a detectable difference in the microbiota from conventional and free-range broilers from selected Irish processing plants. This was done through analysis of the microbiological status of bone-in chicken thighs over the duration of the meat shelf-life. It was found that the shelf-life of these products was 10 days from arrival in the laboratory, with no statistically significant difference (P > 0.05) evident between free-range and conventionally raised chicken meat. A significant difference, however, was established in the presence of pathogenesis-associated genera in different meat processors. These results reinforce past findings which indicate that the processing environment and storage during shelf-life are key determinants of the microflora of chicken products reaching the consumer.