The objective of the Food Safety department is to provide the science to underpin a total chain risk based approach to food safety, focusing on microbial and chemical contaminants in the ‘farm to fork’ food chain.

Recent Submissions

  • Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome

    Butler, Mary I.; Bastiaanssen, Thomaz F. S.; Long-Smith, Caitriona; Berding, Kirsten; Morkl, Sabrina; Cusack, Anne-Marie; Strain, Conall; Busca, Kizkitza; Porteous-Allen, Penny; Claesson, Marcus J.; et al. (MDPI AG, 2020-05-19)
    Introduction: The gut microbiota plays a role in gut–brain communication and can influence psychological functioning. Diet is one of the major determinants of gut microbiota composition. The impact of unpasteurised dairy products on the microbiota is unknown. In this observational study, we investigated the effect of a dietary change involving intake of unpasteurised dairy on gut microbiome composition and psychological status in participants undertaking a residential 12-week cookery course on an organic farm. Methods: Twenty-four participants completed the study. The majority of food consumed during their stay originated from the organic farm itself and included unpasteurised milk and dairy products. At the beginning and end of the course, participants provided faecal samples and completed self-report questionnaires on a variety of parameters including mood, anxiety and sleep. Nutrient intake was monitored with a food frequency questionnaire. Gut microbiota analysis was performed with 16S rRNA gene sequencing. Additionally, faecal short chain fatty acids (SCFAs) were measured. Results: Relative abundance of the genus Lactobacillus increased significantly between pre- and post-course time points. This increase was associated with participants intake of unpasteurised milk and dairy products. An increase in the faecal SCFA, valerate, was observed along with an increase in the functional richness of the microbiome profile, as determined by measuring the predictive neuroactive potential using a gut–brain module approach. Conclusions: While concerns in relation to safety need to be considered, intake of unpasteurised milk and dairy products appear to be associated with the growth of the probiotic bacterial genus, Lactobacillus, in the human gut. More research is needed on the effect of dietary changes on gut microbiome composition, in particular in relation to the promotion of bacterial genera, such as Lactobacillus, which are recognised as being beneficial for a range of physical and mental health outcomes.
  • An investigation of the ecological niches and seasonal nature of Clostridium estertheticum and Clostridium gasigenes in the Irish beef farm environment

    Esteves, Eden; Whyte, Paul; Gupta, Tanushree B; Bolton, Declan; Teagasc Walsh Fellowship Programme; 6910NF (Wiley, 2020-07)
    Blown pack spoilage (BPS) of vacuum packaged beef is caused by psychrotolerant and psychrophilic Clostridium species (PPC), primarily Clostridium estertheticum and Clostridium gasigenes. The aim of this study was to investigate the environmental niches and impact of season on these BPS Clostridium spp. on Irish beef farms. On each of 5 different beef farms, faecal (10), soil (5), silage (5), bedding straw (5), drinking water (5), puddle/ditch water (5) and air (5) samples were collected during Spring, Summer, Autumn and Winter and tested for C. estertheticum and C. gasigenes using culture (direct plating and enrichment) and molecular, (conventional PCR and quantitative PCR (qPCR)), based techniques. C. estertheticum and C. gasigenes were detected in all sample types, with qPCR detection rates ranging from 4% to 50% and at concentrations of up to 1.5 log10 cfu g‐1 and 3.5 log10 cfu g‐1, respectively. The impact of season was not clear as the results were mixed depending on the detection method used. It was concluded that BPS causing C. estertheticum and C. gasigenes are widely distributed in the beef farm environment.
  • An investigation of anticoccidial veterinary drugs as emerging organic contaminants in groundwater

    Mooney, D.; Richards, Karl G.; Danaher, Martin; Grant, Jim; Gill, L.; Mellander, Per-Erik; Coxon, C.E.; Teagasc Walsh Scolarship Programme; Science Foundation Ireland; European Union; et al. (Elsevier BV, 2020-12)
    Intensification of the food production system to meet increased global demand for food has led to veterinary pharmaceuticals becoming a critical component in animal husbandry. Anticoccidials are a group of veterinary products used to control coccidiosis in food-producing animals, with primary prophylactic use in poultry production. Excretion in manure and subsequent land-spreading provides a potential pathway to groundwater. Information on the fate and occurrence of these compounds in groundwater is scant, therefore these substances are potential emerging organic contaminants of concern. A study was carried out to investigate the occurrence of anticoccidial compounds in groundwater throughout the Republic of Ireland. Twenty-six anticoccidials (6 ionophores and 20 synthetic anticoccidials) were analysed at 109 sites (63 boreholes and 46 springs) during November and December 2018. Sites were categorised and selected based on the following source and pathway factors: (a) the presence/absence of poultry activity (b) predominant aquifer category and (c) predominant groundwater vulnerability, within the zone of contribution (ZOC) for each site. Seven anticoccidials, including four ionophores (lasalocid, monensin, narasin and salinomycin) and three synthetic anticoccidials (amprolium, diclazuril and nicarbazin), were detected at 24% of sites at concentrations ranging from 1 to 386 ng L−1. Monensin and amprolium were the two most frequently detected compounds, detected at 15% and 7% of sites, respectively. Multivariate statistical analysis has shown that source factors are the most significant drivers of the occurrence of anticoccidials, with no definitive relationships between occurrence and pathway factors. The study found that the detection of anticoccidial compounds is 6.5 times more likely when poultry activity is present within the ZOC of a sampling point, compared to the absence of poultry activity. This work presents the first detections of these contaminants in Irish groundwater and it contributes to broadening our understanding of the environmental occurrence and fate of anticoccidial veterinary products.
  • Conserved redox-dependent DNA binding of ROXY glutaredoxins with TGA transcription factors

    Gutsche, Nora; Holtmannspötter, Michael; Maß, Lucia; O'Donoghue, Martin; Busch, Andrea; Lauri, Andrea; Schubert, Veit; Zachgo, Sabine; Deutsche Forschungsgemeinschaft; SPP 1710 ZA 259/7‐1; et al. (Wiley, 2017-12-14)
    The Arabidopsis thaliana CC‐type glutaredoxin (GRX) ROXY1 and the bZIP TGA transcription factor (TF) PERIANTHIA (PAN) interact in the nucleus and together regulate petal development. The CC‐type GRXs exist exclusively in land plants, and in contrast to the ubiquitously occurring CPYC and CGFS GRX classes, only the CC‐type GRXs expanded strongly during land plant evolution. Phylogenetic analyses show that TGA TFs evolved before the CC‐type GRXs in charophycean algae. MpROXY1/2 and MpTGA were isolated from the liverwort Marchantia polymorpha to analyze regulatory ROXY/TGA interactions in a basal land plant. Homologous and heterologous protein interaction studies demonstrate that nuclear ROXY/TGA interactions are conserved since the occurrence of CC‐type GRXs in bryophytes and mediated by a conserved ROXY C‐terminus. Redox EMSA analyses show a redox‐sensitive binding of MpTGA to the cis‐regulatory as‐1‐like element. Furthermore, we demonstrate that MpTGA binds together with MpROXY1/2 to this motif under reducing conditions, whereas this interaction is not observed under oxidizing conditions. Remarkably, heterologous complementation studies reveal a strongly conserved land plant ROXY activity, suggesting an ancestral role for CC‐type GRXs in modulating the activities of TGA TFs. Super‐resolution microscopy experiments detected a strong colocalization of ROXY1 with the active form of the RNA polymerase II in the nucleus. Together, these data shed new light on the function of ROXYs and TGA TFs and the evolution of redox‐sensitive transcription regulation processes, which likely contributed to adapt land plants to novel terrestrial habitats.
  • Development and validation of a quantitative confirmatory method for 30 β-lactam antibiotics in bovine muscle using liquid chromatography coupled to tandem mass spectrometry

    Di Rocco, Melissa; Moloney, Mary; O’Beirne, T.; Earley, S.; Berendsen, B.; Furey, A.; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Elsevier BV, 2017-06)
    A method was developed for the confirmatory and quantitative analysis of 30 β-lactam antibiotic residues in bovine muscle. The method includes 12 penicillins (amoxicillin, ampicillin, cloxacillin, dicloxacillin, mecillinam, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, ticarcillin), 12 cephalosporins (cefacetrile, cefadroxil, cephalexin, cefalonium, cefazolin, cefoperazone, cefotaxime, cefquinome, cefuroxime, desacetyl cephapirin, desfuroylceftiofur cysteine disulfide, desfuroylceftiofur dimer), five carbapenems (biapenem, doripenem, ertapenem, imipenem, meropenem) and faropenem. Samples were extracted using a simple solvent extraction with acetonitrile:water (80:20, v/v) and C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC–MS/MS) detection. Chromatography was performed on a reversed phase CSH C18 column, using a binary gradient separation comprising of 0.01% formic acid and 0.2 mM ammonium acetate in water (mobile phase A) and 0.01% formic acid in acetonitrile (mobile phase B). The mass spectrometer was operated in the positive electrospray ionisation mode (ESI(+)). Validation was performed following the 2002/657/EC guidelines. Trueness ranged between 69% and 143% and precision ranged between 2.0% and 29.9% under within-laboratory reproducibility conditions. The developed method uses minimal sample preparation and 30 test samples can be analysed by a single analyst in a single day. To the best of our knowledge, this is the first method for carbapenems in foodstuff that does not require derivatisation.
  • Improving the chromatographic selectivity of β-lactam residue analysis in milk using phenyl-column chemistry prior to detection by tandem mass spectrometry

    Di Rocco, Melissa; Moloney, Mary; Haren, Deirdre; Gutierrez, Montserrat; Earley, Seán; Berendsen, Bjorn; Furey, Ambrose; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Springer Science and Business Media LLC, 2020-05-23)
    Analyte isobaric interferences can limit the development of a comprehensive analytical method for the quantitative liquid chromatography-tandem mass spectrometry profiling of an important cohort of veterinary drugs. In this work, a selective chromatographic separation was developed for the analysis of 32 β-lactam antibiotic residues (12 penicillins, 14 cephalosporins, five carbapenems and faropenem) in milk samples. A range of analytical columns with different stationary phases and mobile phases were evaluated for retention and separation of the β-lactam compounds. Results showed that, among the columns tested, only phenyl-hexyl could adequately separate ampicillin from cephalexin and amoxicillin from cefadroxil, which had shown isobaric interferences on a number of stationary phases. Chromatography was performed using a water/acetonitrile binary gradient with formic acid and ammonium acetate. The β-lactam residues were extracted from the milk samples using a water:acetonitrile solution and purified by C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by concentration under nitrogen and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) determination. Analytes were monitored in positive electrospray ionisation mode (ESI(+)). Possible interfering matrix effects were overcome by using 13 internal standards. The method was fully validated according to 2002/657/EC guidelines, showing satisfactory performance characteristics. Under within-laboratory reproducibility conditions, trueness and precision ranged from 91 to 130% and from 1.4 to 38.6%, respectively. Decision limits (CCα) were in the range 2.1–133 μg kg−1. Limits of detection (LODs) and quantitation (LOQs) ranged between 0.0090 and 1.5 μg kg−1 and from 0.030 to 5.0 μg kg−1, respectively.
  • Determination of the presence of pathogens and anthelmintic drugs in raw milk and raw milk cheeses from small scale producers in Ireland

    Lourenco, Antonio; Fraga-Corral, Maria; De Colli, Lorenzo; Moloney, Mary; Danaher, Martin; Jordan, Kieran; Depart of Agriculture, Food and the Marine; 15/F/690 (Elsevier, 2020-04-03)
    This aim of this study was to assess the microbiological and anthelmintic drug residue risks associated with raw milk used for cheesemaking and raw milk cheese, over an 18-month period. Samples of raw milk, milk filters, curd and cheese from nine raw milk artisan cheese producers in the south of Ireland were tested. Numbers of presumptive Bacillus cereus group, Escherichia coli, Salmonella spp., Staphylococcus aureus and Listeria monocytogenes were determined. The determination of anthelmintic drug residues, including benzimidazoles, flukicides, macrocyclic lactone (avermectin and milbemycins), levamisole and morantel was also performed. Neither L. monocytogenes, nor Salmonella spp. were detected in any of the samples tested and no anthelmintic drug residues were detected. Only one of the samples did not conform with regulatory numbers for other bacteria. This survey has shown a good microbiological and residue quality (and low risk) of the raw milk cheese and raw milk used for raw milk cheese produced in Ireland. Moreover, it has shown the importance of frequent assessment of raw milk used for cheesemaking and for raw milk cheese, as it allows the identification of potential problems facilitating resolution of these issues before they cause any public health threat.
  • Bacterial resistance to antibiotic alternatives: a wolf in sheep’s clothing?

    Willing, Benjamin P; Pepin, Deanna M; Marcolla, Camila S; Forgie, Andrew J; Diether, Natalie E; Bourrie, Benjamin C T (Oxford University Press, 2018-04-28)
    Implications • Substantial pressure to reduce antibiotic use has necessitated the development of antibiotic alternatives. However, relatively little consideration has been given to the development of resistance to these alternatives. • Whether we come up with antibiotic alternatives that are bacteriocidal or inhibitory, bacteria will continue to adapt and evolve. • Some antibiotic alternatives support the development of antibiotic resistance necessitating caution. • There are opportunities to optimize antibiotic alternative effectiveness as well as to minimize the development of resistance mechanisms.
  • The effects of sequential heat treatment on microbial reduction and spore inactivation during milk processing

    Li, Fang; Hunt, Karen; Buggy, Aoife K.; Murphy, Kevin; Ho, Quang Tri; O'Callaghan, Tom; Butler, Francis; Jordan, Kieran; Tobin, John; Department of Agriculture, Food and the Marine; et al. (Elsevier BV, 2020-05)
    Sequential heating processes are commonly applied to milk by the dairy industry as part of their microbiological control strategy. Often pasteurisation at 72 °C is followed by a sequential high heat treatment step of up to 125 °C; however, such severe heat treatment can lead to reduced protein quality. Nine temperature combinations (80–90 °C) were evaluated to assess microbial reduction and whey protein nitrogen index values during pilot scale milk processing. A total of 110 bacterial isolates were identified to species level by 16S rDNA sequencing, with Bacillus licheniformis identified as the dominant species. While the experimental treatments did not achieve microbial reductions comparable with the control heating process, the results of this study provide a benchmark for milk processors relative to the effects of sequential heat treatments on milk and their impact on the survival of both thermally resistant microbial populations and thermally labile milk components during processing.
  • Expression, purification and antimicrobial activity of recombinant pediocin PA-1 M31L, a PA-1 derivative with enhanced stability

    Kuniyoshi, Taís Mayumi; O’ Connor, Paula M.; Arbulu, Sara; Mesa-Pereira, Beatriz; Pinheiro de Souza Oliveira, Ricardo; Hill, Collin; Ross, Paul; Cotter, Paul D. (Microbiology Society, 2019-03-01)
    Pediocin, the prototypical class IIa bacteriocin, is an efficient antilisterial molecule. Loss of pediocin PA-1 activity is attributed to methionine oxidation at position 31 and this can be overcome by substituting methionine for leucine (pediocin M31L). The aim of this study was to produce pediocin M31L with enhanced stability by recombinant expression in E. coli cells.
  • A Live Bio-Therapeutic for Mastitis, Containing Lactococcus lactis DPC3147 With Comparable Efficacy to Antibiotic Treatment

    Kitching, Michael; Mathur, Harsh; Flynn, James; Byrne, Noel; Dillon, Pat; Sayers, Riona; Rea, Mary; Hill, Colin; Ross, R. Paul; Enterprise Ireland; et al. (Frontiers Media SA, 2019-09-27)
    Bovine mastitis is an ongoing significant concern in the dairy and agricultural industry resulting in substantial losses in milk production and revenue. Among the predominant etiological agents of bovine mastitis are Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, and Escherichia coli. Currently, the treatment of choice for bovine mastitis involves the use of commercial therapeutic antibiotic formulations such as TerrexineTM, containing both kanamycin and cephalexin. Such antibiotics are regularly administered in more than one dose resulting in the withholding of milk for processing for a number of days. Here, we describe the optimization of a formulation of Lactococcus lactis DPC3147, that produces the two-component bacteriocin lacticin 3147, in a liquid paraffin-based emulsion (formulation hereafter designated ‘live bio-therapeutic’) for the first time and compare it to the commercial antibiotic formulation TerrexineTM, with a view to treating cows with clinical/sub-clinical mastitis. Critically, in a field trial described here, this ‘ready-to-use’ emulsion containing live L. lactis DPC3147 cells exhibited comparable efficacy to TerrexineTM when used to treat mastitic cows. Furthermore, we found that the L. lactis cells within this novel emulsion-based formulation remained viable for up to 5 weeks, when stored at 4, 22, or 37◦C. The relative ease and cost-effective nature of producing this ‘live bio-therapeutic’ formulation, in addition to its enhanced shelf life compared to previous aqueous-based formulations, indicate that this product could be a viable alternative therapeutic option for bovine mastitis. Moreover, the singledose administration of this ‘live bio-therapeutic’ formulation is a further advantage, as it can expedite the return of the milk to the milk pool, in comparison to some commercial antibiotics. Overall, in this field trial, we show that the live bio-therapeutic formulation displayed a 47% cure rate compared to a 50% cure rate for a commercial antibiotic control, with respect to curing cows with clinical/sub-clinical mastitis. The study suggests that a larger field trial to further demonstrate efficacy is warranted.
  • Ultrasound-Assisted Marination: Role of Frequencies and Treatment Time on the Quality of Sodium-Reduced Poultry Meat

    Inguglia, Elena Sofia; Burgess, Catherine; Kerry, Joseph P.; Tiwari, Brijesh K; Teagasc Walsh Fellowship Programme (MDPI AG, 2019-10-11)
    The objective of this study was to evaluate the influence of high-power ultrasound (US) to accelerate marination of chicken breast; the effect of ultrasonic frequencies and marination times were investigated on samples containing full sodium levels (FS) or 25% sodium reduction, either by reducing NaCl (R50) or by its partial substitution with KCl (SR). Chicken breasts were marinated in plastic bags immersed in an ultrasonic bath operating with a frequency of 25, 45 or 130 kHz for 1, 3 or 6 h at a temperature of 2.5 ± 0.5 ◦C. Chicken marinated using US had a significantly higher uptake (p < 0.05) of sodium compared to control samples (no US) marinated for the same amount of time. No significant changes were observed in the quality parameters of sonicated chicken samples compared to controls. However, significant decreases (p < 0.05) in lipid oxidation were observed in SR samples when treated by US. These results suggest the use of ultrasound in the meat processing industry as a novel technology for enhancing marination processes and formulation of reduced sodium meat products.
  • The ability of Listeria monocytogenes to form biofilm on surfaces relevant to the mushroom production environment

    Dygico, Lionel Kenneth; Gahan, Cormac G.M.; Grogan, Helen; Burgess, Catherine; Department of Agriculture, Food and the Marine; 14F881 (Elsevier BV, 2020-03-16)
    Due to its ubiquitous nature, Listeria monocytogenes is a threat to all fresh fruits and vegetables, including mushrooms, which are Ireland's largest horticultural crop. Although fresh cultivated mushrooms (Agaricus bisporus) have not been previously linked with listeriosis outbreaks, the pathogen still poses a threat to the industry, particularly due to its ability to form biofilms. This threat is highlighted by the multiple recalls of mushroom products caused by L. monocytogenes contamination and by previous studies demonstrating that L. monocytogenes is present in the mushroom production environment. In this study, the biofilm formation potential of L. monocytogenes strains isolated from the mushroom production environment was investigated on materials and at temperatures relevant to mushroom production. A preliminary assessment of biofilm formation of 73 mushroom industry isolates was undertaken using a crystal violet assay on polystyrene microtitre plates. The biofilm formation of a subset (n = 7) of these strains was then assessed on twelve different materials, including materials that are representative of the materials commonly found in the mushroom production environments, using the CDC biofilm reactor. Vertical scanning interferometry was used to determine the surface roughness of the chosen materials. All the strains tested using the CDC biofilm reactor were able to form biofilms on the different surfaces tested but material type was found to be a key determining factor on the levels of biofilm formed. Stainless steel, aluminium, rubber, polypropylene and polycarbonate were all able to support biofilm levels in the range of 4–4.9 log10 CFU/cm2, for seven different L. monocytogenes strains. Mushroom industry-specific materials, including growing nets and tarpaulins, were found to support biofilms levels between 4.7 and 6.7 log10 CFU/cm2. Concrete was found to be of concern as it supported 7.7 log10 CFU/cm2 of biofilm for the same strains; however, sealing the concrete resulted in an approximately 2-log reduction in biofilm levels. The surface roughness of the materials varied greatly between the materials (0.7–3.5 log10 Ra) and was found to have a positive correlation with biofilm formation (rs = 0.573) although marginally significant (P = 0.051). The results of this study indicate that L. monocytogenes can readily form biofilms on mushroom industry relevant surfaces, and additionally identifies surfaces of specific concern, where rigorous cleaning and disinfection is required.
  • The response of foodborne pathogens to osmotic and desiccation stresses in the food chain

    Burgess, Catherine; Gianotti, Andrea; Gruzdev, Nadia; Holah, John; Knøchel, Susanne; Lehner, Angelika; Margas, Edyta; Esser, Stephan Schmitz; Sela (Saldinger), Shlomo; Tresse, Odile; et al. (Elsevier BV, 2016-01-02)
    In combination with other strategies, hyperosmolarity and desiccation are frequently used by the food processing industry as a means to prevent bacterial proliferation, and particularly that of foodborne pathogens, in food products. However, it is increasingly observed that bacteria, including human pathogens, encode mechanisms to survive and withstand these stresses. This review provides an overview of the mechanisms employed by Salmonella spp., Shiga toxin producing E. coli, Cronobacter spp., Listeria monocytogenes and Campylobacter spp. to tolerate osmotic and desiccation stresses and identifies gaps in knowledge which need to be addressed to ensure the safety of low water activity and desiccated food products.
  • A new sensitive method for the simultaneous chromatographic separation and tandem mass spectrometry detection of anticoccidials, including highly polar compounds, in environmental waters

    Mooney, D; Coxon, C; Richards, Karl G.; Gill, L.W.; Mellander, Per-Erik; Danaher, Martin; Science Foundation Ireland; European Union; Teagasc Walsh Fellowship Programme; Irish Centre for Research in Applied Geosciences (iCRAG); et al. (Elsevier, 2020-01-10)
    A sensitive and selective method was developed and validated for the determination of 26 anticoccidial compounds (six ionophores and twenty chemical coccidiostats) in surface and groundwater samples at parts-per-quadrillion (pg L−1) to parts-per-trillion (ng L−1) levels by ultra-high performance liquid chromatography with tandem mass spectrometry detection (UHPLC–MS/MS). A range of different analytical columns and mobile phase compositions were evaluated to enhance selectivity and retention of a number of highly polar and basic anticoccidials along with other non-polar coccidiostats. A combined separation, including these problematic polar compounds, was achieved on a phenyl-hexyl column, by binary gradient elution with water/acetonitrile using ammonium formate and formic acid as additives. The anticoccidial residues were extracted from raw, unfiltered, water samples (250 mL) using polymeric divinylbenzene solid phase extraction (SPE) cartridges, with subsequent elution (methanol:acetonitrile:ethyl acetate, 40:40:20, v/v) and concentration prior to determination. The method recovery (at a concentration representative of realistic expected environmental water concentrations based on literature review) ranged from 81% to 105%. The method was successfully validated for 26 anticoccidials, at four concentration levels, in accordance to Commission Decision 2002/657/EC and SANTE/11813/2017 guidelines. Trueness and precision, under within-laboratory reproducibility conditions, ranged from 88% to 111% and 0.9% to 10.3% respectively.
  • Antimicrobial Resistance Determinants Circulating among Thermophilic Campylobacter Isolates Recovered from Broilers in Ireland Over a One-Year Period

    Lynch, Caoimhe T.; Lynch, Helen; Burke, Sarah; Hawkins, Kayleigh; Buttimer, Colin; McCarthy, Conor; Egan, John; Whyte, Paul; Bolton, Declan; Coffey, Aidan; et al. (MDPI AG, 2020-06-08)
    Campylobacteriosis is the leading cause of human bacterial gastroenteritis, very often associated with poultry consumption. Thermophilic Campylobacter (Campylobacter jejuni and Campylobacter coli) isolates (n = 158) recovered from broiler neck skin and caecal contents in Ireland over a one-year period, resistant to at least one of three clinically relevant antimicrobial classes, were screened for resistance determinants. All ciprofloxacin-resistant isolates (n = 99) harboured the C257T nucleotide mutation (conferring the Thr-86-Ile substitution) in conjunction with other synonymous and nonsynonymous mutations, which may have epidemiological value. The A2075G nucleotide mutation and amino acid substitutions in L4 and L22 were detected in all erythromycin-resistant isolates (n = 5). The tetO gene was detected in 100% (n = 119) of tetracycline-resistant isolates and three of which were found to harbour the mosaic tetracycline resistance gene tetO/32/O. Two streptomycin-resistant C. jejuni isolates (isolated from the same flock) harboured ant(6)-Ib, located in a multidrug resistance genomic island, containing aminoglycoside, streptothricin (satA) and tetracycline resistance genes (truncated tetO and mosaic tetO/32/O). The ant(6)-Ie gene was identified in two streptomycin-resistant C. coli isolates. This study highlights the widespread acquisition of antimicrobial resistance determinants among chicken-associated Campylobacter isolates, through horizontal gene transfer or clonal expansion of resistant lineages. The stability of such resistance determinants is compounded by the fluidity of mobile genetic element.
  • The response of foodborne pathogens to osmotic and desiccation stresses in the food chain

    Burgess, Catherine; Gianotti, Andrea; Gruzdev, Nadia; Holah, John; Knøchel, Susanne; Lehner, Angelika; Margas, Edyta; Schmitz Esser, Stephan; Sela (Saldinger), Shlomo; Tresse, Odile; et al. (Elsevier, 2016-01-02)
    In combination with other strategies, hyperosmolarity and desiccation are frequently used by the food processing industry as a means to prevent bacterial proliferation, and particularly that of foodborne pathogens, in food products. However, it is increasingly observed that bacteria, including human pathogens, encode mechanisms to survive and withstand these stresses. This review provides an overview of the mechanisms employed by Salmonella spp., Shiga toxin producing E. coli, Cronobacter spp., Listeria monocytogenes and Campylobacter spp. to tolerate osmotic and desiccation stresses and identifies gaps in knowledge which need to be addressed to ensure the safety of low water activity and desiccated food products.
  • Deltamethrin Residues in Milk and Cheese of Lactating Goats (Capra hircus)

    Marrone, Raffaele; Ramkumar, Abilasha; Smaldone, Giorgio; Rufrano, Domenico; Chirollo, Claudia; Veneziano, Vincenzo; Danaher, Martin; Anastasio, Aniello; University of Naples Federico II (MDPI AG, 2019-01-31)
    The distribution of pyrethroid insecticide deltamethrin (DLM) in goat milk and cheese (caciotta) following pour-on administration at the sheep dosage (DLMS-10 mL/60 kg body weight) and double dosage (DLMD-20 mL/60 kg body weight) was studied. DLM concentrations were measured in milk collected from study animals (No.14) before treatment and at 2, 4, 8, 12, 16, 24, 30, 36, 48, 56, until 168 h (7 days) post treatment and in caciotta cheese at 12 and 24 h post treatment. At both dosages, the maximum level of DLM residues in goat milk and cheese was below the maximum residue limit (MRL) of 20 μg kg−1 established for bovine milk (EU No 37/2010) at all time points. However, in terms of public health, higher DLM residues in cheese show that further specific studies should be performed on double dosage efficacy and pharmacokinetic and pharmacodynamics properties of ectoparasites in lactating goats.
  • Investigation of the Causes of Shigatoxigenic Escherichia coli PCR Positive and Culture Negative Samples

    Macori, Guerrino; McCarthy, Siobhán C.; Burgess, Catherine; Fanning, Séamus; Duffy, Geraldine; Department of Agriculture, Food and the Marine; 15/F/629 (MDPI AG, 2020-04-18)
    Molecular methods may reveal the presence of pathogens in samples through the detection of specific target gene(s) associated with microorganisms, but often, the subsequent cultural isolation of the pathogen is not possible. This discrepancy may be related to low concentration of the cells, presence of dead cells, competitive microflora, injured cells and cells in a viable but non-culturable state, free DNA and the presence of free bacteriophages which can carry the target gene causing the PCR-positive/culture-negative results. Shiga-toxigenic Escherichia coli (STEC) was used as a model for studying this phenomenon, based on the phage-encoded cytotoxins genes (Stx family) as the detection target in samples through real-time qPCR. Stx phages can be integrated in the STEC chromosome or can be isolated as free particles in the environment. In this study, a combination of PCR with culturing was used for investigating the presence of the stx1 and stx2 genes in 155 ovine recto-anal junction swab samples (method (a)-PCR). Samples which were PCR-positive and culture-negative were subjected to additional analyses including detection of dead STEC cells (method (b)-PCR-PMA dye assay), presence of Stx phages (method (c)-plaque assays) and inducible integrated phages (method (d)-phage induction). Method (a) showed that even though 121 samples gave a PCR-positive result (78%), only 68 samples yielded a culturable isolate (43.9%). Among the 53 (34.2%) PCR-positive/culture-negative samples, 21 (39.6%) samples were shown to have STEC dead cells only, eight (15.1%) had a combination of dead cells and inducible stx phage, while two samples (3.8%) had a combination of dead cells, inducible phage and free stx phage, and a further two samples had Stx1 free phages only (3.8%). It was thus possible to reduce the samples with no explanation to 20 (37.7% of 53 samples), representing a further step towards an improved understanding of the STEC PCR-positive/culture-negative phenomenon.
  • Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation

    Ageorges, Valentin; Monteiro, Ricardo; Leroy, Sabine; Burgess, Catherine; Pizza, Mariagrazia; Chaucheyras-durand, Frédérique; Desvaux, Mickaël; INRAE; European Union; RA-FEDER-Bpifrance; et al. (Oxford University Press (OUP), 2020-04-02)
    Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.

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