• Antibiotic resistance in foodborne pathogens

      Duffy, Geraldine; Walsh, Ciara (Teagasc, 2005-02)
      Wide-spread antibiotic resistance among bacterial pathogens is now a serious public health issue and multi-antibiotic resistance has been reported in many foodborne pathogens including Salmonella and E. coli.
    • Automated detection and characterisation of foodborne pathogens

      Duffy, Geraldine; O'Hanlon, Karen; Catarame, Terese; Smyth, Davida S.; McCann, Máiréad (Teagasc, 2007-06)
      This study focused on the development of molecular tools for the rapid detection and characterisation of food-borne pathogens including Verocytotoxigenic Escherichia coli (VTEC) (serotypes O157, O26 and O111) and Salmonella spp. The study involved the development of enrichment systems and the identification of unique genetic targets in these pathogens which could be amplified and detected by Real Time Polymerase Chain Reaction (PCR).
    • Comparative effect of different cooking methods on the physicochemical and sensory characteristics of high pressure processed marinated pork chops

      O'Neill, Ciara M.; Cruz-Romero, Malco C.; Duffy, Geraldine; Kerry, J. P.; Department of Agriculture, Food and the Marine; 11/F/031 (Elsevier, 2019-03-13)
      The objective of this study was to assess the effect of griddle and steam cooking on the physicochemical and sensory characteristics of high pressure processed (HPP) piri-piri marinated pork chops (MPC). Raw MPC that were HPP at 400 MPa had higher (P < 0.05) marinade absorption compared to untreated samples. After cooking, griddled MPC were significantly (P < 0.05) darker, less red, less yellow, tougher and had higher cook loss compared to steam cooked samples. The appearance of the griddled MPC was preferred while the texture, tenderness, juiciness and overall sensory acceptability (OSA) were preferred in steam cooked MPC. The increased marinade absorption in MPC that were HPP modified the fatty acid composition resulting in increased (P < 0.05) levels of oleic acid (C18:1c). Steam cooked MPC had a lower (P < 0.05) n-6: n-3 PUFA ratio and were preferred by the sensory panel compared to griddled MPC. Overall, from the cooking methods assessed steam cooking was the best cooking method for untreated and MPC that were HPP.
    • Comparative effect of different cooking methods on the physicochemical and sensory characteristics of high pressure processed marinated pork chops

      O'Neill, Ciara M.; Cruz-Romero, Malco C.; Duffy, Geraldine; Kerry, Joseph P.; Department of Agriculture, Fisheries & Food; 11/F/031 (Elsevier, 2019-03-13)
      The objective of this study was to assess the effect of griddle and steam cooking on the physicochemical and sensory characteristics of high pressure processed (HPP) piri-piri marinated pork chops (MPC). Raw MPC that were HPP at 400 MPa had higher (P < 0.05) marinade absorption compared to untreated samples. After cooking, griddled MPC were significantly (P < 0.05) darker, less red, less yellow, tougher and had higher cook loss compared to steam cooked samples. The appearance of the griddled MPC was preferred while the texture, tenderness, juiciness and overall sensory acceptability (OSA) were preferred in steam cooked MPC. The increased marinade absorption in MPC that were HPP modified the fatty acid composition resulting in increased (P < 0.05) levels of oleic acid (C18:1c). Steam cooked MPC had a lower (P < 0.05) n-6: n-3 PUFA ratio and were preferred by the sensory panel compared to griddled MPC. Overall, from the cooking methods assessed steam cooking was the best cooking method for untreated and MPC that were HPP. Industrial relevance: Processed meat manufacturers are constantly looking for new ways to increase yield, safety and shelf life of meat products. While high pressure processing (HPP) of raw meat has been shown to increase the safety and shelf life of these products; however, negative effects on the physicochemical characteristics of raw meat products have been reported. For example, HPP of raw meat products causes a whitening effect which may negatively affect consumers' acceptance of these products. In this study, we used a novel approach (a combination of HPP, marinade and a mix of organic acids Inbac™) which showed great potential not only for enhancing the yield of marinated pork chops but also enhancement of the sensory properties, safety and shelf life and particularly the piri-piri marinade masked the discoloration of raw pork meat caused by HPP. This study also provides consumers, retailers and caterers with information on how to best prepare HPP meat products and showed that steam cooked HPP marinated pork chops had the best physicochemical and sensory characteristics compared to griddled marinated pork chops.
    • Control and detection of food-borne pathogens

      Duffy, Geraldine; Cloak, Orla; Sheridan, James J.; Department of Agriculture, Food and the Marine, Ireland (Teagasc, Ballsbridge, Dublin 4, 1998-08)
      The objective of this study was to develop rapid methods for the detection of bacteria from food.
    • Development of a critical control step for E.coli 0157:H7 in pepperoni

      Duffy, Geraldine; Riordan, Denise C.; Sheridan, James J.; US-Ireland Co-operation Programme in Agriculture Science and Technology (Teagasc, 1999-10)
      Verocytotoxin producing Escherichia coli (VTEC) and particularly strains of serogroup O157, have emerged as food poisoning pathogens which can cause a severe and potentially fatal illness. The symptoms of VTEC infection include haemorrhagic colitis with bloody diarrhoea and severe abdominal pain. The infection may lead to renal failure as a result of haemolytic uraemic syndrome. Because of the severity of the illness and the low infectious dose, this pathogen is classed as a serious food safety issue. It is recommended by the United States Department of Agriculture that the production process for ready to eat foods such as fermented meats (pepperoni, salami etc.) should be capable of addressing a worst case scenario ie. the production process should be able to yield a log105.0cfu /g (105 cfu/g) reduction in numbers of E. coli O157:H7 on the raw meat. The aim of this study was to develop an industrially viable critical control step(s) which could be implemented into the pepperoni production process.
    • Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples.

      O'Regan, Edel; McCabe, Evonne; Burgess, Catherine; McGuinness, Sheila; Barry, Thomas; Duffy, Geraldine; Whyte, Paul; Fanning, Seamus; Department of Agriculture, Food and the Marine, Ireland (Biomed Central, 21/09/2008)
      Background: A real-time multiplex PCR assay was developed for the detection of multiple Salmonella serotypes in chicken samples. Poultry-associated serotypes detected in the assay include Enteritidis, Gallinarum, Typhimurium, Kentucky and Dublin. The traditional cultural method according to EN ISO 6579:2002 for the detection of Salmonella in food was performed in parallel. The real-time PCR based method comprised a pre-enrichment step in Buffered Peptone Water (BPW) overnight, followed by a shortened selective enrichment in Rappaport Vasilliadis Soya Broth (RVS) for 6 hours and subsequent DNA extraction. Results: The real-time multiplex PCR assay and traditional cultural method showed 100% inclusivity and 100% exclusivity on all strains tested. The real-time multiplex PCR assay was as sensitive as the traditional cultural method in detecting Salmonella in artificially contaminated chicken samples and correctly identified the serotype. Artificially contaminated chicken samples resulted in a detection limit of between 1 and 10 CFU per 25 g sample for both methods. A total of sixty-three naturally contaminated chicken samples were investigated by both methods and relative accuracy, relative sensitivity and relative specificity of the real-time PCR method were determined to be 89, 94 and 87%, respectively. Thirty cultures blind tested were correctly identified by the real-time multiplex PCR method. Conclusion: Real-time PCR methodology can contribute to meet the need for rapid identification and detection methods in food testing laboratories.
    • Emerging Technologies for Aerial Decontamination of Food Storage Environments to Eliminate Microbial Cross-Contamination

      Oliveira, Márcia; Tiwari, Brijesh K; Duffy, Geraldine (MDPI AG, 2020-11-30)
      Air is recognized as an important source of microbial contamination in food production facilities and has the potential to contaminate the food product causing food safety and spoilage issues for the food industry. Potential for aerial microbial contamination of food can be a particular issue during storage in cold rooms when the food is not packaged and is exposed to contaminated air over a prolonged period. Thus, there are potential benefits for the food industry for an aerial decontamination in cold storage facilities. In this paper, aerial decontamination approaches are reviewed and challenges encountered for their applications are discussed. It is considered that current systems may not be completely e ective and environmentally friendly, therefore, it is of great significance to consider the development of nonresidual and verified decontamination technologies for the food industry and, in particular, for the cold storage rooms.
    • A European study on animal food & biomedical aspects of E.coli 0157:H7

      Duffy, Geraldine; Garvey, Patricia; Sheridan, James J.; European Union; CT98-3935 (Teagasc, 2002-02)
      Verocytotoxin producing Escherichia coli (VTEC) and, in particular, strains of serogroup O157, have emerged as significant pathogens causing a range of severe and potentially fatal illnesses. The European Union has recognised the threat posed by E coli O157:H7 and the need to devise control strategies based on an understanding of VTEC pathogenicity, transmission, survival and growth. It acknowledges the importance of informing farmers, veterinarians, food producers and health authorities so that each of these groups can act appropriately to reduce the overall hazards posed by these organisms. To contribute to the development and dissemination of effective control strategies, the European Commission funded this Concerted Action Project 1
    • Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

      Ojha, K. Shikha; Burgess, Catherine; Duffy, Geraldine; Kerry, Joseph P.; Tiwari, Brijesh K; Teagasc Walsh Fellowship Programme (PLOS, 2018-01-25)
      The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores “sonoporation”. Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.
    • Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei

      Ojha, K. Shikha; Burgess, Catherine; Duffy, Geraldine; Kerry, Joseph P.; Tiwari, Brijesh K; Teagasc Walsh Fellowship Programme (Public Library of Science (PLoS), 2018-01-25)
      The lethal effects of soundwaves on a range of microorganisms have been known for almost a century whereas, the use of ultrasound to promote or control their activity is much more recent. Moreover, the fundamental molecular mechanism influencing the behaviour of microorganisms subjected to ultrasonic waves is not well established. In this study, we investigated the influence of ultrasonic frequencies of 20, 45, 130 and 950 kHz on growth kinetics of Lactobacillus sakei. A significant increase in the growth rate of L. sakei was observed following ultrasound treatment at 20 kHz despite the treatment yielding a significant reduction of ca. 3 log cfu/mL in cells count. Scanning electron microscopy showed that ultrasound caused significant changes on the cell surface of L. sakei culture with the formation of pores “sonoporation”. Phenotypic microarrays showed that all ultrasound treated L. sakei after exposure to various carbon, nitrogen, phosphorus and sulphur sources had significant variations in nutrient utilisation. Integration of this phenotypic data with the genome of L. sakei revealed that various metabolic pathways were being influenced by the ultrasound treatments. Results presented in this study showed that the physiological response of L. sakei in response to US is frequency dependent and that it can influence metabolic pathways. Hence, ultrasound treatments can be employed to modulate microbial activity for specialised applications.
    • 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.
    • Longitudinal Study of Two Irish Dairy Herds: Low Numbers of Shiga Toxin-Producing Escherichia coli O157 and O26 Super-Shedders Identified

      Murphy, Brenda P.; McCabe, Evonne; Murphy, Mary; Buckley, James F.; Crowley, Dan; Fanning, Seamus; Duffy, Geraldine; Department of Agriculture, Food and the Marine, Ireland; 11/F/051 (Frontiers, 2016-11-18)
      A 12-month longitudinal study was undertaken on two dairy herds to ascertain the Shiga-toxin producing Escherichia coli (STEC) O157 and O26 shedding status of the animals and its impact (if any) on raw milk. Cattle are a recognized reservoir for these organisms with associated public health and environmental implications. Animals shedding E. coli O157 at >10,000 CFU/g of feces have been deemed super-shedders. There is a gap in the knowledge regarding super-shedding of other STEC serogroups. A cohort of 40 lactating cows from herds previously identified as positive for STEC in a national surveillance project were sampled every second month between August, 2013 and July, 2014. Metadata on any potential super-shedders was documented including, e.g., age of the animal, number of lactations and days in lactation, nutritional condition, somatic cell count and content of protein in milk to assess if any were associated with risk factors for super-shedding. Recto-anal mucosal swabs (RAMS), raw milk, milk filters, and water samples were procured for each herd. The swabs were examined for E. coli O157 and O26 using a quantitative real time PCR method. Counts (CFU swab-1) were obtained from a standard calibration curve that related real-time PCR cycle threshold (Ct) values against the initial concentration of O157 or O26 in the samples. Results from Farm A: 305 animals were analyzed; 15 E. coli O157 (5%) were recovered, 13 were denoted STEC encoding either stx1 and/or stx2 virulence genes and 5 (2%) STEC O26 were recovered. One super-shedder was identified shedding STEC O26 (stx1&2). Farm B: 224 animals were analyzed; eight E. coli O157 (3.5%) were recovered (seven were STEC) and 9 (4%) STEC O26 were recovered. Three super-shedders were identified, one was shedding STEC O157 (stx2) and two STEC O26 (stx2). Three encoded the adhering and effacement gene (eae) and one isolate additionally encoded the haemolysin gene (hlyA). All four super-shedders were only super-shedding once during the 1-year sampling period. The results of this study show, low numbers of super-shedders in the herds examined, with high numbers of low and medium shedding. Although four super-shedding animals were identified, no STEC O157 or O26 were recovered from any of the raw milk, milk filter, or water samples. The authors conclude that this study highlights the need for further surveillance to assess the potential for environmental contamination and food chain security.
    • Microevolution of antimicrobial resistance and biofilm formation of Salmonella Typhimurium during persistence on pig farms

      Tassinari, Eleonora; Duffy, Geraldine; Bawn, Matt; Burgess, Catherine; McCabe, Evonne M.; Lawlor, Peadar G.; Gardiner, Gillian; Kingsley, Robert A.; BBSRC Institute Strategic Programme Microbes in the Food Chain; Teagasc Walsh Fellowship Programme; et al. (Springer Nature, 2019-06-20)
      Salmonella Typhimurium and its monophasic variant S. 4,[5],12:i:- are the dominant serotypes associated with pigs in many countries. We investigated their population structure on nine farms using whole genome sequencing, and their genotypic and phenotypic variation. The population structure revealed the presence of phylogenetically distinct clades consisting of closely related clones of S. Typhimurium or S. 4,[5],12:i:- on each pig farm, that persisted between production cycles. All the S. 4,[5],12:i:- strains carried the Salmonella genomic island-4 (SGI-4), which confers resistance to heavy metals, and half of the strains contained the mTmV prophage, harbouring the sopE virulence gene. Most clonal groups were highly drug resistant due to the presence of multiple antimicrobial resistance (AMR) genes, and two clades exhibited evidence of recent on-farm plasmid-mediated acquisition of additional AMR genes, including an IncHI2 plasmid. Biofilm formation was highly variable but had a strong phylogenetic signature. Strains capable of forming biofilm with the greatest biomass were from the S. 4,[5],12:i:- and S. Typhimurium DT104 clades, the two dominant pandemic clones found over the last 25 years. On-farm microevolution resulted in enhanced biofilm formation in subsequent production cycle.
    • A nationwide surveillance study on E.coli 0157:H7 and enterobacteriaceae in Irish minced beef products

      Duffy, Geraldine; Cagney, Claire; Crowley, Helen; Sheridan, James J.; Food Safety Authority of Ireland (Teagasc, 2003-04)
      A surveillance study on prevalence and numbers of E . coli O157: H7 in minced beef (unpackaged or packaged) and beefburgers (frozen, fresh and unpackaged or packaged) was carried out over a period of 12 months in the Republic of Ireland. A total of 1533 products were tested with approximately 15 products collected from each of the 26 counties every 3 months. Mince and beefburgers were collected from both supermarkets and butcher shop outlets. A standard analysis was conducted by sample enrichment, IMS extraction and plating onto SMAC agar with confirmation by PCR. The results showed that 43 retail beef products (2.8 %) contained E .coli O157:H7. The number of E .coli O157: H7 in 21 of these samples ranged from log100.51 - 4.03 cfu g-1 ( i.e. 3 to 10,700 bacteria per gram) while in the remaining 22 the pathogen was detectable by enrichment only. There was a seasonal effect observed with 33 of 43 positive samples detected in January (n = 8), April /May(n=20) and August (n=5) and the remaining 10 positive samples detected over the other 8 months. Of the beef products testing positive, 32 were purchased from supermarkets and 11 from butcher shops. E .coli O157:H7 was recovered from 2.8% (13 / 457) of fresh packaged mince and from 1.88 % (3 / 160) of fresh unpackaged burgers purchased from butcher shops. Of the 43 isolates recovered, 41 contained the virulence genes v t1, v t2, E aeA and H lyA while the remaining 2 isolates contained only one of the vtproducing genes (v t1or v t2).
    • A quantitative risk assessment of E.coli 0157:H7 in Irish minced beef

      Duffy, Geraldine; O'Brien, Stephen; Carney, Eimear; Butler, Francis; Cummins, Enda; Nally, Padraig; Mahon, Denise; Henchion, Maeve; Cowan, Cathal (Teagasc, 2005-02)
      A national quantitative risk assessment was undertaken for minced beef in the Republic of Ireland. The objective was to estimate the probability of E. coli O157:H7 infection from consumption of Irish beef and to investigate the parts of the beef chain contributing most to the risk posed by this pathogen.The quantitative risk assessment was broken into 3 main modules: 1) production of boxed beef trimmings; 2) processing of trimmings and burger formation and 3) retail/domestic consumption phase. Key points in each module (beef hide, beef trimmings and beef products at retail) were validated using data derived from microbiology sampling at beef abattoirs, supermarkets and butchers’ shops in Ireland.
    • Recovery and identification of emerging campylobacteraceae from food

      Duffy, Geraldine; Cagney, Claire; Lynch, Orla (Teagasc, 2007-02)
      The family Campylobacteraceae includes 23 different species of Campylobacter and Arcobacter.To date, clinical and epidemiological interest has focused almost exclusively on just two of these species, C. jejuni and C. coli. Current routine examination methods for both clinical and food samples look exclusively for these two species. Recent clinical research indicates that some of the other, previously ignored Campylobacter species may be linked to human infection. The focus of this research was to develop a routine procedure which would allow recovery of all 23 species of Campylobacteraceae from food samples.
    • Recovery and identification of emerging Campylobacteraceae from food

      Duffy, Geraldine; Cagney, Claire; Lynch, Orla; Downey, Gerard (Teagasc, 01/02/2007)
      The family Campylobacteraceae includes 23 different species of Campylobacter and Arcobacter.To date, clinical and epidemiological interest has focused almost exclusively on just two of these species, C. jejuni and C. coli. Current routine examination methods for both clinical and food samples look exclusively for these two species. Recent clinical research indicates that some of the other, previously ignored Campylobacter species may be linked to human infection. The focus of this research was to develop a routine procedure which would allow recovery of all 23 species of Campylobacteraceae from food samples.
    • Routine diagnostic tests for food-borne pathogens

      Duffy, Geraldine; Kilbride, Brendan; Fitzmaurice, Justine; Sheridan, James J. (Teagasc, 2001-01)
      Rapid techniques were developed and applied to the determination of total viable bacteria and to the detection of food borne pathogens (Listeria monocytogenes, Salmonella, Campylobacter jejuni and E. coli O157:H7). The method developed for total viable counts is based on membrane filtration and fluorescent staining and the technique can be performed and a result obtained within 20 min. The results correlate well with the standard plate count and the technique is now being implemented in Irish food factories.
    • A study of cryptosporidium parvum in beef

      Duffy, Geraldine; McEvoy, John M.; Moriarty, Elaine M.; Sheridan, James J.; European Union; QLK1 CT 1999 00775 (Teagasc, 2003-07)
      There is increasing concern that foods, particularly those of animal origin, may play a role in the transmission of C ryptosporidium parvum to humans. Studies were undertaken to examine the risk posed by C . parvum in the beef chain.