• 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.
    • Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

      Zhongyi, Yu; Gunn, Lynda; Brennan, Evan; Reid, Rachael; Wall, Patrick G.; O Gaora, Peadar; Hurley, Daniel; Bolton, Declan; Fanning, Seamus; Department of Agriculture, Food and the Marine, Ireland (Frontiers, 2016-11-10)
      Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT R sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3- like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain.
    • Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

      Yu, Zhongyi; Gunn, Lynda; Brennan, Evan; Reid, Rachael; Wall, Patrick G.; O Gaora, Peadar; Hurley, Daniel; Bolton, Declan; Fanning, Seamus; Department of Agriculture, Food and the Marine (Frontiers, 2016-11-11)
      Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT® sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain.
    • Control of Blown Pack Spoilage in Vacuum Packaged Meat

      Bolton, Declan; Moschonas, Galatios; Sheridan, James J.; Downey, Gerard; National Development Plan (Teagasc, 01/10/2009)
      Blown pack spoilage (BPS) represents a significant commercial loss to Irish meat processors. This research discovered that the organisms causing BPS are ubiquitous in the abattoir environment, making eradication very difficult. The risk of BPS is best managed through a process of regular treatment of plant and equipment with a sporicidal agent such as peroxyacetic acid, good hygiene to minimise carcass contamination and removal of the heat shrinkage stage during vacuum packaging as this activates the spores and reduces the time to spoilage.
    • Control of escherichia coli 0157:H7 in beefburgers

      Bolton, Declan; Byrne, Catriona; Catarame, Terese; Sheridan, James J. (Teagasc, 2001-04)
      The inactivation of E. coli O157:H7 by heating, freezing, pulsed electric field, sodium lactate, lactic acid and citric acid, alone or in combination was investigated. The industrial process for beefburger manufacture did not significantly reduce E.coli O157:H7 numbers regardless of the burger recipe and method of tempering used. Fast freezing of the burgers (to -18°C in 30 minutes as opposed to 36 hours), pulsed electric field, sodium lactate, lactic acid and citric acid, individually and in combination, did not significantly reduce E. coli O157:H7 numbers when applied at different stages throughout the beef burger manufacturing process. Beefburger safety is therefore reliant on proper storage, handling and thermal processing in the domestic or catering kitchen. The lethal effect of thermal processing may be enhanced by the addition of sodium lactate to the burger during mixing. These results are presented and discussed.
    • Controlling Blown Pack Spoilage Using Anti-Microbial Packaging

      Reid, Rachael; Bolton, Declan; Tiuftin, Andrey; Kerry, Joseph P.; Fanning, Seamus; Whyte, Paul (MDPI, 12/08/2017)
      Active (anti-microbial) packaging was prepared using three different formulations; Auranta FV; Inbac-MDA and sodium octanoate at two concentrations (2.5 and 3.5 times their minimum inhibitory concentration (MIC, the lowest concentration that will inhibit the visible growth of the organisms) against Clostridium estertheticum, DSMZ 8809). Inoculated beef samples were packaged using the active packaging and monitored for 100 days storage at 2 °C for blown pack spoilage. The time to the onset of blown pack spoilage was significantly (p < 0.01) increased using Auranta FV and sodium octanoate (caprylic acid sodium salt) at both concentrations. Moreover, sodium octanoate packs had significantly (p < 0.01) delayed blown pack spoilage as compared to Auranta FV. It was therefore concluded that Auranta FV or sodium octanoate, incorporated into the packaging materials used for vacuum packaged beef, would inhibit blown pack spoilage and in the case of the latter, well beyond the 42 days storage period currently required for beef primals
    • Current food safety priorities : report on the European Union risk analysis information network (EU - RAIN)

      Maunsell, Bláithín; Bolton, Declan; Downey, Gerard (Teagasc, 2006-04)
      An estimated 10 to 30% of the population in industrialised countries suffers food-borne illness annually, resulting in an unacceptable social (human suffering) and economic (health care and lost working days) cost. Risk analysis, a proactive preventative approach to food safety, was the focus of the European Union Risk Analysis Information Network (EU-RAIN) concerted action project. Funded by the European Commission, this project commenced in March 2003 and concluded in February 2006.
    • The Development and/or Validation of Novel Intervention Technologies to Assure Meat Food Safety

      Bolton, Declan; Byrne, Brian; Lyng, James G.; Downey, Gerard; Department of Agriculture, Food and the Marine, Ireland; Food Safety Authority of Ireland (Teagasc, 01/02/2007)
      This project was undertaken to fill some of the knowledge gaps in meat food safety from farm to fork. The data provide the scientific basis for a clean sheep policy to reduce the impact of fleece as a source of microbial contamination on ovine carcasses at the beginning of the slaughter process. At the other end of the slaughter-line, a polyurethane sponge swabbing technology was developed for ovine and bovine carcass sampling as required in 2001/471/EC and the new European Commission Hygiene Regulations. At the processing stages, studies were undertaken to determine the most effective media for the recovery and culture of Cl. perfringens cells and spores; the results were then applied to thermal inactivation studies on these bacteria. Thermal resistance data were also obtained for Bacillus cereus and a radio frequency cook for meat products was validated in terms of the destruction of Cl. perfringens and B. cereus cells and spores. Finally, an aerobiology study investigated the effectiveness of a range on measures to prevent air acting as a vector for bacterial dispersion in a meat processing plant.
    • The development and/or validation of novel intervention technologies to assure meat food safety

      Bolton, Declan; Byrne, Brian; Lyng, James G. (Teagasc, 2007-02)
      This project was undertaken to fill some of the knowledge gaps in meat food safety from farm to fork. The data provide the scientific basis for a clean sheep policy to reduce the impact of fleece as a source of microbial contamination on ovine carcasses at the beginning of the slaughter process. At the other end of the slaughter-line, a polyurethane sponge swabbing technology was developed for ovine and bovine carcass sampling as required in 2001/471/EC and the new European Commission Hygiene Regulations. At the processing stages, studies were undertaken to determine the most effective media for the recovery and culture of Cl. perfringens cells and spores; the results were then applied to thermal inactivation studies on these bacteria. Thermal resistance data were also obtained for Bacillus cereus and a radio frequency cook for meat products was validated in terms of the destruction of Cl. perfringens and B. cereus cells and spores. Finally, an aerobiology study investigated the effectiveness of a range on measures to prevent air acting as a vector for bacterial dispersion in a meat processing plant.
    • The effect of antimicrobials on verocytotoxin bacteriophage transduction under bovine rumen fluid and broth conditions

      Nyambe, Sepa; Burgess, Catherine; Whyte, Paul; Bolton, Declan; Department of Agriculture, Food and the Marine, Ireland; 11/F/051 (Teagasc (Agriculture and Food Development Authority), Ireland, 15/11/2017)
      The verocytotoxin genes in verocytotoxigenic Escherichia coli (VTEC) are carried by bacteriophages, incorporated into the bacterial genome (prophage). Antibiotics may promote phage replication and release to infect other cells (transduction), thus leading to the emergence of new VTEC strains. This study investigated transduction of a verocytotoxin2-encoding bacteriophage (3538(vtx2::cat)) under laboratory conditions, including the effect of antibiotic treatments. Luria-Bertani Miller broth and rumen fluid (raw and sterilised by irradiation) were inoculated with the donor (C600φ3538(Δvtx2::cat)) and recipient (E. coli C600::kanamycinR) strains (4 log10 cfu/mL) and incubated at 38°C. Antibiotic treatments (minimal inhibitory and sub-inhibitory concentrations of ampicillin, cefquinome, oxytetracycline and sodium sulfamethazine) were applied after 3 h. Samples were tested for donor, recipient, cell-free phage and transductants at times t = 0, 3, 4, 6, 27 (24 h post-antibiotic treatment) and 51 h. Free phage was detected in the untreated broth and rumen samples, as were the transductants confirmed by polymerase chain reaction. The antibiotic treatments did not significantly (P > 0.01) increase the concentrations of free phage or transductants detected. It was therefore concluded that, under laboratory conditions, the antibiotics tested did not induce bacteriophage lysis, release and infection of new bacterial cells beyond that constitutively found in the phage population.
    • The effect of organic acid and sodium chloride dips on the shelf-life of refrigerated Irish brown crab (Cancer pagurus) meat

      McDermott, A.; Whyte, Paul; Brunton, Nigel; Lyng, L.; Fagan, John; Bolton, Declan; Department of Agriculture, Food and the Marine; 13F529 (Elsevier, 2018-08-18)
      Crab (Cancer pagurus) meat (white and brown) has a short shelf-life. Chemical treatments may inhibit microbial spoilage and extend shelf-life. The effect of 5% organic acids (lactic acid (LA), acetic acid (AA) and citric acid (CA)) and 5% sodium chloride (NaCl) on TVC (mesophiles and psychrophiles), Enterobacteriaceae, Pseudomonas spp. and lactic acid bacteria (LAB) were investigated during storage (2 °C for 12 days). AA was the most effective treatment for white meat, reducing the initial TVCm and TVCp by 1.6 and 1.8 log10 cfu/g, respectively, and extended the shelf life to 8–11.5 days, compared to 5 days for untreated control samples. LA treatment also significantly (P < 0.05) reduced the initial TVC, but the shelf life was only increased by 3 days. CA and NaCl treatments had no significant effect (P > 0.05). A similar pattern was observed for brown meat samples, although the shelf life was increased by a maximum of 1–3 days. The growth of Enterobacteriaceae, Pseudomonas spp. and LAB was significantly (P < 0.05) reduced on AA treated samples only. It was concluded that the shelf-life of crab meat may be extended by up to 3 days using lactic acid and more than doubled using acetic acid.
    • The Effect of Organic Acid, Trisodium Phosphate and Essential Oil Component Immersion Treatments on the Microbiology of Cod (Gadus morhua) during Chilled Storage

      Smyth, Conor; Brunton, Nigel P.; Fogarty, Colin; Bolton, Declan; Department of Agriculture Food and the Marine; 13F458 (MDPI, 2018-12-08)
      Spoilage is a major issue for the seafood sector with the sale and exportation of fish limited by their short shelf-life. The immediate and storage effects of immersion (30 s at 20 °C) with 5% (w/v) citric acid (CA), 5% (v/v) lactic acid (LA), 5% (w/v) capric acid (CP) and 12% trisodium phosphate (TSP) (experiment 1) and essential oil components (EOC) (1% (v/v) citral (CIT), 1% (v/v) carvacrol (CAR), 1% (w/v) thymol (THY) and 1% (v/v) eugenol (EUG)) (experiment 2) on the concentrations of indicator (total viable counts (TVC) (mesophilic and psychrophilic) and total Enterobacteriaceae counts (TEC)), and spoilage organisms (Pseudomonas spp., lactic acid bacteria (LAB), Brochothrix thermosphacta, Photobacterium spp. and hydrogen sulphide producing bacteria (HSPB)) on cod (Gadus morhua) (stored aerobically at 2 °C) was investigated. There was no significant reduction for most treatment-bacteria combinations, with the following exceptions; TSP and TVCm (time t = 6), TSP and TVCp (t = 6), CP and LAB (t = 6, 8 and 10), CP and Br. thermosphacta (t = 4, 6, 8, 10, 14 and 16), TSP and Photobacterium spp. (t = 4), CAR and Br. thermosphacta (t = 6) and CAR and HSPB (t = 3, 6, 9, 12, 15 and 18). Although the majority of treatments did not significantly (P > 0.05) reduce bacterial counts, the limited success with CP and CAR warrants further investigation.
    • Efficacy of ultraviolet light (UV-C) and pulsed light (PL) for the microbiological decontamination of raw salmon (Salmo salar) and food contact surface materials

      Pedrós-Garrido, S.; Condón-Abanto, S.; Clemente, I.; Beltrán, J.A.; Lyng, James G.; Bolton, Declan; Brunton, Nigel; Whyte, Paul; Department of Agriculture, Food and the Marine; 13F458 (Elsevier, 2018-10-03)
      The decontamination effect of two light-based technologies on salmon, polyethylene (PE) and stainless steel (SS) was evaluated. Optimization of treatment conditions for ultraviolet light (UV-C) and pulsed light (PL) was carried out on raw salmon, obtaining inactivation levels of 0.9 and 1.3 log CFU/g respectively. The effects of treatments on several microbial groups present in salmon were then evaluated. For both technologies, Pseudomonas spp. were found to be the most resistant group of microorganisms tested. Three different strains from within this group were isolated and speciated, including a P. fluorescens strain which was selected for subsequent studies. PE and SS surfaces were inoculated with a suspension of the P. fluorescens suspended in a ‘salmon juice’ solution, and treated with UV-C and PL at different doses (mJ/cm2). PE surfaces were effectively decontaminated a low doses for both technologies, with a reduction of >4 log cycles observed. Decontamination of SS was also effective when treated with PL, although at higher doses than for PE. When SS was treated with UV-C, the maximum reduction of P. fluorescens achieved was 2 log cycles, even at the highest dose.
    • Escherichia coli 0157:H7: implications for HACCP on the farm and in the abattoir

      Bolton, Declan; Byrne, Catriona; Sheridan, James J.; Riordan, Denise C.; European Union (Teagasc, 1999-01)
      Experiments were designed to assess the risks associated with Escherichia coli O157:H7 on the farm, through the abattoir and into the butcher shop. Data was also generated for application in model building and the reliability of pathogen models for predicting pathogen growth in different foods was examined.
    • HACCP for Irish beef, pork and lamb slaughter

      Bolton, Declan; Sheridan, James J.; US-Ireland Co-operation Programme in Agriculture Science and Technology; Department of Agriculture, Food and the Marine, Ireland (Teagasc, 2002-02)
      It is generally accepted that HACCP principles should be incorporated into the food safety control systems in meat processing plants to better assure food safety. The objective of this project was to publish detailed HACCP slaughter documents for the Irish beef, pork and lamb processing industries. These would provide the necessary information and detail to facilitate the implementation of HACCP on the slaughter floor (from lairage to chilling) in Irish meat plants. To this end `HACCP for Irish Beef Slaughter' was published in October 2000, `HACCP for Irish Pork Slaughter' in December 2001 and `HACCP for Irish Lamb Slaughter' will be available early in 2002. These are non-generic, detailed documents which provide the scientific basis for establishing critical control points (CCP), critical limits, monitoring and corrective action procedures.
    • Hazard analysis and critical control point (HACCP) and hygiene control auditing in Irish beef abattoirs

      Bolton, Declan; Pearce, Rachel; Tergny, Annabel; Howlett, Brendan (Teagasc, 2007-06)
      This project validated two innovative technologies for use in improving the safety of Irish beef. Online monitoring was developed and successfully tested as a tool for controlling faecal contamination on beef carcasses with the resultant reduction in microbial counts. A novel anti-microbial, LactiSAL®, was also tested and validated for use in the beef industry. Sponge swabbing using a polyurethane sponge was developed and validated for use in carcass testing as required in European Commission Decision 2001/471/EC. The costs of developing and implementing a HACCP system in Irish beef slaughter plants were assessed. Furthermore, a guide to relevant food safety legislation, including the development and auditing of HACCP and prerequisites for beef slaughter (in compliance with 2001/471/EC and the European Commission Hygiene Regulations), was developed and published.
    • Impact of direct and indirect heating systems in broiler units on environmental conditions and flock performance

      Smith, Shaun; Meade, Joseph; Gibbons, James; McGill, Kevina; Bolton, Declan; Whyte, Paul; Department of Agriculture, Food and Marine; 11SF328 (Elsevier, 2016-11-11)
      This study compared the impact of three indirect heating systems to direct gas flame heaters on a selection of flock performance and environmental indicators in commercial broiler units. No statistically significant differences (P≥0.05) were found in flock mortality rates, bird weight, water consumption, stress response, carbon dioxide, ammonia, temperature, relative humidity, litter quality, within-flock Campylobacter levels or mean Campylobacter counts when flock data from any of the three indirect heating systems were compared to flocks reared in houses with direct heating systems. Differences in litter quality were observed between upper and lower litter layers in all houses, regardless of heating type, which may have implications for bird health and welfare. Carbon dioxide concentrations in houses with direct heating systems were significantly higher than those in houses with indirect heating systems during the first 10 days of bird life (P≤0.05). This was due to the increased use of heating systems during this period of the flock cycle. Differences in CO2 concentrations had no effect on flock performance, possibly due to the fact that concentrations did not exceed known safe levels. A statistically significant increase in stress response was observed in birds as a result of partial depopulation (thinning) within houses, irrespective of heating system type used (P≤0.05). Stress associated with thinning may have consequences for bird welfare and food safety. In conclusion, the results of our study suggest that indirect heating systems do not appear to negatively impact on flock performance, stress response, within-flock Campylobacter levels or mean Campylobacter counts and do not appear to significantly alter environmental conditions within broiler houses when compared to houses equipped with direct heating systems. Indirect systems are a viable alternative for heating broiler houses in terms of flock performance, bird welfare and food safety.
    • 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.
    • Irish Domestic Food Safety Knowledge, Practice and Microbiology with Particular Emphasis on Staphylococcus aureus

      Bolton, Declan; Kennedy, Jean; Cowan, Cathal; Safefood (Teagasc, 01/06/2005)
      This study examined consumer food safety knowledge on the island of Ireland. Domestic refrigerators were tested for the presence of a range of pathogenic bacteria. The effect of refrigerated storage on the antibiotic resistance and thermal resistance of S . aureus were also investigated. Irish consumers displayed a considerable lack of knowledge about correct refrigeration temperatures and proper hygiene procedures to prevent crosscontamination in the kitchen. Domestic refrigerators were contaminated with a range of bacterial pathogens including S . aureus (41%), S almonella spp. (7%), E scherichia. coli (6%), L isteria monocytogenes (6%) and Y ersinia enterocolitica (2%).
    • Irish domestic food safety knowledge, practice and microbiology with particular emphasis on staphylococcus aureus

      Bolton, Declan; Kennedy, Jean; Cowan, Cathal (Teagasc, 2005-06)
      This study examined consumer food safety knowledge on the island of Ireland. Domestic refrigerators were tested for the presence of a range of pathogenic bacteria. The effect of refrigerated storage on the antibiotic resistance and thermal resistance of S . aureus were also investigated. Irish consumers displayed a considerable lack of knowledge about correct refrigeration temperatures and proper hygiene procedures to prevent crosscontamination in the kitchen. Domestic refrigerators were contaminated with a range of bacterial pathogens including S . aureus (41%), S almonella spp. (7%), E scherichia. coli (6%), L isteria monocytogenes (6%) and Y ersinia enterocolitica (2%). Viewing Options