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

  • Determination of Listeria monocytogenes numbers at less than 10 cfu/g

    Hunt, K.; Vacelet, M.; Jordan, Kieran; Department of Agriculture, Food and the Marine; Dairy Processing Technology Centre; 11/F/008; TC 2014 0016. (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-06-09)
    Listeria monocytogenes is a foodborne pathogen that causes a relatively rare foodborne disease called listeriosis, with a high mortality rate of 20%-30% and an undefined dose response. Current European Union regulations permit up to 100 colony-forming units (cfu)/g in food at the end of its shelf life, where the food has been shown not to support the growth of this pathogenic bacterium. Therefore, enumeration of L. monocytogenes at low numbers in food is important. The objective of this study was to reduce the detection limit of L. monocytogenes in food by a factor of 10. The International Organisation for Standardisation (ISO) 11290-2 method for enumeration of L. monocytogenes in food recommends spreading 0.1 mL of a 1:10 dilution of the food on the surface of an agar plate (detection limit 100 cfu/g), or 1.0 mL spread in equal parts on the surface of three agar plates (detection limit: 10 cfu/g). The pour-plate method (using 1 or 10 mL of an appropriate dilution) was compared to the spread-plate method using the ISO-approved chromogenic medium Agar Listeria according to Ottaviani and Agosti (ALOA). Using the pour-plate method, the colony morphology and halo formation were similar to the spread-plate method from pure cultures and inoculated foods. Using the pour-plate method in a 140 mm Petri dish, 10 mL of a 1:10 dilution of food allowed determination of numbers as low as 1 cfu/g. Applying this method, L. monocytogenes in naturally contaminated food samples were enumerated at numbers as low as 1-9 cfu/g.
  • The effect of antimicrobials on verocytotoxin bacteriophage transduction under bovine rumen fluid and broth conditions

    Nyambe, Sepa; Burgess, Catherine; Whyte, P.; Bolton, Declan; Department of Agriculture, Food and the Marine; 11/F/051 (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-11-15)
    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.
  • A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

    CaoYu; Fanning, Seamus; Proos, Sinead; Jordan, Kieran; Srikumar, Shabarinath; Department of Agriculture, Food and the Marine; SMART-PIF; 13/F/423 (Frontiers, 2017)
    The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
  • Controlling Blown Pack Spoilage Using Anti-Microbial Packaging

    Reid, Rachael; Bolton, Declan; Tiuftin, Andrey; Kerry, Joe P.; Fanning, Seamus; Whyte, Paul (MDPI, 2017-08-12)
    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
  • Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

    Zhongyi, Yu; Gunn, Lynda; Brennan, Evan; Reid, Rachel; Wall, Patrick G.; O'Gaora, Peadar; Hurley, Daniel; Bolton, Declan; Fanning, Seamus (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.
  • 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 (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.
  • Survival characteristics of monophasic Salmonella Typhimurium 4,[5],12:i:- strains derived from pig feed ingredients and compound feed

    Burns, Ann Marie; Duffy, Geraldine; Walsh, Des; Tiwari, Brijish K.; Grant, Jim; Lawlor, Peadar G; Gardiner, Gillian E. (Elsevier, 2015-12-09)
    The presence of Salmonella in animal feed or feed ingredients at the feed mill or on-farm is a cause for concern, as it can be transmitted to food-producing animals and subsequently to humans. The objective of this study was to determine the survival characteristics of five feed ingredient- and feed-derived monophasic Salmonella Typhimurium 4,[5],12:i:- strains. The first part of the study investigated thermal inactivation using an immersed heating coil apparatus. A Weibull model provided a good fit, with low RMSE values (0.04–0.43) and high R2 values (0.93–0.99) obtained. There was considerable inter-strain variation in heat resistance, with D-values ranging from 397.83 to 689 s at 55 °C, 11.35–260.95 s at 60 °C and 1.12 to 6.81 at 65 °C. Likewise, z-values ranged from 2.95 to 5.44 °C. One strain demonstrated a significantly higher thermal tolerance, even though it had been isolated from a meal feed. However, overall the strains investigated do not appear to be that much more heat resistant than Salmonella previously studied. The second part of this study involved assessing the ability of the five Salmonella strains to survive during storage over a 28-day period in pelleted weaner pig feed treated with 0.3% sodium butyrate. While a mean reduction in the Salmonella count of 0.79 log10 CFU was seen in the treated feed during the storage period, a reduction (albeit only 0.49 log10 CFU) was also observed in the control feed. Although there was no overall effect of treatment, sodium butyrate resulted in reductions in Salmonella counts of 0.75 and 0.22 log10 CFU at days 14 and 24 of feed storage, respectively but at the end of the 28-day storage period counts were 0.25 log10 CFU higher in the treated feed. Therefore, the sodium butyrate used appears unsuitable as an agent for feed treatment perhaps due to the protective coating on the particular feed additive used. Overall, the results of this study enhance knowledge about the behaviour and survival characteristics of monophasic S. Typhimurium 4,[5],12:i:- strains in animal feed and may assist the feed industry and pig producers in implementing effective intervention strategies for their control.
  • Listeria monocytogenes in Milk Products

    Jordan, Kieran; Hunt, Karen; Dalmasso, Marion (Springer International Publishing, 2016-04-13)
    Milk and milk products are frequently identified as vectors for transmission of Listeria monocytogenes. Milk can be contaminated at farm level either by indirect external contamination from the farm environment or less frequently by direct contamination of the milk from infection in the animal. Pasteurisation of milk will kill L. monocytogenes, but post-pasteurisation contamination, consumption of unpasteurised milk and manufacture of unpasteurised milk products can lead to milk being the cause of outbreaks of listeriosis. Therefore, there is a concern that L. monocytogenes in milk could lead to a public health risk. To protect against this risk, there is a need for awareness surrounding the issues, hygienic practices to reduce the risk and adequate sampling and analysis to verify that the risk is controlled. This review will highlight the issues surrounding L. monocytogenes in milk and milk products, including possible control measures. It will therefore create awareness about L. monocytogenes, contributing to protection of public health.
  • A note on challenge trials to determine the growth of Listeria monocytogenes on mushrooms (Agaricus bisporus)

    Leong, Dara; Alvarez-Ordonez, Avelino; Jordan, Kieran (Teagasc (Agriculture and Food Development Authority), Ireland, 2015-12-30)
    In the EU, food is considered safe with regard to Listeria monocytogenes if the number of micro-organisms does not exceed 100 colony forming units (cfu)/g throughout its shelf-life. Therefore, it is important to determine if a food supports growth of L. monocytogenes. Guidelines for conducting challenge tests for growth assessment of L. monocytogenes on foods were published by the European Union Reference Laboratory (EURL) in 2014. The aim of this study was to use these guidelines to determine if refrigerated, fresh, whole, closed-cap, prepackaged mushrooms (Agaricus bisporus) support the growth of L. monocytogenes. Three batches of mushrooms were artificially inoculated at approximately 100 cfu/g with a three-strain mix of L. monocytogenes and incubated for 2 days at 8°C followed by 4 days at 12°C. L. monocytogenes numbers were determined (in triplicate for each batch) on days 0, 2 and 6. Water activity, pH and total bacterial counts were also determined. There was no increase in the number of L. monocytogenes above the threshold of 0.5 log cfu/g in any of the replicates. In 8 of 9 replicates, the numbers decreased indicating that A. bisporus do not support the growth of L. monocytogenes. As the EU regulations allow < 100 cfu/g if the food cannot support growth of L. monocytogenes, the significance of this study is that mushrooms with < 100 cfu/g may be within the regulations and therefore, quantitative rather than qualitative determination may be required.
  • Irish Domestic Food Safety Knowledge, Practice and Microbiology with Particular Emphasis on Staphylococcus aureus

    Bolton, Declan J.; Kennedy, Jean; Cowan, Cathal (Teagasc, 2005-06-01)
    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%).
  • A Risk Assessment and Hazard Analysis and Critical Control Point (HACCP) Study for the Irish Catering Industry

    Bolton, Declan J.; Meally, Aisling; Downey, Gerard (Teagasc, 2007-02-01)
    This report provides details of a food safety knowledge survey, a microbiological survey, a chilled temperature survey and an audit conducted in 200 restaurants throughout the island of Ireland. The results suggest a low incidence of several bacterial pathogens (including Salmonella enterica) and identify areas in which food safety knowledge, procedures and practices should be improved. Salmonella enterica isolates were characterised and the results suggested distinct pockets of different serotypes. Growth curves for L. monocytogenes isolates suggest considerably reduced shelf-life for a variety of foods. For example, lettuce should not be stored at room temperature or the shelf-life is reduced from 6.5 days (chilled storage) to 3.3 days.The predicted shelf-life for fresh milk was 4.5 days (chilled storage). Chlorine (sodium hypochlorite, 5 ppm), 1-monolauroyl-rac-glycerol and a laurate ester (ester-glucoside laurate) were also tested for application as vegetable decontaminating agents in restaurant kitchens. The report concludes with recommendations for improved food safety and hygiene in Irish restaurants.
  • The Development and/or Validation of Novel Intervention Technologies to Assure Meat Food Safety

    Bolton, Declan J.; Byrne, Brian; Lyng, James; Downey, Gerard (Teagasc, 2007-02-01)
    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.
  • Determining the Prevalence and Seasonality of Fasciola hepatica in Pasture-based Dairy herds in Ireland using a Bulk Tank Milk ELISA

    Bloemhoff, Yris; Forbes, Andrew; Danaher, Martin; Good, Barbara; Morgan, Eric; Mulcahy, Grace; Sekiya, Mary; Sayers, Riona (Biomed Central, 2015-07-09)
    Background Fasciola hepatica is a helminth parasite of global importance in livestock, with major economic impact. However information on F. hepatica infections in Irish pasture-based dairy herds is limited. Therefore this study was conducted in order to determine the prevalence, seasonality and management factors associated with F. hepatica. A total of 319 Irish dairy herds were selected for this study. Bulk tank milk (BTM) samples were collected from 290 dairy farms on a quarter year basis, while from a further 29 dairy farms BTM samples were collected on a monthly basis to provide a more detailed pattern of F. hepatica exposure in Irish herds. BTM samples were analysed using a commercially available F. hepatica antibody detection ELISA. Furthermore, within-herd prevalence of F. hepatica was assessed in a subset of these 29 herds (n = 17); both individual serum samples and bulk tank milk samples were collected. Results A within-herd prevalence of ≤ 50 % was found for herds with negative bulk tank milk samples. The mean prevalence of the 290 study herds was 75.4 % (Range 52 %–75.1 %), with the highest prevalence being observed in November (75.1 %). The seasonal pattern of F. hepatica shows elevated antibodies as the grazing season progressed, reaching a peak in January. A significant association was found between F. hepatica and age at first calving. Conclusion This study demonstrates that F. hepatica is present in a large proportion of Irish dairy herds and provides a basis on which control practices, particularly in adult dairy cows, can be reviewed.
  • Tracking of Salmonella through the Pork Slaughter Process

    Prendergast, Deirdre M.; Duggan, Sharon J.; Duffy, Geraldine; Downey, Gerard (Teagasc, 2009-10-01)
    To help address the problem of salmonellosis in the Republic of Ireland (RoI), a national Salmonella control programme was introduced in 1997 with a view to reducing the prevalence of Salmonella in pigs on the farm and on pig carcasses. The primary objective of this present study was to determine the correlation between the Salmonella serological and bacteriological status of pigs presented for slaughter and the Salmonella status of pork cuts following slaughter, dressing and chilling. Two additional studies investigated the prevalence and numbers of Salmonella spp. in the boning halls of four commercial pork abattoirs and at retail level in butcher shops and supermarkets in the RoI. The results indicated that categorisation of pig herds on the basis of a historical serological test for Salmonella was not a good predictor of the bacteriological Salmonella status of individual pigs at time of slaughter. However, it is acknowledged that serological testing does help in giving a rough estimate of the overall Salmonella status of a pig herd. There was a linear correlation between prevalence of Salmonella in caecal contents and on pork cuts at factory level; therefore, if the number of herds presented for slaughter with high levels of Salmonella (category 3) was reduced, there would be less potential for contamination of the lairage, equipment etc. and so less likelihood of Salmonella contamination on pork. The impact of crosscontamination during transport, lairage, processing and distribution cannot be ignored and measures to diminish this would significantly reduce the dissemination of Salmonella in the chain and the consequent risk posed. A key finding was the considerable variation in the incidence of Salmonella on different sampling days and in different slaughter plants.
  • Control of Blown Pack Spoilage in Vacuum Packaged Meat

    Bolton, Declan J.; Moschonas, Galatios; Sheridan, James J.; Downey, Gerard (Teagasc, 2009-10-01)
    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.
  • Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network

    Condell, Orla; Power, Karen A.; Handler, Kristian; Finn, Sarah; Sheridan, Aine; Sergeant, Kjell; Renaut, Jenny; Burgess, Catherine M.; Hinton, Jay C.D.; Nally, Jarlath E.; Fanning, Seamus (Frontiers Media SA, 2014-08-01)
    Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24CHX) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent.
  • Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility

    Casey, Aidan; Fox, Edward M.; Schmitz-Esser, Stephan; Coffey, Aidan; McAuliffe, Olivia; Jordan, Kieran (Frontiers Media SA, 2014-02-28)
    Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing the transcriptome of L. monocytogenes 6179 in the presence (4 ppm) and absence of BZT, and mapping each data set to the sequenced genome of strain 6179. Hundreds of differentially expressed genes were identified, and subsequent analysis suggested that many biological processes such as peptidoglycan biosynthesis, bacterial chemotaxis and motility, and carbohydrate uptake, were involved in the response of L. monocyotogenes to the presence of BZT. The information generated in this study further contributes to our understanding of the response of bacteria to environmental stress. In addition, this study demonstrates the importance of using the bacterium's own genome as a reference when analysing RNA-Seq data.
  • Antimicrobial antagonists against food pathogens; a bacteriocin perspective

    O'Connor, Paula M.; Ross, R Paul; Hill, Colin; Cotter, Paul D. (Elsevier, 2015-02-03)
    Efforts are continuing to find novel bacteriocins with enhanced specificity and potency. Traditional plating techniques are still being used for bacteriocin screening studies, however, the availability of ever more bacterial genome sequences and the use of in silico gene mining tools have revealed novel bacteriocin gene clusters that would otherwise have been overlooked. Furthermore, synthetic biology and bioengineering-based approaches are allowing scientists to harness existing and novel bacteriocin gene clusters through expression in different hosts and by enhancing functionalities. The same principles apply to bacteriocin producing probiotic cultures and their application to control pathogens in the gut. We can expect that the recent developments on bacteriocins from Lactic Acid Bacteria (LAB) described here will contribute greatly to increased commercialisation of bacteriocins in food systems.
  • Determination and Occurrence of Phenoxyacetic Acid Herbicides and Their Transformation Products in Groundwater Using Ultra High Performance Liquid Chromatography Coupled to Tandem Mass Spectrometry

    McManus, Sarah-Louise; Moloney, Mary; Richards, Karl G.; Coxon, Catherine E.; Danaher, Martin (MDPI AG., Basel, Switzerland, 10/12/2014)
    A sensitive method was developed and validated for ten phenoxyacetic acid herbicides, six of their main transformation products (TPs) and two benzonitrile TPs in groundwater. The parent compounds mecoprop, mecoprop-p, 2,4-D, dicamba, MCPA, triclopyr, fluroxypr, bromoxynil, bentazone, and 2,3,6-trichlorobenzoic acid (TBA) are included and a selection of their main TPs: phenoxyacetic acid (PAC), 2,4,5-trichloro-phenol (TCP), 4-chloro-2-methylphenol (4C2MP), 2,4-dichlorophenol (DCP), 3,5,6-trichloro-2-pyridinol (T2P), and 3,5-dibromo-4-hydroxybenzoic acid (BrAC), as well as the dichlobenil TPs 2,6-dichlorobenzamide (BAM) and 3,5-dichlorobenzoic acid (DBA) which have never before been determined in Irish groundwater. Water samples were analysed using an efficient ultra-high performance liquid chromatography (UHPLC) method in an 11.9 min separation time prior to detection by tandem mass spectrometry (MS/MS). The limit of detection (LOD) of the method ranged between 0.00008 and 0.0047 µg·L−1 for the 18 analytes. All compounds could be detected below the permitted limits of 0.1 µg·L−1 allowed in the European Union (EU) drinking water legislation [1]. The method was validated according to EU protocols laid out in SANCO/10232/2006 with recoveries ranging between 71% and 118% at the spiked concentration level of 0.06 µg·L−1. The method was successfully applied to 42 groundwater samples collected across several locations in Ireland in March 2012 to reveal that the TPs PAC and 4C2MP were detected just as often as their parent active ingredients (a.i.) in groundwater.
  • Protocols and strategies to study the migration of veterinary drug residues into milk and dairy products in licensed trials – Corrigendum

    Power, C.; Sayers, Riona; O'Brien, Bernadette; Furey, A.; Danaher, Martin; Jordan, Kieran (Teagasc (Agriculture and Food Development Authority), Ireland, 2014)

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