Browsing by Author "Butler, Francis"
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- An alternative framework to conduct inferential statistics for low microbial counts in foods: the poisson-gamma regressionPublication . Gonzales-Barron, Ursula; Cadavez, Vasco; Butler, FrancisThe objective of this article was to compare four Poisson-gamma regression models to assess the effect of chilling on the concentration of coliforms from beef carcasses. A total of 600 carcasses were sampled before and after chilling at eight large Irish abattoirs, and the total coliforms were determined. With a coded variable (pre-chill/post-chill) as treatment, and extracting the variability of batches nested in abattoirs, random-effects models confirmed that chilling had a decreasing effect on the overall recovery of coliforms. Furthermore, the expected coliforms concentrations on pre-chill and post-chill carcasses were estimated on a CFU/cm2 scale, as well as their between-batch variability. This study introduced an alternative conceptual framework that can find interesting applications in stochastic risk assessment and in the design of more efficient sampling plans.
- An assessment of the processing and physicochemical factors contributing to the microbial contamination of salpicão, a naturally-fermented Portuguese sausagePublication . Cadavez, Vasco; Gonzales-Barron, Ursula; Pires, P.; Fernandes, E.; Pereira, Ana Paula; Gomes, Aline; Araújo, José Pedro; Lopes-da-Silva, M.F.; Rodrigues, Paula; Fernandes, Conceição; Saavedra, Maria José; Butler, Francis; Dias, TeresaComplete microbiological, physicochemical and environmental longitudinal data were obtained from factory surveys in order to elucidate risk factors leading to the survival of Enterobacteriaceae, Staphylococcus aureus and Listeria monocytogenes in salpicão sausage. A total of six batches were surveyed from two factories; one added nitrite and polyphosphates in their formulation (Factory II). The addition of polyphosphates slowed down fermentation, which favoured the increase in Enterobacteriaceae (∼0.5 log CFU/g), S. aureus (∼0.5 log CFU/g) and L. monocytogenes (∼70 CFU/g) until maceration. Maceration should be regarded as a critical stage in the control of S. aureus in salpicão, as longer maceration (p = 0.033), higher temperatures of maceration (p = 0.018) and pH of macerated meat (p = 0.079) led to higher S. aureus counts in the final product. The main hurdle controlling S. aureus in salpicão is the pH. For L. monocytogenes and Enterobacteriaceae, at least three hurdles hinder their viability: low Aw (p = 0.010; 0.012), smoking (p < 0.0001; 0.020) and nitrite (p = 0.158; 0.105). Cross-contamination, especially during mixing, should be avoided as it is an important factor explaining the increase in Enterobacteriaceae (p = 0.041), S. aureus (p = 0.015) and L. monocytogenes (p = 0.082) on a batch basis. There is a need to optimise the acidification process and reinforce good hygiene practices
- A Bayesian approach to estimating the uncertainty in the distribution of Cronobacter spp. in powdered infant formula arising from microbiological criteria test outcomesPublication . Westerholt, Friedrich von; Gonzales-Barron, Ursula; Butler, FrancisThe application of microbiological criteria related to foods has become well established for the protection of public health. Sampling plans will more likely detect a microorganism when the level of contamination is high. However, as the concentration of the microorganism drops, detection becomes more and more infrequent. Cronobacter spp. is an opportunistic pathogen that can occur infrequently and in low concentrations in powdered infant formula (PIF) with a distribution that is typically heterogeneous. This paper developed a Bayesian approach to quantify the uncertainty in the concentration of Cronobacter spp. clusters that may be present in a batch of PIF depending on the outcome of a sampling plan. Two approaches were developed. The first was a Bayesian methodology using a spreadsheet approach to develop the appropriate likelihood and posterior distributions based on an uninformed prior distribution. The second approach was similar but used an algebraic approach rather than a spreadsheet numerical approximation to characterise the uncertainty. Different sampling plans were considered based on the EC Microbiological Criteria for Cronobacter spp. When a zero positive test was the outcome of the sampling plans considered, the Bayesian analysis indicated that while the most likely outcome for all the sampling plans considered was zero clusters present, the analysis indicated that the true number of clusters present could be as high as several thousand clusters per tonne of powder depending on the sampling plan. The algebraic approach demonstrated that for zero or one positive tests, the uncertainty distribution could be approximated by a gamma distribution. Choice of the prior distribution influenced the level of uncertainty. The Bayesian approach demonstrates that even when zero positives are detected for a given sampling plan, there remains a considerable uncertainty in the true number of microorganisms that may be present undetected in a consignment of powder.
- Conducting inferential statistics for low microbial counts in foods using the Poisson-gamma regressionPublication . Gonzales-Barron, Ursula; Cadavez, Vasco; Butler, FrancisMixed Poisson distributions have been shown to be able to represent low microbial counts more efficiently than the lognormal distribution because of its greater flexibility to model microbial clustering even when data consist of a large proportion of zero counts. The objective of this study was to develop an alternative modelling framework for low microbial counts based on heterogeneous Poisson regressions. As an illustration, Poisson-gamma regression models were used to assess the effect of chilling on the concentration of total coliforms from beef carcasses (n=600) sampled at eight large Irish abattoirs. Three Poisson-gamma and three zero-modified (hurdle and zero-inflated) models were appraised with a series of random-effects variants in order to extract any variability in microbial mean concentration, dispersion and/or proportion of zero counts. Models were compared and validated in their ability to predict the coliforms counts on carcasses after chilling. In all five test batches, the hurdle Poisson-gamma distributions predicted the observed post-chill counts closer than the Poisson-gamma distributions. This is justified by the better capacity of the hurdle model to represent a higher proportion of zero counts, which were in fact observed in the post-chill batches. Thus, with a coded variable (pre-chill/post-chill) as treatment, and extracting the significant variability of batches nested in abattoirs for the coliforms mean concentration (σ 2 u =2.68), the dispersion measure (σ 2 v =2.39) and the probability of zero counts (σ 2 w =0.89), the validated hurdle Poisson-gamma model confirmed that chilling has a decreasing effect on the viability of coliforms from beef carcasses, and that the concentration is reduced by an average (pre-chill to post-chill) factor of 2.2 (95% CI: 2.15-2.24) at batch level. The model also indicated that chilling increases the odds of producing a zero count from a carcass swab in about 13.5 times, and that the higher the coliforms concentration in a batch, the weaker the effect that chilling has to reduce such contamination on the beef carcasses.
- Estimación meta-analítica de la reducción de coliformes totales en canales de bovino debido al enfriamientoPublication . Gonzales-Barron, Ursula; Cadavez, Vasco; Butler, FrancisEl objetivo principal del meta-análisis es comparar e integrar los resultados de varios estudios primarios que investigan el mismo tema. El meta-análisis produce un estimado más preciso del efecto de un tratamiento o intervención, así como también permite explicar las posibles diferencias entre los estudios independientes. Este estimado meta-analítico – llamado ‘efecto promedio’ – tendrá un mayor poder estadístico y una mayor capacidad de generalización que cualquier resultado individual. La prevención de enfermedades humanas, causadas por agentes zoonóticos en carnes, es compleja debido a las múltiples etapas en su procesamiento. Antes de implementar cualquier programa de inocuidad alimentaria, es necesario identificar los tratamientos que sean efectivos en la reducción de la contaminación. Así, existe una necesidad de conducir meta-análisis en los campos de zootecnia e inocuidad alimentaria con la finalidad de identificar, evaluar y sintetizar los resultados de muchas fuentes bibliográficas. Esta información proveer las autoridades nacionales información resumida sobre la eficacia de intervenciones para el control de las enfermedades transmitidas por alimentos. El objetivo de este trabajo fue utilizar métodos meta-analíticos para cuantificar el efecto del enfriamiento convencional de canales de bovino en la concentración de coliformes totales, integrando resultados de diferentes estudios llevados a cabo en mataderos irlandeses de carne de exportación.
- A meta-analysis of the between-batch variability in the effect of chilling on the salmonella incidence on pig carcassesPublication . Gonzales-Barron, Ursula; Cadavez, Vasco; Butler, FrancisThe objective of this work was to study the effect of chilling on the occurrence of Salmonella on pig carcasses at batch level by meta-analysis. Fixed-effects and random-effects metaanalysis were conducted, and the random-effects solution was preferred to account for the significant variability in effect size estimated from 51 sampled batches extracted from 13 primary studies. This study results indicated that chilling reduces the Salmonella incidence on pig carcasses by a mean ratio of ~1.92 (95% CI: 1.36 – 2.70). Multilevel meta-analyses models investigating study characteristics that could explain the heterogeneity (τ2) in the true effect size among sampled batches (τ2=0.373), revealed that ‘total sample size’ and ‘carcass swabbed area’ impact (p<0.05) on the measured effect size of chilling. The fact that swabbed area explained 62% and total sample size 38% of the total heterogeneity in the chilling true effect size, gives rise to an awareness that differences in experimental design greatly affects our substantive conclusion about the effect of chilling on Salmonella recovery. Higher swabbed areas and greater sample sizes led to more precise and greater estimates of the decreasing effect of chilling on Salmonella.
- A meta-analytical assessment os the variability between abattoirs in the effect of chilling on the salmonella incidence on pig carcassesPublication . Gonzales-Barron, Ursula; Sheridan, James; Butler, Francis; Cadavez, VascoThe aim of the study was to estimate the overall effect of chilling on the Salmonella occurrence on pig carcasses during pork processing. Meta-analyses were conducted on the outcomes of research studies conducted in 32 abattoirs.
- Modelling the effect of chilling on the occurrence of Salmonella on pig carcasses at study, abattoir and batch levels by meta-analysisPublication . Gonzales-Barron, Ursula; Cadavez, Vasco; Sheridan, James; Butler, FrancisThe effect of chilling on the occurrence of Salmonella on pig carcasses was investigated at study, abattoir and batch level by meta-analysis. Both the fixed-effects and random-effects model confirmed (p b 0.05) the significant effect of chilling in decreasing Salmonella occurrence on pig carcasses; although the random-effects solution was preferred to account for the significant variability in effect size (p b 0.001) estimated from the 13 primary studies considered, the 32 abattoirs surveyed, and the 51 sampled batches. Conservatively, it can be said that chilling reduces the Salmonella incidence on pig carcasses by a mean ratio of ~1.6 (95% CI: 1.0–2.6). Multilevel meta-analysismodels investigating study characteristics that could explain the heterogeneity (τ2) in the true effect size among primary studies (τ2 = 0.578), among surveyed abattoirs (τ2 = 0.431), and among sampled batches (τ2 = 0.373), revealed that study size (represented by the moderating variables of ‘total sample size’ and ‘number of batches sampled in an abattoir’) and ‘carcass swabbed area’ have a significant impact (p b 0.05) on the measured effect size of chilling. The fact that swabbed area explained between 56 and 62% and total sample size between 23 and 38% of the total heterogeneity in the chilling true effect size, indicates that differences in experimental design greatly affect our substantive conclusion about the effect of chilling on Salmonella occurrence. This inconsistency to elucidate the effect of chilling arises because of themany factors influencing both the performance of the chilling operation and themeasurement itself.Meta-analysis was not only instrumental to showthat small-size studies (i.e., only one batch sampled per abattoir, total number of sampled carcasses per batch b 50) and small swabbed areas (b100 cm2) lead to imprecise and even conflicting conclusions, but most importantly, enabled definition of the characteristics of a well-designed study having aminimumstatistical power to produce precise results. A sound experimental design derived by multilevel meta-analysis consists of swabbing carcass areas of at least 500 cm2 from 25 pre-chill and 25 post-chill carcasses from a single production batch, with a minimum of two batches sampled per surveyed abattoir. If the survey were to be conducted in more than one abattoir, the total sample size should not be less than 400. Two methods to test for publication bias, a common problem in meta-analysis, suggested that whilst the presence of unpublished small-size studies is probable, it is not likely that this would significantly bias the overall chilling effect estimated in this study.
- Modelling the inhibitory effect of LAB on L. monocytogenes and Enterobacteriaceae in a fermented sausage during ripeningPublication . Cadavez, Vasco; Butler, Francis; Gonzales-Barron, UrsulaEarlier research has shown that the survivability of Enterobacteriaceae (ENT) and L. monocytogenes (LM) in a Portuguese fermented sausage (linguiça) decreases during the ripening stage, and that such inhibition arises from the adverse conditions caused by the competition with autochthonous lactic acid bacteria (LAB) and the progressively lower water activity and pH. The objective of this work was to mathematically characterise the competition or interactions between LAB, LM and ENT that takes place in fermenting linguiça during ripening.
- Omnibus modeling of listeria monocytogenes growth rates at low temperaturesPublication . Pennone, Vincenzo; Gonzales-Barron, Ursula; Hunt, Kevin; Cadavez, Vasco; McAuliffe, Olivia; Butler, FrancisListeria monocytogenes is a pathogen of considerable public health importance with a high case fatality. L. monocytogenes can grow at refrigeration temperatures and is of particular concern for ready-to-eat foods that require refrigeration. There is substantial interest in conducting and modeling shelf-life studies on L. monocytogenes, especially relating to storage temperature. Growth model parameters are generally estimated from constant-temperature growth experiments. Traditionally, first-order and second-order modeling (or primary and secondary) of growth data has been done sequentially. However, omnibus modeling, using a mixed-effects nonlinear regression approach, can model a full dataset covering all experimental conditions in one step. This study compared omnibus modeling to conventional sequential first-order/second-order modeling of growth data for five strains of L. monocytogenes. The omnibus model coupled a Huang primary model for growth with secondary models for growth rate and lag phase duration. First-order modeling indicated there were small significant differences in growth rate depending on the strain at all temperatures. Omnibus modeling indicated smaller differences. Overall, there was broad agreement between the estimates of growth rate obtained by the first-order and omnibus modeling. Through an appropriate choice of fixed and random effects incorporated in the omnibus model, potential errors in a dataset from one environmental condition can be identified and explored.