Ana Sofia Ribeiro Duarte

Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food.

Background Diarrhoeal diseases are major contributors to the global burden of disease, particularly in children. However, comprehensive estimates of the incidence and mortality due to specific aetiologies of diarrhoeal diseases are not available. The objective of this study is to provide estimates of the global and regional incidence and mortality of diarrhoeal diseases caused by nine pathogens that are commonly transmitted through foods. Methods and Findings We abstracted data from systematic reviews and, depending on the overall mortality rates of the country, applied either a national incidence estimate approach or a modified Child Health Epidemiology Reference Group (CHERG) approach to estimate the aetiology-specific incidence and mortality of diarrhoeal diseases, by age and region. The nine diarrhoeal diseases assessed caused an estimated 1.8 billion (95% uncertainty interval [UI] 1.1–3.3 billion) cases and 599,000 (95% UI 472,000–802,000) deaths worldwide in 2010. The largest number of cases were caused by norovirus (677 million; 95% UI 468–1,153 million), enterotoxigenic Escherichia coli (ETEC) (233 million; 95% UI 154–380 million), Shigella spp. (188 million; 95% UI 94–379 million) and Giardia lamblia (179 million; 95% UI 125–263); the largest number of deaths were caused by norovirus (213,515; 95% UI 171,783–266,561), enteropathogenic E. coli (121,455; 95% UI 103,657–143,348), ETEC (73,041; 95% UI 55,474–96,984) and Shigella (64,993; 95% UI 48,966–92,357). There were marked regional differences in incidence and mortality for these nine diseases. Nearly 40% of cases and 43% of deaths caused by these nine diarrhoeal diseases occurred in children under five years of age. Conclusions Diarrhoeal diseases caused by these nine pathogens are responsible for a large disease burden, particularly in children. These aetiology-specific burden estimates can inform efforts to reduce diarrhoeal diseases caused by these nine pathogens commonly transmitted through foods.

Human risk from thermotolerant Campylobacter on broiler meat in Denmark.

This paper describes a new approach by which changes over time in the relative risk of human campylobacteriosis from broiler meat are evaluated through quantitative microbiological risk assessment modelling. Danish surveillance data collected at retail from 2001 to 2010 on numbers of thermotolerant Campylobacter spp. on Danish produced and imported chilled and frozen broiler meat were the basis for the investigation. The aim was to explore if the risk from the different meat categories had changed over time as a consequence of implemented intervention strategies. The results showed a slight decrease from 2005 to 2008 in the human risk from Danish produced broiler meat, and a decrease from 2005 to 2010 in the risk from imported chilled meat. This risk reduction coincides with control measures implemented to reduce Campylobacter in Danish and imported chilled broiler meat. The human risk of campylobacteriosis from Danish frozen meat increased but remained lower compared to chilled meat. In total, the relative risk from broiler meat available for sale in Denmark increased from 2001 to 2005 after which the risk decreased to a level similar to the period 2001-2002. The use of QMRA in the evaluation of intervention strategies based on monitoring data provided an added value, compared to the traditional approach of only using changes in prevalence. The estimated human health risk is a function of prevalence and the distribution of concentrations, and therefore takes best usage of the available data, while providing the most relevant outcome for food safety risk managers.

Effect of slaughterhouse and day of sample on the probability of a pig carcass being Salmonella-positive according to the Enterobacteriaceae count in the largest Brazilian pork production region

Sources of contamination of carcasses during slaughter include infected pigs as well as environmentally related sources. There are many microbial indicators that can be used in the processing of food to assess food hygiene and the safety of food processing. The presence of some microbial indicators can be viewed as a result of direct or indirect contamination of a food with fecal material. The presence of Enterobacteriaceae is often used as a hygiene indicator, as they are found both in the environment and in the intestine of warm-blooded animals. An association between Salmonella isolation and Enterobacteriaceae count (EC) on pre-chill carcasses has been described, however the impact of slaughterhouse and the day of sampling on the occurrence of Salmonella has not been previously investigated. To this end, mixed logistic regressions (MLRs) with random effects and fixed slopes were performed to assess the change in EC and its correlation with Salmonella occurrence using two data sets. The first describes the EC and Salmonella isolation in 60 pork carcasses in one slaughterhouse sampled at 11 different slaughter steps, including the carcass as a random effect. The second describes the EC and Salmonella isolation on 1150 pre-chill carcasses sampled in 13 slaughterhouses over 230 sampling days, and the model combined two random intercepts, slaughterhouse and date of sampling nested with slaughterhouse (day/slaughterhouse). Statistically significant associations (p<0.0001) between the log of the EC and Salmonella occurrence were found in all models. Nevertheless, although a strong association was found between Enterobacteriaceae and Salmonella contamination in pork carcasses, this association was not constant, given that there was a high variation in the probability of a carcass being positive for Salmonella according to the EC mainly between days of samples. The effect of the day of sampling on Salmonella prevalence was so large that the predictive value of the EC count for Salmonella isolation on a daily basis was compromised. It is possible that on some days batches with a high prevalence of Salmonella carriers shedding a high number of Salmonella were slaughtered. On these days, the potential for contamination/cross-contamination of carcasses will be so large that even hygienic slaughter, confirmed by the low EC on carcasses, will not be able to prevent the presence of Salmonella on some carcasses. The results of this study demonstrate that, despite the statistically significant association found, it may be difficult to predict when hygiene failure measured via EC actually indicates Salmonella contamination, and neither the inverse.

Fitting a distribution to microbial counts: making sense of zeroes.

The accurate estimation of true prevalence and concentration of microorganisms in foods is an important element of quantitative microbiological risk assessment (QMRA). This estimation is often based on microbial detection and enumeration data. Among such data are artificial zero counts, that originated by chance from contaminated food products. When these products are not differentiated from uncontaminated products that originate true zero counts, the estimates of true prevalence and concentration may be inaccurate. This inaccuracy is especially relevant in situations where highly pathogenic bacteria are involved and where growth can occur along the food pathway. Our aim was to develop a method that provides accurate estimates of concentration parameters and differentiates between artificial and true zeroes, thus also accurately estimating true prevalence. We first show the disadvantages of using a limit of quantification (LOQ) threshold for the analysis of microbial enumeration data. We show that, depending on the original distribution of concentrations and the LOQ value, it may be incorrect to treat artificial zeroes as censored below a quantification threshold. Next, a method is developed that estimates the true prevalence of contamination within a food lot and the parameters characterizing the within-lot distribution of concentrations, without assuming a LOQ, and using raw plate count data as an input. Counts resulting both from contaminated and uncontaminated sample units are analysed together. This procedure allows the estimation of the proportion of artificial zeroes among the total of zero counts, and therefore the estimation of true prevalence from enumeration results. We observe that this method yields best estimates of mean, standard deviation and prevalence at low true prevalence levels and low expected standard deviation. Furthermore, we conclude that the estimation of prevalence and the estimation of the distribution of concentrations are interrelated and therefore should be estimated simultaneously. We also conclude that one of the keys to an accurate characterization of the overall microbial contamination is the correct identification and separation of true and artificial zeroes. Our method for the analysis of quantitative microbial data shows a good performance in the estimation of true prevalence and the parameters of the distribution of concentrations, which indicates that it is a useful data analysis tool in the field of QMRA.

Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial.

Background Atopic dermatitis (AD) patients may benefit from using textiles coated with skin microbiome–modulating compounds. Chitosan, a natural biopolymer with immunomodulatory and antimicrobial properties, has been considered potentially useful. Objective This randomized controlled trial assessed the clinical utility of chitosan-coated garment use in AD. Methods Of the 102 patients screened, 78 adult and adolescents were randomly allocated to overnight use of chitosan-coated or uncoated cotton long-sleeved pyjama tops and pants for 8 weeks. The primary outcome was change in disease severity assessed by Scoring Atopic dermatitis index (SCORAD). Other outcomes were changes in quality of life, pruritus and sleep loss, days with need for rescue medication, number of flares and controlled weeks, and adverse events. Changes in total staphylococci and Staphylococcus aureus skin counts were also assessed. Comparisons were made using analysis of variance supplemented by repeated measures analysis for the primary outcome. Interaction term between time and intervention was used to compare time trends between groups. Results Chitosan group improved SCORAD from baseline in 43.8%, (95%CI: 30.9 to 55.9), P = 0.01, placebo group in 16.5% (-21.6 to 54.6); P = 0.02 with no significant differences between groups; Dermatology Quality of life Index Score significantly improved in chitosan group (P = 0.02) and a significant increase of skin Coagulase negative Staphylococci (P = 0.02) was seen. Conclusions Chitosan coated textiles may impact on disease severity by modulating skin staphylococcal profile. Moreover, a potential effect in quality of life may be considered. Trial Registration ClinicalTrials.gov NCT01597817

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.Metagenomic analyses of European pig and poultry farms show differing resistome profiles and an association with country-level antibiotic use.

The impact of screening-test negative samples not enumerated by MPN.

In microbiological surveys, false negative results in detection tests precluding the enumeration by MPN may occur. The objective of this study was to illustrate the impact of screening test failure on the probability distribution of Salmonella concentrations in pork using a Bayesian method. A total of 276 swab samples in four slaughter steps (69 samples in each slaughter step: after dehairing, after singeing, after evisceration, and before chilling) were screened for Salmonella and enumerated by the MPN method. Salmonella contamination data were fitted to a lognormal distribution by using a Bayesian model that uses the number of positive tubes at each dilution in an MPN analysis to estimate the parameters of the concentration distribution. With Salmonella paired data, three data sets were used for each slaughter step: one that includes the positives in the screening test only, a second one that includes false negative results from the screening, and a third that considers the entire data set. The relative sensitivity of the screening test was also calculated assuming as gold standard samples with confirmed Salmonella. Salmonella was confirmed by a reference laboratory in 29 samples either by screening or MPN method. The relative sensitivity of the screening test was 69% (CI 95%: 52%-85%). The data set that included enumerations from screen-negative samples (false negative results) tended to have higher μ̂ and smaller σ̂ in comparison with the data set that discards false negative results, suggesting that the lack of sensitivity of the screening test affects the distribution that describes the contamination across the population. Numerous surveys on fitting distribution methods of microbial censored data have been published and discuss source of bias due to fitting method. Results of this survey contribute with that discussion by illustrating another possible source of bias due to failure of the screening methods preceding the MPN.

Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Meal-exercise challenge and physical activity reduction impact on immunity and inflammation (MERIIT trial)

Background The effect of a pre-exercise meal as countermeasure to exercise induced immunodepression is poorly known. Also, sedentary behavior is associated with increased cardiometabolic risk but studies on immune changes are lacking. Therefore, we aimed to assess: 1) the impact of a pre-exercise Mediterranean meal (MdM) compared with a fast-food type meal (FFM) on exercise-induced immunological changes and 2) the impact of an induced acute period of sedentary behavior on neuro-immune-endocrine status. Methods /Design: This is a two steps clinical trial including: (a) randomized crossover clinical trial, comparing the effect a high-fat/low-nutrient dense meal, FFM, with an isoenergetic similar high-nutrient dense meal, MdM, in the immune response to an exercise challenge (EC) and (b) a pilot trial assessing the neuro-immune-endocrine change induced by acute decreasing by half the usual physical activity level. Results A total of 46 participants (26 females), median aged 25 years were included. Of those 39-completed protocol, including overweight, physical active and inactive and participants with asthma. There were no differences in the EC between interventions. Dietary factors and physical activity were closely monitored during interventions and kept similar. During physical inactivity induction, 31% reached the target of 50% reduction in mean step number and 77% reached a 30% reduction. Conclusion The use of a pre-exercise meal to modulate immune response and the understanding of the immunological impact of physical inactivity might help to establish future recommendations on how to practice exercise in a safer way and to recognize the potential impact of inactivity.