Qualitative and quantitative risk assessment for human salmonellosis due to multi-resistant Salmonella Typhimurium DT104 from consumption of Danish dry-cured pork sausages

Veterinary bacteriology in Denmark from the 1880s to 2022

This paper gives an account of the history of veterinary bacteriology including clinical veterinary bacteriology as well as the area of veterinary public health in Denmark from the 1880s to 2022. We describe key persons, including B. Bang, C.O. Jensen, K.A. Jensen and others who made important contributions to the development of these areas of microbiological expertise, and we discuss how challenges ranging from bovine tuberculosis to bacterial antimicrobial resistance have been met. Further, we describe progress in research on important bacterial pathogens both with regard to animal clinical aspects and zoonotic food-related aspects. Finally, we describe current issues in relation to One Health and research organization.

Animal sources of antimicrobial-resistant bacterial infections in humans: a systematic review

Bacterial antimicrobial resistance (AMR) is among the leading global health challenges of the century. Animals and their products are known contributors to the human AMR burden, but the extent of this contribution is not clear. This systematic literature review aimed to identify studies investigating the direct impact of animal sources, defined as livestock, aquaculture, pets, and animal-based food, on human AMR. We searched four scientific databases and identified 31 relevant publications, including 12 risk assessments, 16 source attribution studies, and three other studies. Most studies were published between 2012 and 2022, and most came from Europe and North America, but we also identified five articles from South and South-East Asia. The studies differed in their methodologies, conceptual approaches (bottom-up, top-down, and complex), definitions of the AMR hazard and outcome, the number and type of sources they addressed, and the outcome measures they reported. The most frequently addressed animal source was chicken, followed by cattle and pigs. Most studies investigated bacteria-resistance combinations. Overall, studies on the direct contribution of animal sources of AMR are rare but increasing. More recent publications tailor their methodologies increasingly towards the AMR hazard as a whole, providing grounds for future research to build on.

Identification of risk profiles for Salmonella prevalence in pig supply chains in South Korea using meta-analysis and a quantitative microbial risk assessment model

International travel and the globalization of food supplies have increased the risk of epidemic foodborne infections. Salmonella strains, particularly non-typhoidal Salmonella (NTS), are major zoonotic pathogens responsible for gastrointestinal diseases worldwide. In this study, the prevalence and Salmonella contamination in pigs/carcasses throughout the South Korean pig supply chain and the associated risk factors were evaluated using Systematic reviews and meta-analyses (SRMA), and quantitative microbial risk assessment (QMRA). The prevalence of Salmonella in finishing pigs, which is one of the major starting inputs of the QMRA model was calculated through SRMA of studies conducted in south Korea in order to complement and enhance the robustness of the model. Our findings revealed that the pooled Salmonella prevalence in pigs was 4.15% with a 95% confidence interval (CI) of 2.56 to 6.66%. Considering the pig supply chain, the highest prevalence was detected in slaughterhouses (6.27% [95% CI: 3.36; 11.37]), followed by farms (4.16% [95% CI: 2.32; 7.35]) and meat stores (1.21% [95% CI: 0.42; 3.46]). The QMRA model predicted a 3.9% likelihood of Salmonella-free carcasses and a 96.1% probability of Salmonella-positive carcasses at the end of slaughter, with an average Salmonella concentration of 6.38 log CFU/carcass (95% CI: 5.17; 7.28). This corresponds to an average contamination of 1.23 log CFU/g (95% CI: 0.37; 2.48) of pork meat. Across the pig supply chain, the highest Salmonella contamination was predicted after transport and lairage, with an average concentration of 8 log CFU/pig (95% CI: 7.15; 8.42). Sensitivity analysis indicated that Salmonella fecal shedding (r = 0.68) and Salmonella prevalence in finishing pigs (r = 0.39) at pre-harvest were the most significant factors associated with Salmonella contamination in pork carcasses. Although disinfection and sanitation interventions along the slaughter line can reduce contamination levels to some extent, effective measures should be taken to reduce Salmonella prevalence at the farm level to improve the safety of pork consumption.

Quantitative Risk Assessment of Susceptible and Ciprofloxacin-Resistant Salmonella from Retail Pork in Chiang Mai Province in Northern Thailand

The adverse human health effects as a result of antimicrobial resistance have been recognized worldwide. Salmonella is a leading cause of foodborne illnesses while antimicrobial resistant (AMR) Salmonella has been isolated from foods of animal origin. The quantitative risk assessment (RA) as part of the guidelines for the risk analysis of foodborne antimicrobial resistance was issued by the Codex Alimentarius Commission more than a decade ago. However, only two risk assessments reported the human health effects of AMR Salmonella in dry-cured pork sausage and pork mince. Therefore, the objective of this study was to quantitatively evaluate the adverse health effects attributable to consuming retail pork contaminated with Salmonella using risk assessment models. The sampling frame covered pork at the fresh market (n = 100) and modern trade where pork is refrigerated (n = 50) in Chiang Mai province in northern Thailand. The predictive microbiology models were used in the steps where data were lacking. Susceptible and quinolone-resistant (QR) Salmonella were determined by antimicrobial susceptibility testing and the presence of AMR genes. The probability of mortality conditional to foodborne illness by susceptible Salmonella was modeled as the hazard characterization of susceptible and QR Salmonella. For QR Salmonella, the probabilistic prevalences from the fresh market and modern trade were 28.4 and 1.9%, respectively; the mean concentrations from the fresh market and modern trade were 346 and 0.02 colony forming units/g, respectively. The probability of illness (P_I) and probability of mortality given illness (P_MI) from QR Salmonella-contaminated pork at retails in Chiang Mai province were in the range of 2.2 × 10⁻⁸–3.1 × 10⁻⁴ and 3.9 × 10⁻¹⁰–5.4 × 10⁻⁶, respectively, while those from susceptible Salmonella contaminated-pork at retails were in the range 1.8 × 10⁻⁴–3.2 × 10⁻⁴ and 2.3 × 10⁻⁷–4.2 × 10⁻⁷, respectively. After 1000 iterations of Monte Carlo simulations of the risk assessment models, the annual mortality rates for QR salmonellosis simulated by the risk assessment models were in the range of 0–32, which is in line with the AMR adverse health effects previously reported. Therefore, the risk assessment models used in both exposure assessment and hazard characterization were applicable to evaluate the adverse health effects of AMR Salmonella spp. in Thailand.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.

Critical Analysis of Pork QMRA Focusing on Slaughterhouses: Lessons from the Past and Future Trends

Foodborne microbial diseases have a significant impact on public health, leading to millions of human illnesses each year worldwide. Pork is one of the most consumed meat in Europe but may also be a major source of pathogens introduced all along the farm-to-fork chain. Several quantitative microbial risk assessment (QMRA) have been developed to assess human health risks associated with pork consumption and to evaluate the efficiency of different risk reduction strategies. The present critical analysis aims to review pork QMRA. An exhaustive search was conducted following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) methodology. It resulted in identification of a collection of 2489 papers including 42 on QMRA, after screening. Among them, a total of 29 studies focused on Salmonella spp. with clear concern on impacts at the slaughterhouse, modeling the spreading of contaminations and growth at critical stages along with potential reductions. Along with strict compliance with good hygiene practices, several potential risk mitigation pathways were highlighted for each slaughterhouse step. The slaughterhouse has a key role to play to ensure food safety of pork-based products but consideration of the whole farm-to-fork chain is necessary to enable better control of bacteria. This review provides an analysis of pork meat QMRA, to facilitate their reuse, and identify gaps to guide future research activities.

Prevalence and characteristics of Salmonella isolates recovered from retail raw chickens in Shaanxi Province, China

In this study, we evaluated the prevalence of Salmonella in retail raw chickens in Shaanxi Province, China, on a monthly basis. In addition, we studied the antibiotic susceptibility, serotype, and genotype of Salmonella isolates and explored their relationships with sampling time, location, market type, and chicken type. The results showed that Salmonella was more prevalent in chickens sampled during the spring and summer than during the autumn and winter. Thirty-nine serotypes were identified from 406 Salmonella isolates, of which Salmonella typhimurium (16.7%) was the most prevalent. Other prevalent serotypes included S. thompson (12.8%), S. essen (9.1%), S. infantis (6.9%), S. rissen (5.7%), and S. enteritidis (5.4%). Approximately 71.4% of the 406 isolates were resistant to 3 or more antibiotics, 11.8% to 12 or more, and 1.7% to all 14 antibiotics tested. The most frequently detected resistance was to trimethoprim/sulfamethoxazole (82.0%), followed by nalidixic acid (71.9%) and tetracycline (59.4%). The frequencies of resistance to ampicillin, chloramphenicol, and amoxicillin/clavulanic acid were moderately high (∼50% each). Resistance to kanamycin, ceftiofur, streptomycin, gentamicin, and ciprofloxacin was less common (<40% each). Serotype distribution and antibiotic susceptibility of Salmonella isolates were related to sampling time, location, chicken type, and market type. Isolates recovered from the same sampling time, market type, location, and chicken type commonly exhibited identical or similar genotypes and antibiotic resistance profiles. However, DNA profiles and antibiotic resistance phenotypes of isolates within some serotypes were diverse. Our results revealed that multiple Salmonella subtypes with antibiotic resistance were prevalent in retail raw chickens in Shaanxi Province. Our study findings provide information for developing preventive measures against contamination of retail foods with Salmonella.

Source Attribution and Risk Assessment of Antimicrobial Resistance

Source attribution and microbial risk assessment methods have been widely applied for the control of several foodborne pathogens worldwide by identifying (i) the most important pathogen sources and (ii) the risk represented by specific foods and the critical points in these foods' production chains for microbial control. Such evidence has proved crucial for risk managers to identify and prioritize effective food safety and public health strategies. In the context of antimicrobial resistance (AMR) from livestock and pets, the utility of these methods is recognized, but a number of challenges have largely prevented their application and routine use. One key challenge has been to define the hazard in question: Is it the antimicrobial drug use in animals, the antimicrobial-resistant bacteria in animals and foods, or the antimicrobial resistance genes that can be transferred between commensal and pathogenic bacteria in the animal or human gut or in the environment? Other important limitations include the lack of occurrence and transmission data and the lack of evidence to inform dose-response relationships. We present the main principles, available methods, strengths, and weaknesses of source attribution and risk assessment methods, discuss their utility to identify sources and estimate risks of AMR from livestock and pets, and provide an overview of conducted studies. In addition, we discuss remaining challenges and current and future opportunities to improve methods and knowledge of the sources and transmission routes of AMR from animals through food, direct contact, or the environment, including improvements in surveillance and developments in genotypic typing methods.

A Quantitative Microbiological Risk Assessment for Salmonella in Pigs for the European Union

A farm-to-consumption quantitative microbiological risk assessment (QMRA) for Salmonella in pigs in the European Union has been developed for the European Food Safety Authority. The primary aim of the QMRA was to assess the impact of hypothetical reductions of slaughter-pig prevalence and the impact of control measures on the risk of human Salmonella infection. A key consideration during the QMRA development was the characterization of variability between E.U. Member States (MSs), and therefore a generic MS model was developed that accounts for differences in pig production, slaughterhouse practices, and consumption patterns. To demonstrate the parameterization of the model, four case study MSs were selected that illustrate the variability in production of pork meat and products across MSs. For the case study MSs the average probability of illness was estimated to be between 1 in 100,000 and 1 in 10 million servings given consumption of one of the three product types considered (pork cuts, minced meat, and fermented ready-to-eat sausages). Further analyses of the farm-to-consumption QMRA suggest that the vast majority of human risk derives from infected pigs with a high concentration of Salmonella in their feces (≥10(4) CFU/g). Therefore, it is concluded that interventions should be focused on either decreasing the level of Salmonella in the feces of infected pigs, the introduction of a control step at the abattoir to reduce the transfer of feces to the exterior of the pig, or a control step to reduce the level of Salmonella on the carcass post-evisceration.

Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

Status and future of Quantitative Microbiological Risk Assessment in China

Since the implementation of the Food Safety Law of the People's Republic of China in 2009 use of Quantitative Microbiological Risk Assessment (QMRA) has increased. QMRA is used to assess the risk posed to consumers by pathogenic bacteria which cause the majority of foodborne outbreaks in China. This review analyses the progress of QMRA research in China from 2000 to 2013 and discusses 3 possible improvements for the future. These improvements include planning and scoping to initiate QMRA, effectiveness of microbial risk assessment utility for risk management decision making, and application of QMRA to establish appropriate Food Safety Objectives.

Assessing risk profiles for Salmonella serotypes in breeding pig operations in Portugal using a Bayesian hierarchical model

Background

The EU Regulation No 2160/2003 imposes a reduction in the prevalence of Salmonella in pigs. The efficiency of control programmes for Salmonella in pigs, reported among the EU Member States, varies and definitive eradication seems very difficult. Control measures currently recommended for Salmonella are not serotype-specific. Is it possible that the risk factors for different Salmonella serotypes are different? The aim of this study was to investigate potential risk factors for two groups of Salmonella sp serotypes using pen faecal samples from breeding pig holdings representative of the Portuguese pig sector.

Methods

The data used come from the Baseline Survey for the Prevalence of Salmonella in breeding pigs in Portugal. A total of 1670 pen faecal samples from 167 herds were tested, and 170 samples were positive for Salmonella. The presence of Salmonella in each sample (outcome variable) was classified in three categories: i) no Salmonella, ii) Salmonella Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-, , and iii) other serotypes. Along with the sample collection, a questionnaire concerning herd management and potential risk factors was utilised. The data have a “natural” hierarchical structure so a categorical multilevel analysis of the dataset was carried out using a Bayesian hierarchical model. The model was estimated using Markov Chain Monte Carlo methods, implemented in the software WinBUGS.

Results

The significant associations found (when compared to category “no Salmonella”), for category “serotype Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-” were: age of breeding sows, size of the herd, number of pigs/pen and source of semen. For the category “other serotypes” the significant associations found were: control of rodents, region of the country, source of semen, breeding sector room and source of feed.

Conclusions

The risk factors significantly associated with Salmonella shedding from the category “serotype Typhimurium or serotype 1,4,5,12:i:-“ were more related to animal factors, whereas those associated with “other serotypes” were more related to environmental factors. Our findings suggest that different control measures could be used to control different Salmonella serotypes in breeding pigs.

Development of a self-regulated dynamic model for the propagation of Salmonella Typhimurium in pig farms

A self-regulated epidemic model was developed to describe the dynamics of Salmonella Typhimurium in pig farms and predict the prevalence of different risk groups at slaughter age. The model was focused at the compartment level of the pig farms and it included two syndromes, a high and a low propagation syndrome. These two syndromes generated two different classes of pigs, the High Infectious and the Low Infectious, respectively, which have different shedding patterns. Given the two different classes and syndromes, the Infectious Equivalent concept was used, which reflected the combination of High and Low Infectious pigs needed for the high propagation syndrome to be triggered. Using the above information a new algorithm was developed that decides, depending on the Infectious Equivalent, which of the two syndromes should be triggered. Results showed that the transmission rate of S. Typhimurium for the low propagation syndrome is around 0.115, pigs in Low Infectious class contribute to the transmission of the infection by 0.61-0.80 of pigs in High Infectious class and that the Infectious Equivalent should be above 10-14% of the population in order for the high propagation syndrome to be triggered. This self-regulated dynamic model can predict the prevalence of the classes and the risk groups of pigs at slaughter age for different starting conditions of infection.

Causal hidden variable model of pathogenic contamination from pig to pork

Risk assessments relating to food safety over more than one step along a production chain are frequently hampered by lack of detailed quantitative data. This study set out to develop a Bayesian hidden variable model to integrate available limited data of the combined occurrence of three bacterial pathogens, Listeria monocytogenes, Yersinia enterocolitica and Yersinia pseudotuberculosis, with causal assumptions along three steps of pork production chain. The pathogen occurrence data were animal specific both on conventional and organic pig farms and at the abattoir, but merely farm specific at meat cutting plants. The model was able to incorporate all data concerning different types of testing at different steps of the chain, and missing data values were dealt with in a straightforward manner. It provides a tool for quantitative risk assessments and for estimating the causal risk mitigation effects by combining external data with the specific follow-up data. Intervention effects are provided with Bayesian credible intervals indicating the uncertainty due to all information sources included in the model. Combined prevalence in Finnish pork was estimated to be 1–11% and it could be reduced to 0–2% if head was removed intact and rectum sealed off.

Salmonella serosurveillance: different statistical methods to categorise pig herds based on serological data

This study proposes three different statistical methods that can be applied in order to categorise pig herds into two groups (high seroreactors vs. low seroreactors) based on serological test results for Salmonella-specific antibodies in pigs. All proposed statistical methods were restricted to allocate about 10% of the herds into the group defined by each of the statistical approaches as high seroreactors. Previously, semi-parametric quantile regression has been used for this purpose, and here we compare it with two other alternatives: a naive method (based on the mean values) and another based on activity region finder methodology in combination with random forest regression models. The serological response values (the sample-to-positive ratio (S/P ratio)) of 13 649 pigs from 314 Belgian pig herds were used for this comparison. Nearly 14% of these herds were assigned to the high-seroreactor-herd group by at least one of these three methods. The corrected level of agreement was calculated together with the pair-wise agreement among all three methods in order to classify herds as high- or low-level seroreactors, resulting in an agreement level greater than 92%. The results obtained from a fourth method, which is adopted by the Belgian Federal Agency for the Safety of the Food Chain (FASFC), were also compared to the previous three methods. The methods were compared in terms of their agreement as well as their advantages and disadvantages. Recommendations for each applied method are presented in relation to the objectives and the requisite policy for classifying pig herds based on serological data.

Risk-based analysis of the Danish pork Salmonella program: past and future

The Danish pork Salmonella control program was initiated in 1993 in response to a prominent pork-related outbreak in Copenhagen. It involved improved efforts at slaughter hygiene (postharvest) and on-farm (preharvest) surveillance and control. After 10 years, 95 million Euros, significant reductions in seropositive herds, Salmonella positive carcasses, and pork-attributable human cases (PAHC), questions have arisen about how best to continue this program. The objective of this study was to provide some analysis and information to address these questions. The methods used include a computer simulation model constructed of a series of Excel workbooks, one for each simulated year and scenario (http://www.ifss.iastate/DanSalmRisk). Each workbook has three modules representing the key processes affecting risk: seropositive pigs leaving the farm (Production), carcass contamination after slaughter (Slaughter), and PAHC of Salmonella (Attribution). Parameter estimates are derived from an extensive farm-to-fork database collected by industry and government and managed by the Danish Zoonosis Centre (http://www.food.dtu.dk). Retrospective (1994-2003) and prospective (2004-2013) simulations were evaluated. The retrospective simulations showed that, except for the first few years (1994-1998), the on-farm program had minimal impact in reducing the number of positive carcasses and PAHC. Most of the reductions in PAHC up to 2003 were, according to this analysis, due to various improvements in abattoir processes. Prospective simulations showed that minimal reductions in human health risk (PAHC) could be achieved with on-farm programs alone. Carcass decontamination was shown as the most effective means of reducing human risk, reducing PAHC to about 10% of the simulated 2004 level.

Factors influencing the prevalence of Salmonella spp. in swine farms: a meta-analysis approach

A systematic review and meta-analysis was conducted to identify study-level variables that could explain the variation in apparent Salmonella spp. prevalence estimates. Electronic and non-electronic literature searches from 1990 until 2005 were carried out to identify all studies related to the prevalence of subclinical Salmonella infection in swine. The searches were restricted to studies published in English, Spanish, and French. Clinical trials or any other study where an intervention was evaluated were excluded from this analysis. A template was designed to retrieve the most relevant variables and data abstraction was performed in duplicate. A total of 98 papers containing 82 animal-level and 156 farm-level studies were used in the analyses. The median farm-level and animal-level prevalences were 59% and 17%, respectively. Meta-regression analyses were carried out on both farm and animal-level data. Diagnostic procedure, sample size, and country where study was conducted were the three most important predictors in explaining the differences in Salmonella prevalences between studies. When compared to a farm with a apparent prevalence of 50% determined by the blood ELISA, prevalences based on culture of fecal samples were 39% lower and prevalences based on cecum and tissue cultures were 16% and 19% lower, respectively. Similar to farm-level models, animal-level models did not show any difference among serological tests and prevalence values based culture procedures were, on average, 9% lower than those from serological tests. Sample size was negatively associated with prevalence estimates. In conclusion, the methodology was useful for identifying and quantifying sources of variation in Salmonella apparent prevalence among studies and for establishing prevalence distributions that could be used as input parameters in risk assessment and decision models. The analysis provides some guidelines when interpreting and comparing apparent Salmonella prevalence results from studies using different study designs.

Prevalence of multidrug resistant (MDR) Salmonella in bovine dairy herds in western France

As a part of our effort in quantitative risk analysis of food-borne diseases, we carried out an epidemiologic study to estimate the prevalence of multidrug resistant (MDR) Salmonella in dairy herds situated in western France. The study population consisted of 489 farms in the region and manure or slurry was sampled from these operations and tested for the Salmonella spp. All strains isolated during the study were serotyped and tested for their antimicrobial susceptibility. Salmonella spp. was isolated from 8.1% (95% confidence interval (CI 95%): 4.5-13.3%) of the sampled herds. The herd prevalence of MDR Salmonella among the sampled herds was 1.9% (CI 95%: 0.5-5.4%). Spatial statistics were used to check for sampling representativeness and to determine if infected herds were clustered spatially.

In vitro effects of essential oils fromOstericum koreanum against antibiotic-resistantSalmonella spp

The essential oil fraction of Ostericum koreanum was analyzed by GC-MS. Inhibiting activities of this oil and its main components were tested by the broth dilution assay and disk diffusion test against one antibiotic-susceptible and two resistant strains of Salmonella enteritidis and S. typhimurium, respectively. The GC-MS analysis revealed thirty-four compounds; the main components were alpha-pinene (41.12%), rho-cresol (17.99%) and 4-methylacetophenone (7.90%). The essential oil of O. koreanum and its main components were significantly effective against the tested antibiotic-susceptible strains as well as against the resistant strains of the two Salmonella species, with MICs (minimum inhibitory concentrations) ranging from 2 mg/mL to 16 mg/mL. The anti-Salmonella effects of the oils were dose-dependent on Müller-Hinton agar plates in this experiment. Additionally, checkerboard titer test results demonstrated significant combined effects of streptomycin and O. koreanum oil or cresol, one of the main components of this oil, against the two streptomycin resistant strains of S. typhimurium, with FICIs ranging from 0.12 to 0.37.

An epidemiologic critique of current microbial risk assessment practices: the importance of prevalence and test accuracy data

Data deficiencies are impeding the development and validation of microbial risk assessment models. One such deficiency is the failure to adjust test-based (apparent) prevalence estimates to true prevalence estimates by correcting for the imperfect accuracy of tests that are used. Such adjustments will facilitate comparability of data from different populations and from the same population over time as tests change and the unbiased quantification of effects of mitigation strategies. True prevalence can be estimated from apparent prevalence using frequentist and Bayesian methods, but the latter are more flexible and can incorporate uncertainty in test accuracy and prior prevalence data. Both approaches can be used for single or multiple populations, but the Bayesian approach can better deal with clustered data, inferences for rare events, and uncertainty in multiple variables. Examples of prevalence inferences based on results of Salmonella culture are presented. The opportunity to adjust test-based prevalence estimates is predicated on the availability of sensitivity and specificity estimates. These estimates can be obtained from studies using archived gold standard (reference) samples, by screening with the new test and follow-up of test-positive and test-negative samples with a gold standard test, and by use of latent class methods, which make no assumptions about the true status of each sampling unit. Latent class analysis can be done with maximum likelihood and Bayesian methods, and an example of their use in the evaluation of tests for Toxoplasma gondii in pigs is presented. Guidelines are proposed for more transparent incorporation of test data into microbial risk assessments.

Microbial contamination of carcasses, meat, and equipment from an Iberian pork cutting plant

An assessment and follow-up of the microbial contamination of an Iberian pork cutting room is presented. Samples were taken from carcasses (n = 76), meat pieces (three types, n = 71), meat for dry-cured sausages (3 types, n = 66), and surfaces of equipment (n = 158). Aerobic plate counts (APC) at 37 degrees C on meat pieces (primal cuts) were lower than on carcasses (3.62 log CFU/10 cm2 against 4.63 log CFU/10 cm2), probably owing to the removal of the skin. However, more than 80% of the meat pieces showed presence of Escherichia coli. For the three types of meat intended for dry-cured sausages, higher counts (P < 0.001) were found for meat type 3--an important cut obtained from the vertebral column--at 2.62 log CFU/g for E. coli; the particular surface used in the handling of meat type 3 also showed high counts (P < 0.001) for E. coli. Consequently, attention should be paid to the hazard analysis critical control point plan at this stage. Salmonella was isolated from 3.94% of the carcass surfaces (perianal zone), 4.46% of meat pieces, and 13.58% of meat for dry-cured sausages. Moreover, the percentages for isolation of Salmonella from carcasses of Iberian pigs (extensive rearing) in our study were lower than those generally reported in the literature for "white pigs" (intensive rearing). Coagulase-positive Staphylococcus aureus was isolated in 31.82% of meat samples for dry-cured sausages, in 16.90% of meat pieces, and in 15.50% of the equipment after 4 h of work. Of the coagulase-positive strains isolated, 47.61% were producers of enterotoxin.