Barbara Wilhelm

The Effect of Hazard Analysis Critical Control Point Programs on Microbial Contamination of Carcasses in Abattoirs: A Systematic Review of Published Data

Hazard analysis critical control point (HACCP) programs have been endorsed and implemented globally to enhance food safety. Our objective was to identify, assess, and summarize or synthesize the published research investigating the effect of HACCP programs on microbial prevalence and concentration on food animal carcasses in abattoirs through primary processing. The results of microbial testing pre- and post-HACCP implementation were reported in only 19 studies, mostly investigating beef (n=13 studies) and pork (n=8 studies) carcasses. In 12 of 13 studies measuring aerobic bacterial counts, reductions were reported on beef (7/8 studies), pork (3/3), poultry (1/1), and sheep (1/1). Significant (p<0.05) reductions in prevalence of Salmonella spp. were reported in studies on pork (2/3 studies) and poultry carcasses (3/3); no significant reductions were reported on beef carcasses (0/8 studies). These trends were confirmed through meta-analysis of these data; however, powerful meta-analysis was precluded because of an overall scarcity of individual studies and significant heterogeneity across studies. Australia reported extensive national data spanning the period from 4 years prior to HACCP implementation to 4 years post-HACCP, indicating reduction in microbial prevalence and concentration on beef carcasses in abattoirs slaughtering beef for export; however, the effect of abattoir changes initiated independent of HACCP could not be excluded. More primary research and access to relevant proprietary data are needed to properly evaluate HACCP program effectiveness using modeling techniques capable of differentiating the effects of HACCP from other concurrent factors.

Prevalence of Zoonotic or Potentially Zoonotic Bacteria, Antimicrobial Resistance, and Somatic Cell Counts in Organic Dairy Production: Current Knowledge and Research Gaps

The reviews objective was to identify, evaluate, and summarize the findings of all primary research published in English or French, investigating prevalence of zoonotic or potentially zoonotic bacteria, bacterial resistance to antimicrobials, and somatic cell count (SCC) in organic dairy production, or comparing organic and conventional dairy production, using a systematic review methodology. Among 47 studies included in the review, 32 comparison studies were suitable for quality assessment. Fifteen studies were not assessed for quality, due to their descriptive nature or a low sample size (n <or= 2 farms). Overall, bacterial outcomes were reported in 17 studies, and prevalence of antimicrobial resistance (AMR) and multidrug resistance (MDR) of zoonotic or potentially zoonotic bacteria in 12 and 7 studies, respectively. Campylobacter spp., Escherichia coli including Shiga toxin-producing strains, Salmonella spp., Staphylococcus aureus, and SCC were investigated in 2, 7, 4, 6, and 15 studies, respectively. Contradictory findings were reported for differences in bacterial outcomes and SCC between dairy production types (organic vs. conventional). Lower prevalence of AMR on organic dairy farms was reported more consistently in studies conducted in the United States, as opposed to those conducted in Europe. These conflicting findings may result from geographic differences in organic production regulations governing antimicrobial usage, use of antimicrobials in conventional dairy production, and baseline prevalence, as well as laboratory methods, study designs, or methods of analysis employed. The majority (four of seven) of MDR investigations reported no significant differences in prevalence. Overall, only 9 of 32 studies met all five methodological soundness criteria. More well designed, executed, and reported primary research is needed at the farm and post-farm levels.

The application of knowledge synthesis methods in agri-food public health: recent advancements, challenges and opportunities.

Knowledge synthesis refers to the integration of findings from individual research studies on a given topic or question into the global knowledge base. The application of knowledge synthesis methods, particularly systematic reviews and meta-analysis, has increased considerably in the agri-food public health sector over the past decade and this trend is expected to continue. The objectives of our review were: (1) to describe the most promising knowledge synthesis methods and their applicability in agri-food public health, and (2) to summarize the recent advancements, challenges, and opportunities in the use of systematic review and meta-analysis methods in this sector. We performed a structured review of knowledge synthesis literature from various disciplines to address the first objective, and used comprehensive insights and experiences in applying these methods in the agri-food public health sector to inform the second objective. We describe five knowledge synthesis methods that can be used to address various agri-food public health questions or topics under different conditions and contexts. Scoping reviews describe the main characteristics and knowledge gaps in a broad research field and can be used to evaluate opportunities for prioritizing focused questions for related systematic reviews. Structured rapid reviews are streamlined systematic reviews conducted within a short timeframe to inform urgent decision-making. Mixed-method and qualitative reviews synthesize diverse sources of contextual knowledge (e.g. socio-cognitive, economic, and feasibility considerations). Systematic reviews are a structured and transparent method used to summarize and synthesize literature on a clearly-defined question, and meta-analysis is the statistical combination of data from multiple individual studies. We briefly describe and discuss key advancements in the use of systematic reviews and meta-analysis, including: risk-of-bias assessments; an overall quality-of-evidence approach; engagement of stakeholders; Bayesian, multivariate, and network meta-analysis; and synthesis of diagnostic test accuracy studies. We also highlight several challenges and opportunities in the conduct of systematic reviews (e.g. inclusion of grey literature, minimizing language bias, and optimizing search strategies) and meta-analysis (e.g. inclusion of observational studies and approaches to address the insufficient reporting of data and significant heterogeneity). Many of these developments have yet to be comprehensively applied and evaluated in an agri-food public health context, and more research is needed in this area. There is a need to strengthen knowledge synthesis capacity and infrastructure at the regional, national, and international levels in this sector to ensure that the best available knowledge is used to inform future decision-making about agri-food public health issues.

Prevalence of Zoonotic Bacteria in Wild and Farmed Aquatic Species and Seafood: A Scoping Study, Systematic Review, and Meta-analysis of Published Research

Increased reliance on seafood has brought to light concerns regarding food safety, but the information to inform risk assessment or surveillance needs is lacking. A scoping study (ScS) was conducted to characterize published research investigating selected zoonotic bacteria and public health topics in various wild and farmed aquatic species and seafood. This was followed by a systematic review (SR) on selected bacteria (Aeromonas spp., generic Escherichia coli, Salmonella spp., and Vibrio spp.) and aquatic species (clams, mussels, oysters, salmon, and shrimp [including prawn]); a meta-analysis (MA) was conducted only at the retail level due to considerable variability among various pathogen/seafood combinations. The ScS revealed the most frequently investigated themes were farm-level prevalence and intervention research for Vibrio spp. and Aeromonas spp. Antimicrobial use (AMU) and the association between AMU and antimicrobial resistance were rarely investigated. The SR indicated a consistent lack of reporting regarding study methodology and results, precluding the use of many studies in and full benefits of MA. MA of Aeromonas, E. coli, and Salmonella prevalence in retail salmon resulted in pooled estimates of 13% (6-27%), 2% (0.1-11%), and 1% (0-5%), respectively. When MA of pathogen/seafood combination resulted in statistically significant heterogeneity (p<0.1), median/range were reported at the region level. The results from our ScS, SR, and MA could be used for better design of future bacteriological surveys of seafood and as inputs for risk assessments or surveillance initiatives in this field.

Survey of Canadian retail pork chops and pork livers for detection of hepatitis E virus, norovirus, and rotavirus using real time RT-PCR.

Over the past 15 years, hepatitis E virus (HEV), norovirus (NoV), and rotavirus (RV) have been hypothesized to be potentially zoonotic; swine and pork have been suggested as possible human infection sources for all 3 viruses. Our objective was to estimate HEV, NoV, and RV prevalence and load on Canadian retail pork chops and livers. Using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) sampling platform, pork livers (n=283) and chops (n=599) were collected, processed, and assayed for the 3 viruses by four collaborating federal laboratories using validated real time reverse transcriptase polymerase chain reactions (qRT-PCR). Follow-up qRT-PCR estimating viral load in genomic copies/g was followed by nested classical RT-PCR and isolate sequencing of a partial segment of the ORF2 gene. Local alignments were performed using MUSCLE (Multiple Sequence Comparison by Log-Expectation); a phylogenetic tree was created. Twenty-five livers and 6 chops were classified positive (thresholds for viral RNA detected in both replicates of the assay) or suspect (thresholds detected in one of two replicates) for HEV. Follow-up qRT-PCR detected HEV on 16 livers, 0 chops, and nested classical RT-PCR, on 14 livers and 0 chops. Initial qRT-PCR classified 12 chops suspect for NoV. Follow-up qRT-PCR detected viral RNA on only one sample with thresholds greater than 40 in both replicates. No amplicon was yielded, and therefore no isolate was sequenced from this sample. Partial ORF2 genes from 14 HEV isolates were sequenced, and compared via sequence identity and phylogenetic analysis with selected human case isolates listed in NCBI-GenBank. Overall, HEV prevalence on retail pork was comparable with other published reports.

Assessment of the efficacy and quality of evidence for five on-farm interventions for Salmonella reduction in grow-finish swine: A systematic review and meta-analysis

Five on-farm practices for reduction of Salmonella shedding or sero-prevalence in grow-finish swine were selected through scoping study and expert consultation. Specific examples were selected based on supporting evidence from at least one controlled trial (CT), and availability to Canadian swine producers. Efficacy was evaluated using systematic review and meta-analysis (SR-MA) methodology. A modified Grading of Recommendations, Assessment, and Evaluation (GRADE) approach was applied to assess the quality of evidence for each intervention, and a summary of findings table was developed to present findings at-a-glance. MA of the small dataset of CTs investigating feeding meal, and measuring serology, yielded a significant summary estimate of efficacy (odds ratio (OR)=0.21; 95% confidence intervals (CI): 0.14, 0.31) with non-significant heterogeneity (P>0.10). MA of the dataset investigating inclusion of organic acids in the ration, measuring serology, yielded a significant summary estimate with significant heterogeneity across studies (P<0.001, I(2)=91%) precluding presentation of a single summary estimate; a range of results were reported (OR Range: 28 (1.6, 498); 0.07 (CI: 0.042, 0.33)). Pen disinfection between batches of finishers was studied in one large CT measuring both fecal culture (OR 0.84 (0.68, 1.1)) and serology (OR 0.48 (0.40, 0.58)) outcomes. The dataset investigating Salmonella spp. vaccination contained inconsistent findings (OR Range: 4.5 (1.3, 15); 0.07 (0.008, 0.68)), with significant heterogeneity across studies (P=0.005, I(2)=82), assessed measuring fecal culture. MA of the dataset investigating inclusion of in-feed tetracyclines yielded a significant OR indicating a potential harmful effect, measuring fecal culture, (OR Range: 14 (1.9, 108); 1.0 (0.43, 2.5)) with significant heterogeneity (P=0.003, I(2)=82%) across studies, suggesting some potential for withdrawal of in-feed tetracyclines to reduce Salmonella shedding. Therefore our ranking of intervention efficacy is: feeding meal>inclusion of acids in ration, feeder pen disinfection or Salmonella spp. vaccination>in-feed tetrayclines. Study design characteristics increasing risk of bias, including failure to justify sample size (19 of 31 studies) and failure to report random or systematic sampling (13 of 31 studies), resulted in modified GRADE evidence rankings of low for these interventions. This suggests that further research is likely to affect our findings. Field CTs investigating herd-level interventions with measurements at the herd- and individual-levels are recommended. Overall, SR-MA was a useful approach for ranking efficacy, and GRADE offered a transparent method for ranking quality of evidence, although both were limited by the small number of comparable studies available.

A systematic review-meta-analysis of chilling interventions and a meta-regression of various processing interventions for Salmonella contamination of chicken

CONTEXTnThe results of individual studies investigating the efficacy of chilling and other processing interventions on Salmonella prevalence or concentration in broiler chicken carcasses are inconsistent or contradictory.nnnOBJECTIVEnDetermine efficacy of chilling on reducing Salmonella prevalence or concentration on broiler carcasses using systematic review-meta-analysis, and explore sources of heterogeneity among studies investigating various processing interventions through meta-regression.nnnDATA SOURCESnA comprehensive search included electronic search in six databases, manual search of reference lists of topic-related articles, and consultation with five topic experts to assure that all relevant intervention research was identified. STUDY INCLUSION: Primary intervention research, published in English, encompassing control, challenge, cohort, or before-and-after study designs investigating the efficacy of any chilling or other processing interventions on Salmonella prevalence or concentration in broiler chicken carcasses. RISK OF BIAS ASSESSMENT AND DATA EXTRACTION: Data pertaining to study methodology and reported results, chilling or other processing intervention parameters, populations sampled and outcomes measured were assessed for methodological soundness and extracted by two independent reviewers using pretested checklists.nnnRESULTSnRandom-effects meta-analyses of immersion chilling with chlorine (n=9 trials), acetic acid (n=16) and potable water (n=13) trended towards reductions in the odds or log(10)CFU/ml of Salmonella. Significant heterogeneity (P-value≤0.1 and I(2)>25%) precluded the reporting of pooled summary effect estimates. Meta-regression of all processing interventions indicated that serotype, disinfectant type and treatment time and pH were significantly associated with studies reporting reductions in concentration while study design, population sampled, study setting, publication date, intervention and disinfectant type, and treatment pH were significantly associated with studies reporting reductions in prevalence. Methodological and reporting flaws were consistently observed in relevant intervention research as well as a lack of studies conducted under commercial conditions and using Salmonella concentration outcomes.nnnCONCLUSIONSnChilling may be effective at reducing Salmonella concentration and prevalence, but significant heterogeneity precluded reporting of pooled summary effect estimates for many chilling interventions. Investigations into potential sources of heterogeneity among all processing interventions found that the use of other chemical disinfectants, such as organic acids and surfactants might result in larger reductions in Salmonella contamination than more commonly utilized oxidizing agents like chlorine.

A systematic review-meta-analysis and meta-regression on the effect of selected competitive exclusion products on Salmonella spp. prevalence and concentration in broiler chickens.

The effectiveness of various competitive exclusion (CE) products for reducing Salmonella colonization in broiler chickens was evaluated using systematic review-meta-analysis-meta-regression (SR-MA-MR). Relevance screening identified 201 relevant studies that were subjected to methodological assessment. Of these studies, 159 were suitable for data extraction, 66 were presented in a number of MAs and 130 were examined in a meta-regression (MR). Fourteen different CE products were identified, 9 of them commercial products, and the most common route of administration was oral gavage (63.7% of trials). Meta-analyses indicated that a number of CE products reduce Salmonella colonization in broilers, the most effective one being Preempt™ which was formerly known as CF-3. Five study characteristics (publication year, CE type, CE route, sample origin, and Salmonella serovar administered/recovered) and three methodological soundness characteristics (treatment assignment, intervention and laboratory methods description) were retained as statistically significant (p<0.05) in the final MR model. The MR analysis indicated that, undefined CE products outperformed all commercial products, except for: Preempt™ and Broilact(®). Both were considered comparable to the undefined chicken source CE culture products in effectiveness. The administration of CE through spraying the chicks at the hatchery was determined to be just as effective as the oral gavage treatment, and more practical for farmers to administer. The results of this study could be useful in decision-making concerning the on-farm use of CE products in broiler chickens, and as inputs for risk assessments as the industry pushes for more antibiotic-free alternatives. Out of the various interventions to reduce Salmonella colonization in broilers on-farm, CE was the most studied; its inability to be licenced in certain countries and proof of consistent efficacy remains a barrier.

Preliminary molecular epidemiological investigation of hepatitis E virus sequences from Québec, Canada.

Our study objective was to describe the Canadian Hepatitis E virus (HEV) sequences currently cataloged in GenBank from three populations: commercially raised pigs, retail pork, and locally acquired Hepatitis E cases, and to interpret the molecular evidence they provide. We searched the GenBank for any/all Canadian HEV sequences from these populations, and identified highly similar matches using the Basic Local Alignment Search Tool (BLAST) algorithm, studying sequences of the partial ORF2 gene. We validated the findings made using Multiple Sequence Comparison by Log-Expectation (MUSCLE) and Clustal 2 programs for multiple sequence alignments, as inputs to estimate dendrograms using both neighbour-joining and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) methods. The GenBank search yielded 47 sequences collected from pigs: 32 sequences from two to four month old commercial pigs in Québec, one from three to four month old pigs at a research station in Ontario, one from two month old pigs in a commercial Saskatchewan herd, and 13 collected from finisher pigs in a national survey. Additionally, 14 sequences were collected from a national survey of Canadian retail pork livers, and seven sequences from two Canadian pediatric patients with locally acquired Hepatitis E, both from the province of Québec. All sequences belonged to genotype 3. Eight of the 14 sequences from retail pork livers had human-derived sequences in their top ten BLAST matches; six did not. Those eight sequences having close human BLAST matches clustered within a dendrogram, as did those with no close human BLAST matches. Human sequences with close matches to the eight retail sequences included both of the Québec Hepatitis E cases, as well as sequences from Japanese Hepatitis E cases, and Japanese blood donors. Seven of the eight HEV sequences from retail liver with close human BLAST matches originated in Québec. Kulldorffs spatial scan statistic showed a significant (P<0.05) spatial cluster of these sequences, but not of the overall dataset of 12 HEV sequences collected from Québec retail livers. All seven retail liver sequences with close human matches were processed in-store. We conclude that some Canadian sequences of HEV collected from pigs/pork are more closely related to human sequences than others, and hypothesize that detection of some HEV sequences recovered from Canadian retail pork livers may be associated with exposure to human shedding. More research needs to be conducted at the processing level to help understand the molecular epidemiology of HEV in Canadian retail pork.

Presence, viral load and characterization of Torque teno sus viruses in liver and pork chop samples at retail

Torque teno viruses (TTV) are widespread in humans, swine as well as in several other animal species. In market ready swine, the reported prevalence ranges between 11% and 100%. Through a national retail sampling plan from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) program, 283 and 599 liver and pork chop samples, respectively, were collected over a 12-month period from commercial establishments in 5 selected geographical regions of Canada to assess the presence of Torque teno sus viruses (TTSuVs) in these products. TTSuVs were detected in 97.9% of pork chops with viral loads ranging between 1×10(4) and 9.9×10(5) genomic copies (gc)/g and 98.6% of liver samples with viral loads ranging from 1×10(5) to 9.9×10(6) gc/g. A selection of 20 positive samples (10 pork chop and 10 liver) from the 5 geographical regions were further tested for the production, of a 305bp fragment for TTSuV1 and a 253bp fragment for TTSuV2 in the non-coding region. TTSuV1 was present in all 10 liver and 10 pork chops samples while TTSuV2 was detected in 10 liver and 9 pork chop samples. Two different TTSuV1 sequences were simultaneously detected from 5 of 20 samples and 2 different TTSuV2 sequences were detected from 6 of 19 samples. The omnipresence of TTSuVs in commercial pork samples may allow its use as a viral indicator to monitor the effectiveness of cleaning and disinfecting process in slaughtering, cutting, slicing and packaging facilities.