Andrijana Rajić

Scoping Review on Search Queries and Social Media for Disease Surveillance: A Chronology of Innovation

Background The threat of a global pandemic posed by outbreaks of influenza H5N1 (1997) and Severe Acute Respiratory Syndrome (SARS, 2002), both diseases of zoonotic origin, provoked interest in improving early warning systems and reinforced the need for combining data from different sources. It led to the use of search query data from search engines such as Google and Yahoo! as an indicator of when and where influenza was occurring. This methodology has subsequently been extended to other diseases and has led to experimentation with new types of social media for disease surveillance. Objective The objective of this scoping review was to formally assess the current state of knowledge regarding the use of search queries and social media for disease surveillance in order to inform future work on early detection and more effective mitigation of the effects of foodborne illness. Methods Structured scoping review methods were used to identify, characterize, and evaluate all published primary research, expert review, and commentary articles regarding the use of social media in surveillance of infectious diseases from 2002-2011. Results Thirty-two primary research articles and 19 reviews and case studies were identified as relevant. Most relevant citations were peer-reviewed journal articles (29/32, 91%) published in 2010-11 (28/32, 88%) and reported use of a Google program for surveillance of influenza. Only four primary research articles investigated social media in the context of foodborne disease or gastroenteritis. Most authors (21/32 articles, 66%) reported that social media-based surveillance had comparable performance when compared to an existing surveillance program. The most commonly reported strengths of social media surveillance programs included their effectiveness (21/32, 66%) and rapid detection of disease (21/32, 66%). The most commonly reported weaknesses were the potential for false positive (16/32, 50%) and false negative (11/32, 34%) results. Most authors (24/32, 75%) recommended that social media programs should primarily be used to support existing surveillance programs. Conclusions The use of search queries and social media for disease surveillance are relatively recent phenomena (first reported in 2006). Both the tools themselves and the methodologies for exploiting them are evolving over time. While their accuracy, speed, and cost compare favorably with existing surveillance systems, the primary challenge is to refine the data signal by reducing surrounding noise. Further developments in digital disease surveillance have the potential to improve sensitivity and specificity, passively through advances in machine learning and actively through engagement of users. Adoption, even as supporting systems for existing surveillance, will entail a high level of familiarity with the tools and collaboration across jurisdictions.

Comparison of the prevalence of bacterial enteropathogens, potentially zoonotic bacteria and bacterial resistance to antimicrobials in organic and conventional poultry, swine and beef production: a systematic review and meta-analysis

The prevalences of zoonotic and potentially zoonotic bacteria or bacteria resistant to antimicrobials in organic and conventional poultry, swine and beef production were compared using systematic review and meta-analysis methodology. Thirty-eight articles were included in the review. The prevalence of Campylobacter was higher in organic broiler chickens at slaughter, but no difference in prevalence was observed in retail chicken. Campylobacter isolates from conventional retail chicken were more likely to be ciprofloxacin-resistant (odds ratio 9.62, 95% confidence interval 5.67-16.35). Bacteria isolated from conventional animal production exhibited a higher prevalence of resistance to antimicrobials; however, the recovery of some resistant strains was also identified in organic animal production, where there is an apparent reduced antimicrobial selection pressure. Limited or inconsistent research was identified in studies examining the prevalence of zoonotic and potentially zoonotic bacteria in other food-animal species. There is a need for further research of sufficient quality in this area.

Associations between reported on-farm antimicrobial use practices and observed antimicrobial resistance in generic fecal Escherichia coli isolated from Alberta finishing swine farms.

Multilevel random intercept logistic and Poisson regression were used to model associations between various antimicrobial use practices and resistance to individual and multiple antimicrobials among generic fecal Escherichia coli isolated from Alberta finishing swine. In-feed antimicrobial use in finishers was significantly associated with increased risk of resistance to ampicillin, chloramphenicol, streptomycin, and sulfisoxazole in generic E. coli isolates. Chlortetracycline use in grower rations was associated with ampicillin and tetracycline resistance. Use of in-feed antimicrobials in finishers was significantly associated with increased risk of resistance of generic E. coli to multiple antimicrobials. The study findings suggest that certain farm-level interventions related to antimicrobial use might be beneficial in reducing development and emergence of antimicrobial resistance in swine populations.

Knowledge and attitudes towards food safety among Canadian dairy producers

The Canadian dairy industry has recently begun implementing an on-farm food-safety (OFFS) program called Canadian Quality Milk (CQM). For CQM to be effective, producers should be familiar with food-safety hazards in their industry and have an adequate understanding of on-farm good production practices that are necessary to ensure safe food. To assess their knowledge and attitudes towards food safety, a postal questionnaire was administered to all (n=10,474) Canadian dairy producers enrolled in dairy herd-improvement organizations in 2008. The response rate was 20.9% (2185/10,474). Most producers (88.7%) reported that they or their families consume unpasteurized milk from their bulk milk tanks and 36.3% indicated that consumers should be able to purchase unpasteurized milk in Canada. Producers who reported completion of a dairy-health management course (OR=0.74, 95% CI: 0.60, 0.92) and participation in CQM (OR=0.79, 95% CI: 0.64, 0.97) were less likely to support the availability of unpasteurized milk for consumers, while organic producers (OR=2.10, 95% CI: 1.27, 3.47), younger producers (aged <30) and producers with smaller herds were more likely to favour this practice. Two-thirds of producers (66.7%) were concerned that antimicrobial resistance (AMR) might preclude successful treatment of sick cattle. Producers who completed a dairy-health management course (OR=1.37, 95% CI: 1.11, 1.69), organic producers (OR=2.00, 95% CI: 1.09, 3.69) and producers from Quebec compared to each other province were more likely to indicate concern about AMR. Most producers reported that Salmonella (74.2%) and Escherichia coli (73.0%) could be transmitted through contaminated beef or milk to humans, while most were not sure or did not think that Brucella (70.3%) and Cryptosporidium (88.5%) could be transmitted via these routes. Most producers did not perceive that any type of farm visitor has a high risk of introducing infectious agents into their herds. Producers rated veterinarians as very knowledgeable about OFFS (90.9% answered 4 or 5 on a five-point scale) and a favoured (73.1%) source of information about food safety. In contrast, only 13.2% and 30.2% of producers, respectively, indicated that consumers and government personnel are knowledgeable about OFFS. Targeted continuing education for dairy producers in Canada should address the major gaps in knowledge and attitudes towards food safety identified in this study, and veterinarians should be included as key knowledge-transfer informants.

An overview of microbial food safety programs in beef, pork, and poultry from farm to processing in Canada.

Canadas vision for the agri-food industry in the 21st century is the establishment of a national food safety system employing hazard analysis and critical control point (HACCP) principles and microbiological verification tools, with traceability throughout the gate-to-plate continuum. Voluntary on-farm food safety (OFFS) programs, based in part on HACCP principles, provide producers with guidelines for good production practices focused on general hygiene and biosecurity. OFFS programs in beef cattle, swine, and poultry are currently being evaluated through a national recognition program of the Canadian Food Inspection Agency. Mandatory HACCP programs in federal meat facilities include microbial testing for generic Escherichia coli to verify effectiveness of the processors dressing procedure, specific testing of ground meat for E. coli O157:H7, with zero tolerance for this organism in the tested lot, and Salmonella testing of raw products. Health Canadas policy on Listeria monocytogenes divides ready-to-eat products into three risk categories, with products previously implicated as the source of an outbreak receiving the highest priority for inspection and compliance. A national mandatory identification program to track livestock from the herd of origin to carcass inspection has been established. Can-Trace, a data standard for all food commodities, has been designed to facilitate tracking foods from the point of origin to the consumer. Although much work has already been done, a coherent national food safety strategy and concerted efforts by all stakeholders are needed to realize this vision. Cooperation of many government agencies with shared responsibility for food safety and public health will be essential.

A scoping review of published research on the relinquishment of companion animals.

Globally, large populations of companion animals are relinquished each year. The purpose of this scoping review was to identify all published research investigating companion-animal relinquishment to map out and evaluate research gaps, needs, and opportunities. A comprehensive search strategy was implemented in 4 online databases, identified citations were screened, and relevant articles were procured and characterized. From 6,848 unique citations identified, 192 were confirmed relevant, including 115 primary-research articles and 77 reviews and commentaries. The majority of these articles originated from the United States (131; 68.2%); 74 (38.5%) of them have been published since 2006. Among the primary-research articles, 84 (73.0%) investigated reasons for companion-animal relinquishment. The most commonly studied reasons were aggressive companion-animal behaviors (49; 58.3%); moving, rental, or housing issues (45; 53.6%); and caretaker personal issues (42; 50.0%). Only 17 primary-research articles investigated interventions to prevent companion-animal relinquishment. The quantity of research into reasons for relinquishment highlights an opportunity for future knowledge-synthesis activities in this area, including systematic review and meta-analysis. In comparison, the limited research into interventions identifies a priority for new research.

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.

Antimicrobial use and resistance in aquaculture: findings of a globally administered survey of aquaculture-allied professionals.

There is limited published information regarding antimicrobial use (AMU) and antimicrobial resistance (AMR) in aquaculture. Our objective was to determine the opinions of aquaculture‐allied professionals around the world on the frequency of AMU and AMR in common aquatic species. The study questionnaire included five sections: respondent demographics, extent of AMU in aquaculture, frequency of observations of AMR in aquaculture, AMR monitoring and surveillance and antimicrobial susceptibility testing in various jurisdictions. It was administered in English and Spanish to 604 professionals in 25 countries and with varying expertise in aquaculture. The response rate was 33% (199/604). Over half of the participants had >10 years of experience in aquaculture: 70% (140/199) were involved in fish health/clinical work and their primary experience was with salmon, tilapia, trout, shrimp (including prawn) and/or catfish. Tetracycline use was reported by 28%, 46%, 18%, 37% and 9% of respondents working with catfish, salmon, tilapia, trout and shrimp, respectively. Resistance to tetracycline in one or more species of bacteria was reported as ‘frequent‐to‐almost always’ for the same aquaculture species by 39%, 28%, 17%, 52% and 36% of respondents, respectively. ‘Frequent‐to‐almost always’ use of quinolone was reported by 70% (32/46) and 67% (8/12) of respondents from the United States and Canada, respectively, where quinolone products are not approved for aquaculture, and extra‐label fluoroquinolone use is either prohibited (United States) or discouraged (Canada). Similar frequencies of quinolone use were also reported by the majority of respondents from Europe [70% (7/10)] and Asia [90% (9/10)] where labelled indications exist. This baseline information can be used to prioritize research or surveillance for AMU and AMR in aquaculture.