Scoping review to identify potential non-antimicrobial interventions to mitigate antimicrobial resistance in commensal enteric bacteria in North American cattle production systems

Comparison of multiple international metrics for benchmarking antibiotic usage (ABU) using UK beef and sheep data

BACKGROUND

Accurate surveillance of livestock antibiotic usage (ABU) at the farm level is an increasingly important part of national antibiotic stewardship initiatives. Numerous ABU indicators or metrics have been developed in Europe and North America but the comparability of these metrics is poorly understood. For policymakers, understanding the relationship between metrics is important when considering the risks posed by ABU and how to regulate them, at the national level, and regulate international trade access in livestock products between countries who use different ABU metrics.

OBJECTIVES

To quantify the patterns of ABU among beef (cattle) and lamb (sheep) production systems. To explore ABU variation between farm types across seven ABU metrics developed in Europe and North America using a common dataset of sheep and beef farms' antibiotic purchases from the UK.

METHODS

A dataset of >16 200 antibiotic sales events to 686 farm enterprises of different types underwent quantitative analysis. Correlation matrixes were generated for seven international ABU metrics.

RESULTS

ABU was significantly higher among calf-rearers. Across all farm types, tetracyclines and β-lactams were the predominant groups by mass, but represent a similar dose equivalent to macrolides across most farm types. Good agreement (>0.9) was observed between metrics.

CONCLUSIONS

Reliable metrics to accurately benchmark farms are crucial for maintaining confidence of farmers in the fairness of any surveillance system, especially when the ranking of any given system may be linked to financial subsidies or penalties and also when negotiating import and export access for livestock products between countries.

Exploration of plasma metabolite levels in healthy nursery pigs in response to environmental enrichment and disease resilience

The purpose of this study was to explore plasma metabolite levels in young healthy pigs and their potential association with disease resilience and estimate genetic and phenotypic correlation with the change in lymphocyte concentration following disease challenge. Plasma samples were collected from 968 healthy nursery pigs over 15 batches at an average of 28 ± 3.23 d of age. Forty-four metabolites were identified and quantified by nuclear magnetic resonance. Pigs were then introduced into a natural disease challenge barn, and were classified into four groups based on the growth rate of each animal in the grow-to-finish phase (GFGR) and treatment rate (TR): resilient (RES), average (MID), susceptible (SUS), and dead (pigs that died before harvest). Blood samples were collected from all pigs before and 2 wk after disease challenge and complete blood count was determined. Environmental enrichment (inedible point source objects) was provided for half of the pigs in seven batches (N = 205) to evaluate its impact on resilience and metabolite concentrations. Concentration of all metabolites was affected by batch, while entry age affected the concentration of 16 metabolites. The concentration of creatinine was significantly lower for pigs classified as "dead" and "susceptible" when compared to "average" (P < 0.05). Pigs that received enrichment had significantly lower concentrations of six metabolites compared with pigs that did not receive enrichment (P ≤ 0.05). Both, group classification and enrichment affected metabolites that are involved in the same pathways of valine, leucine, and isoleucine biosynthesis and degradation. Resilient pigs had higher increase in lymphocyte concentration after disease challenge. The concentration of plasma l-α-aminobutyric acid was significantly negatively genetically correlated with the change in lymphocyte concentration following challenge. In conclusion, creatinine concentration in healthy nursery pigs was lower in pigs classified as susceptible or dead after disease challenge, whilst l-α-aminobutyric may be a genetic biomarker of lymphocyte response after pathogen exposure, and both deserve further investigation. Batch, entry age, and environmental enrichment were important factors affecting the concentration of metabolites and should be taken into consideration in future studies.

A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project)

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

Enterobacteriaceae in food safety with an emphasis on raw milk and meat

There has been a growing interest in traditional dairy (such as raw milk cheeses) and meat products, in recent years. However, these products are suitable and nutrient medium and may be easily contaminated by microorganisms such as Enterobacteriaceae. Enterobacteriaceae are considered to be the indicator bacteria for microbiological quality of food and hygiene status of a production process. Additionally, the food contaminated by Enterobacteriaceae poses a microbiological risk for consumers. In fact, the contamination of raw milk and meat by Enterobacteriaceae amid manufacturing may easily occur from various environmental sources, and this group of bacteria is frequently detected in dairy and meat products. Therefore, monitoring the microbiological quality of the used raw material and maintaining high standards of hygiene in the production process are mandatory for a high quality of traditional products and the safety of the potential consumers. The goal of this review is to present the most recent survey on Enterobacteriaceae growth, number, and distribution in raw milk cheeses and meat, as well as to discuss the sources of contamination and methods of control. KEY POINTS: • Enterobacteriaceae: role and importance in milk and meat products, EU legal regulations • Dynamics, distribution, and survival of Enterobacteriaceae in milk and meat • Mechanisms of control of Enterobacteriaceae in dairy products.

Age Dependence of Antimicrobial Resistance Among Fecal Bacteria in Animals: A Scoping Review

Introduction: A phenomenon of decreasing antimicrobial resistance (AMR) among fecal bacteria as food animals age has been noted in multiple field studies. We conducted a scoping review to summarize the extent, range, and nature of research activity and the data for the following question: "does AMR among enteric/fecal bacteria predictably shift as animals get older?". Methods: This review followed a scoping review methodology framework. Pertinent literature published up until November 2018 for all animals (except humans) was retrieved using keyword searches in two online databases, namely, PubMed® and the Web of Science™ Core Collection, without filtering publication date, geographic location, or language. Data were extracted from the included studies, summarized, and plotted. Study quality was also assessed using the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) guidelines for all included papers. Results: The publications with detailed relevant data (n = 62) in food animals, poultry, and dogs were identified. These included longitudinal studies (n = 32), cross-sectional studies of different age groups within one food animal production system or small-animal catchment area (n = 16), and experimental or diet trials (n = 14). A decline in host-level prevalence and/or within-host abundance of AMR among fecal bacteria in production beef, dairy cattle, and swine was reported in nearly two-thirds (65%) of the identified studies in different geographic locations from the 1970's to 2018. Mixed results, with AMR abundance among fecal bacteria either increasing or decreasing with age, have been reported in poultry (broiler chicken, layer, and grow-out turkey) and dogs. Conclusions: Quantitative synthesis of the data suggests that the age-dependent AMR phenomenon in cattle and swine is observed irrespective of geographic location and specific production practices. It is unclear whether the phenomenon predates or is related to antimicrobial drug use. However, almost 50% of the identified studies predate recent changes in antimicrobial drug use policy and regulations in food animals in the United States and elsewhere.

Non-antibiotic approaches for disease prevention and control in beef and veal production: a scoping review

Livestock producers are encouraged to reduce the use of antibiotics belonging to classes of medical importance to humans. We conducted a scoping review on non-antibiotic interventions in the form of products or management practices that could potentially reduce the need for antibiotics in beef and veal animals living under intensive production conditions. Our objectives were to systematically describe the research on this broad topic, identify specific topics that could feasibly support systematic reviews, and identify knowledge gaps. Multiple databases were searched. Two reviewers independently screened and charted the data. From the 13,598 articles screened, 722 relevant articles were charted. The number of relevant articles increased steadily from 1990. The Western European research was dominated by veal production studies whereas the North American research was dominated by beef production studies. The interventions and outcomes measured were diverse. The four most frequent interventions included non-antibiotic feed additives, vaccinations, breed type, and feed type. The four most frequent outcomes were indices of immunity, non-specific morbidity, respiratory disease, and mortality. There were seven topic areas evaluated in clinical trials that may share enough commonality to support systemic reviews. There was a dearth of studies in which interventions were compared to antibiotic comparison groups.

Scoping Reviews, Systematic Reviews, and Meta-Analysis: Applications in Veterinary Medicine

Evidence-based decision making is a hallmark of effective veterinary clinical practice. Scoping reviews, systematic reviews, and meta-analyses all are methods intended to provide transparent and replicable ways of summarizing a body of research to address an important clinical or public health issue. As these methods increasingly are being used by researchers and read by practitioners, it is important to understand the distinction between these techniques and to understand what research questions they can, and cannot, address. This review provides an overview of scoping reviews, systematic reviews, and meta-analysis, including a discussion of the method and uses. A sample dataset and coding to conduct a simple meta-analysis in the statistical program R also are provided. Scoping reviews are a descriptive approach, designed to chart the literature around a particular topic. The approach involves an extensive literature search, following by a structured mapping, or charting, of the literature. The results of scoping reviews can help to inform future research by identifying gaps in the existing literature and also can be used to identify areas where there may be a sufficient depth of literature to warrant a systematic review. Systematic reviews are intended to address a specific question by identifying and summarizing all of the available research that has addressed the review question. Questions types that can be addressed by a systematic review include prevalence/incidence questions, and questions related to etiology, intervention efficacy, and diagnostic test accuracy. The systematic review process follows structured steps with multiple reviewers working in parallel to reduce the potential for bias. An extensive literature search is undertaken and, for each relevant study identified by the search, a formal extraction of data, including the effect size, and assessment of the risk of bias is performed. The results from multiple studies can be combined using meta-analysis. Meta-analysis provides a summary effect size, and allows heterogeneity of effect among studies to be quantified and explored. These evidence synthesis approaches can provide scientific input to evidence-based clinical decision-making for veterinarians and regulatory bodies, and also can be useful for identifying gaps in the literature to enhance the efficiency of future research in a topic area.

Synchronous shedding of multiple bat paramyxoviruses coincides with peak periods of Hendra virus spillover

Within host-parasite communities, viral co-circulation and co-infections of hosts are the norm, yet studies of significant emerging zoonoses tend to focus on a single parasite species within the host. Using a multiplexed paramyxovirus bead-based PCR on urine samples from Australian flying foxes, we show that multi-viral shedding from flying fox populations is common. We detected up to nine bat paramyxoviruses shed synchronously. Multi-viral shedding infrequently coalesced into an extreme, brief and spatially restricted shedding pulse, coinciding with peak spillover of Hendra virus, an emerging fatal zoonotic pathogen of high interest. Such extreme pulses of multi-viral shedding could easily be missed during routine surveillance yet have potentially serious consequences for spillover of novel pathogens to humans and domestic animal hosts. We also detected co-occurrence patterns suggestive of the presence of interactions among viruses, such as facilitation and cross-immunity. We propose that multiple viruses may be interacting, influencing the shedding and spillover of zoonotic pathogens. Understanding these interactions in the context of broader scale drivers, such as habitat loss, may help predict shedding pulses of Hendra virus and other fatal zoonoses.

Factors potentially linked with the occurrence of antimicrobial resistance in selected bacteria from cattle, chickens and pigs: A scoping review of publications for use in modelling of antimicrobial resistance (IAM.AMR Project)

Antimicrobial resistance is a complex issue with a large volume of published literature, and there is a need for synthesis of primary studies for an integrated understanding of this topic. Our research team aimed to have a more complete understanding of antimicrobial resistance in Canada (IAM.AMR Project) using multiple methods including the literature reviews and quantitative modelling. To accomplish this goal, qualitative features of publications (e.g., geographical location, study population) describing potential relationships between the occurrence of antimicrobial resistance and factors (e.g., antimicrobial use; management system) were of particular interest. The objectives of this review were to (a) describe the available peer-reviewed literature reporting potential relationships between factors and antimicrobial resistance; and (b) to highlight data gaps. A comprehensive literature search and screening were performed to identify studies investigating factors potentially linked with antimicrobial resistance in Campylobacter species, Escherichia coli and Salmonella enterica along the farm-to-fork pathway (farm, abattoir (slaughter houses) and retail meats) for the major Canadian livestock species (beef cattle, broiler chicken and pigs). The literature search returned 14,966 potentially relevant titles and abstracts. Following screening of titles, abstracts and full-text articles, the qualitative features of retained studies (n = 28) were extracted. The most common factors identified were antimicrobial use (n = 13 studies) and type of farm management system (e.g., antibiotic-free, organic; n = 8). Most studies were conducted outside of Canada and involved investigations at the farm level. Identified data gaps included the effect of vaccination, industry-specific factors (e.g., livestock density) and factors at sites other than farm along the agri-food chain. Further investigation of these factors and other relevant industry activities are needed for the development of quantitative models that aim to identify effective interventions to mitigate the occurrence of antimicrobial resistance along the agri-food chain.

Risk Factors for Antimicrobial Resistance in Escherichia coli in Pigs Receiving Oral Antimicrobial Treatment: A Systematic Review

The aim of this literature review was to identify risk factors in addition to antimicrobial treatment for antimicrobial resistance (AMR) occurrence in commensal Escherichia coli in pigs. A variety of studies were searched in 2014 and 2015. Studies identified as potentially relevant were assessed against eligibility criteria such as observation or experiment (no review), presentation of risk factors in addition to (single dosage) antimicrobial use, risk factors for but not resulting from AMR, and the same antimicrobial used and tested. Thirteen articles (nine on observational, four on experimental studies) were finally selected as relevant. It was reported that space allowance, production size/stage, cleanliness, entry of animals and humans into herds, dosage/frequency/route of administration, time span between treatment and sampling date, herd size, distance to another farm, coldness, and season had an impact on AMR occurrence. Associations were shown by one to four studies per factor and differed in magnitude, direction, and level of significance. The risk of bias was unclear in nearly half of the information of observational studies and in most of the information from experimental studies. Further research on the effects of specific management practices is needed to develop well-founded management advice.