A Critical Review of AMR Risks Arising as a Consequence of Using Biocides and Certain Metals in Food Animal Production.

The focus of this review was to assess what evidence exists on whether, and to what extent, the use of biocides (disinfectants and sanitizers) and certain metals (used in feed and other uses) in animal production (both land and aquatic) leads to the development and spread of AMR within the food chain. A comprehensive literature search identified 3434 publications, which after screening were reduced to 154 relevant publications from which some data were extracted to address the focus of the review. The review has shown that there is some evidence that biocides and metals used in food animal production may have an impact on the development of AMR. There is clear evidence that metals used in food animal production will persist, accumulate, and may impact on the development of AMR in primary animal and food production environments for many years. There is less evidence on the persistence and impact of biocides. There is also particularly little, if any, data on the impact of biocides/metal use in aquaculture on AMR. Although it is recognized that AMR from food animal production is a risk to human health there is not sufficient evidence to undertake an assessment of the impact of biocide or metal use on this risk and further focused in-field studies are needed provide the evidence required.

Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections.

A one-health perspective may provide new and actionable information about Escherichia coli transmission. E. coli colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic E. coli strains from food animals to humans. However, the relative contribution of foodborne zoonotic E. coli (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source E. coli isolates (n = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical E. coli isolates. We estimated that approximately 8 % of human extraintestinal E. coli infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-H22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-E. coli uropathogenic species (e.g., Klebsiella pneumoniae). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal E. coli infections.

Evaluation of changes in the faecal resistome associated with children's exposure to domestic animals and food animal production.

OBJECTIVES: The paediatric gut microbiota is a reservoir of antimicrobial resistance genes. Environmental factors such as a child's exposure to faecal contamination and antimicrobial resistance genes of animal origin likely shape the resistome of infants and children. This study measured how different levels of exposure to domestic or food animals affect the structure of the intestinal resistome in children between 1 and 7 years of age. METHODS: One hundred nineteen faecal samples from 39 children were analysed according to the level of exposure to domestic or food animals and categorized into three risk groups. Using high-throughput sequencing with an Illumina NovaSeq 6000 SP platform, we performed faecal resistome analyses using the ResFinder database. Additionally, ResistoXplorer was used to characterize the resistomes of children differentially exposed to domestic animals. RESULTS: Our data indicated that specific antimicrobial resistance genes such as those that confer resistance to MATFPR (macrolide, aminoglycoside, tetracycline, fluoroquinolone, phenicol, and rifamycin) and tetracyclines were statistically less abundant in the group of children without exposure to animals (group 2), compared with the groups exposed to domestic and food animals (groups 1 and 3). However, the overall resistome structure among the children was not affected by the different levels of exposure to animals. CONCLUSIONS: This study suggests that animal exposure is a risk factor for young children acquiring specific antimicrobial resistance genes from domestic animals or animal production areas. However, the overall resistome structure was not affected.

Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon.

Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall 'low' probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall 'low', but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.

A Review of the Effectiveness of Current US Policies on Antimicrobial Use in Meat and Poultry Production.

PURPOSE: Industrial food animal production accounts for most animal-source protein consumed in the USA. These operations rely on an array of external inputs, which can include antimicrobials of medical importance. The use of these drugs in this context has been the subject of public health debate for decades because their widespread use contributes to the selection for and proliferation of drug-resistant bacteria and their genetic determinants. Here, we describe legislative and regulatory efforts, at different levels of governance in the USA, to curtail food animal consumption of medically important antimicrobials. RECENT FINDINGS: The features and relative success of the US efforts are examined alongside those of selected member states (Denmark and the Netherlands) of the European Union. Evaluation of efforts at all levels of US governance was complicated by shortcomings in prescribed data collection; nevertheless, available information suggests deficiencies in policy implementation and enforcement compromise the effectiveness of interventions pursued to date. The political will, robust systems for collecting and integrating data on antimicrobial consumption and use, and cross-sectoral collaboration that have been integral to the success of efforts in Denmark and The Netherlands have been notably absent in the USA, especially at the federal level.

Antibiotic use by backyard food animal producers in Ecuador: a qualitative study.

BACKGROUND: Antibiotics are increasingly used throughout the world in food animal production for controlling and preventing disease and for promoting growth. But this trend also has the potential for promoting antibiotic resistance, which represents a threat to human, animal, and environmental health. The use of antibiotics and the potential effects of antibiotic dependence has often been associated with large-scale food animal production. But rural households also engage in small-scale production, often operating literally in backyards. While some small-scale producers use veterinary antibiotics, many do not. This paper examines knowledge, attitudes, beliefs, and agricultural practices (KAP) that represent an alternative to dependence on antibiotics. METHODS: Qualitative field research was based on four focus group discussions (FGDs) with non-indigenous backyard food animal producers in four communities near Quito, Ecuador and two FGDs with veterinarians. FGDs were supplemented by structured observations and key informant interviews. They were recorded with digital audio devices and transcriptions were analyzed independently by two researchers using a three-stage coding procedure. Open coding identifies underlying concepts, while axial coding develops categories and properties, and selective coding integrates the information in order to identify the key dimensions of the collective qualitative data. RESULTS: Backyard food animal producers in the Ecuadorian highlands generally do not use antibiotics while rearing small batches of animals and poultry for predominantly non-commercial household consumption. Instead, they rely on low cost traditional veterinary remedies. These practices are informed by their Andean history of agriculture and a belief system whereby physical activity is a holistic lifestyle through which people maintain their health by participating in the physical and spiritual environment. CONCLUSIONS: Backyard food animal producers in the Ecuadorian highlands implement complex strategies based on both economic calculations and sociocultural underpinnings that shape perceptions, attitudes, and practices. They use traditional veterinary remedies in lieu of antibiotics in most cases because limited production of food animals in small spaces contributes to a predictable household food supply, while at the same time conforming to traditional concepts of human and environmental health.

Communication skills training and assessment of food animal production medicine veterinarians: A component of a voluntary Johne's disease control program.

In food animal production medicine (FAPM), the success of control programs for infectious diseases that have serious animal health and economic consequences frequently rely on the veterinarian's effective communication and producer adherence to veterinary recommendations. However, little research has been conducted on communication skills of practicing FAPM veterinarians. During this study, we developed a communication training workshop intervention to support the Atlantic Johne's Disease Initiative. Seventeen FAPM veterinarians across 10 clinics practicing within Maritime Canada participated in a pre-post intervention study design. Communication skills were evaluated utilizing 3 assessment tools; an objective structured clinical exam (OSCE), standardized client feedback, and an instrument designed for veterinary participants to assess their self-efficacy. Study results showed that before training, communication skills of participating veterinarians had limitations, including skill deficits in communication tasks strongly associated with increased adherence to veterinary recommendations. Based on the 3 assessment tools, communication skills of participating veterinarians improved with the training provided. Significant increases were detected in pre- to postintervention self-efficacy percentage scores, OSCE percentage and global scores from expert raters, and OSCE percentage and global scores from standardized client feedback. These improvements emphasize the importance of communication skills training specific to FAPM.

Successful Prevention of Antimicrobial Resistance in Animals-A Retrospective Country Case Study of Sweden.

The misuse and overuse of antibiotics have resulted in an alarmingly high prevalence of antimicrobial resistance (AMR) in human and animal bacteria. European monitoring programmes show that AMR occurrence in food animals is lower in Sweden than in most other EU Member States and that the use of antibiotics for animals is among the lowest in Europe. In this retrospective country case study, we analysed published documents to identify factors contributing to this favourable situation. A fundamental factor identified was early insight into and sustained awareness of the risks of AMR and the need for the prudent use of antibiotics. Early and continuous access to data on antibiotic use and AMR made it possible to focus activities on areas of concern. Another factor identified was the long-term control and eradication of infectious animal diseases, including coordinated activities against endemic diseases, which reduced the need to use antibiotics. Structures and strategies for that purpose established at the national level have since proven useful in counteracting AMR as an integral part of disease prevention and control, guided by a "prevention is better than cure" approach. A third factor identified was consensus among stakeholders on the need to address AMR and their cooperation in the design and implementation of measures.

Antimicrobial Resistance in Agri-Food Chain and Companion Animals as a Re-emerging Menace in Post-COVID Epoch: Low-and Middle-Income Countries Perspective and Mitigation Strategies.

Antimicrobial resistance (AMR) leads to enormous financial losses from issues such as high morbidity, mortality, man-days lost, hospital length of stay, health-care, and social costs. In humans, over prescription of antimicrobials, which is presumably higher during COVID, has been identified as the major source of selection for antimicrobial resistant bacteria; however, use of antimicrobials in food and companion animals, fish, and vegetables, and the environmental resistance gene pool, also play important roles. The possibilities of unnecessary use of antibiotics as prophylaxis during and after COVID in livestock and companion animals exist in low-and middle-income countries. A considerable loss in gross domestic product (GDP) is also projected in low-and middle-income countries (LMICs) due to AMR by the year 2050, which is further going to be reduced due to economic slowdown in the post-COVID period. Veterinary hospitals dedicated to pets have cropped up, especially in urban areas of LMICs where use of antimicrobials has also been increased substantially. The inevitable preventive habit built up during COVID with the frequent use of hand sanitizer might trigger AMR due to the presence of cross-resistance with disinfectants. In LMICs, due to the rising demand for animal protein, industrial food animal production (IFAP) is slowly replacing the small-scale backyard farming system. The lack of stringent regulations and monitoring increased the non-therapeutic use of antimicrobials in industrial farms where the persistence of antimicrobial resistant bacteria has been associated with several factors other than antimicrobial use, such as co-resistance, cross-resistance, bacterial fitness, mixing of new and old animals, and vectors or reservoirs of bacterial infection. The present review describes types of antimicrobials used in agri-food chains and companion animals in LMICs with identification of the gap in data, updated categories of prevalent antimicrobial resistant bacteria, the role of animal farms as reservoirs of resistant bacteria, and mitigation strategies, with a special focus on the pivotal strategy needed in the post-COVID period.

The economics of antimicrobial resistance in veterinary medicine: Optimizing societal benefits through mesoeconomic approaches from public and private perspectives.

Antimicrobial resistance (AMR) is a global public health threat driven by a combination of factors, including antimicrobial use (AMU) and interactions among microorganisms, people, animals and the environment. The emergence and spread of AMR in veterinary medicine (AMR-V) arising from AMU in veterinary medicine (AMU-V) can be linked to individuals' economic behaviour and institutional context. We highlight the limitations of current microeconomic approaches and propose a mesoeconomic conceptual model of AMR-V that integrates actors' strategic and routine behaviours in their context from a dynamic perspective using the concepts of externality, globality and futurity. The global solution to AMR-V management relies on a trade-off between i) the global externality assessment of AMU-V with respect to AMR-V (public perspective) and ii) farm- or value chain-level marginal abatement cost evaluation (private perspective). The improvements realized by the proposed mesoeconomic conceptual model include i) the simultaneous fight against the emergence and spread of AMR-V and ii) a local decrease in AMU-V without any loss of competitiveness for private actors due to the development of adequate production standards. A set of generic equations describing the stepwise change in the scale of analysis is finally proposed. This original contribution to the global challenge of AMR through a mesoeconomic approach bring substantial improvement for better AMU. This model can be considered a way to smoothly promote institutional change and a call for public policies that support public private partnership in the development of adequate incentives. The model requires further development prior to its application in a given value-chain or territory.

A Transdisciplinary Approach Supporting the Implementation of a Big Data Project in Livestock Production: An Example From the Swiss Pig Production Industry.

Big Data approaches offer potential benefits for improving animal health, but they have not been broadly implemented in livestock production systems. Privacy issues, the large number of stakeholders, and the competitive environment all make data sharing, and integration a challenge in livestock production systems. The Swiss pig production industry illustrates these and other Big Data issues. It is a highly decentralized and fragmented complex network made up of a large number of small independent actors collecting a large amount of heterogeneous data. Transdisciplinary approaches hold promise for overcoming some of the barriers to implementing Big Data approaches in livestock production systems. The purpose of our paper is to describe the use of a transdisciplinary approach in a Big Data research project in the Swiss pig industry. We provide a brief overview of the research project named "Pig Data," describing the structure of the project, the tools developed for collaboration and knowledge transfer, the data received, and some of the challenges. Our experience provides insight and direction for researchers looking to use similar approaches in livestock production system research.

Complex System Approaches for Animal Health Surveillance.

Many new and highly variable data are currently being produced by the many participants in farmed animal productions systems. These data hold the promise of new information with potential value for animal health surveillance. The current analytical paradigm for dealing with these new data is to implement syndromic surveillance systems, which focus mainly on univariate event detection methods applied to individual time series, with the goal of identifying epidemics in the population. This approach is relatively limited in the scope and not well-suited for extracting much of the additional information that is contained within these data. These approaches have value and should not be abandoned. However, an additional, new analytical paradigm will be needed if surveillance and disease control agencies wish to extract additional information from these data. We propose a more holistic analytical approach borrowed from complex system science that considers animal disease to be a product of the complex interactions between the many individuals, organizations and other factors that are involved in, or influence food production systems. We will discuss the characteristics of farmed animal food production systems that make them complex adaptive systems and propose practical applications of methods borrowed from complex system science to help animal health surveillance practitioners extract additional information from these new data.

Applying an environmental public health lens to the industrialization of food animal production in ten low- and middle-income countries.

BACKGROUND: Industrial food animal production (IFAP) is characterized by dense animal housing, high throughput, specialization, vertical integration, and corporate consolidation. Research in high-income countries has documented impacts on public health, the environment, and animal welfare. IFAP is proliferating in some low- and middle-income countries (LMICs), where increased consumption of animal-source foods has occurred alongside rising incomes and efforts to address undernutrition. However, in these countries IFAP's negative externalities could be amplified by inadequate infrastructure and resources to document issues and implement controls. METHODS: Using UN FAOSTAT data, we selected ten LMICs where food animal production is expanding and assessed patterns of IFAP growth. We conducted a mixed methods review to explore factors affecting growth, evidence of impacts, and information gaps; we searched several databases for sources in English, Spanish, and Portuguese. Data were extracted from 450+ sources, comprising peer-reviewed literature, government documents, NGO reports, and news articles. RESULTS: In the selected LMICs, not only has livestock production increased, but the nature of expansion appears to have involved industrialized methods, to varying extents based on species and location. Expansion was promoted in some countries by explicit government policies. Animal densities, corporate structure, and pharmaceutical reliance in some areas mirrored conditions found in high-income countries. There were many reported weaknesses in regulation and capacity for enforcement surrounding production and animal welfare. Global trade increasingly influences movement of and access to inputs such as feed. There was a nascent, compelling body of scientific literature documenting IFAP's negative environmental and public health externalities in some countries. CONCLUSIONS: LMICs may be attracted to IFAP for economic development and food security, as well as the potential for increasing access to animal-source foods and the role these foods can play in alleviating undernutrition. IFAP, however, is resource intensive. Industrialized production methods likely result in serious negative public health, environmental, and animal welfare impacts in LMICs. To our knowledge, this is the first systematic effort to assess IFAP trends through an environmental public health lens for a relatively large group of LMICs. It contributes to the literature by outlining urgent research priorities aimed at informing national and international decisions about the future of food animal production and efforts to tackle global undernutrition.

"Ag-Gag" Laws: Evolution, Resurgence, and Public Health Implications.

The term "ag-gag" refers to state laws that intentionally limit public access to information about agricultural production practices, particularly livestock production. Originally created in the 1990s, these laws have recently experienced a resurgence in state legislatures. We discuss the recent history of ag-gag laws in the United States and question whether such ag-gag laws create a "chilling effect" on reporting and investigation of occupational health, community health, and food safety concerns related to industrial food animal production. We conclude with a discussion of the role of environmental and occupational health professionals to encourage critical evaluation of how ag-gag laws might influence the health, safety, and interests of day-to-day agricultural laborers and the public living proximal to industrial food animal production.

Incidence and characteristics of juvenile tarsocrural osteochondrosis in purebred Angus bulls.

Osteochondrosis (OC) of the bovine tarsus has been suggested to contribute to osteoarthritis. The objective of this prospective cohort study was to provide data specific to the Angus breed. Clinical and radiographic exams evaluating OC lesions, effusion and osteoarthritis were performed in 50 purebred bull calves at three time points between 5.8 and 21 months of age. The likelihood of OC was lower at a median age of 12.4 months (P<0.001), primarily due to resolution of distal talus changes (P<0.01). Significant associations were observed between medial malleolus lesions and effusion at median age of 7.4 months (P<0.001). This study suggests that clinical and radiographic screening performed at approximately one year of age may be beneficial in detecting tarsal OC lesions in Angus breeding herds.

Residential proximity to high-density poultry operations associated with campylobacteriosis and infectious diarrhea.

Poultry carry zoonotic bacteria that can cause gastroenteritis in humans. Environmental transmission of pathogens from poultry operations may increase gastrointestinal infection risk in surrounding communities. To evaluate associations between residential proximity to high-density poultry operations and individual-level diarrheal illnesses, we conducted a nested case-control study among 514,488 patients in Pennsylvania (2006-2015). Using electronic health records, we identified cases of five gastrointestinal outcomes: three pathogen-specific infections, including Escherichia coli (n = 1425), Campylobacter (n = 567), and Salmonella (n = 781); infectious diarrhea (n = 781); and non-specific diarrhea (2012-2015; n = 28,201). We estimated an inverse-distance squared activity metric for poultry operations based on farm and patient addresses. Patients in the second and fourth (versus first) quartiles of the poultry operation activity metric had increased odds of Campylobacter (AOR [CI], Q2: 1.36 [1.01, 1.82]; Q3: 1.38 [0.98, 1.96]; Q4: 1.75 [1.31, 2.33]). Patients in the second, third, and fourth quartiles had increased odds of infectious diarrhea (Q2: 1.76 [1.29, 2.39]; Q3: 1.76 [1.09, 2.85]; Q4: 1.60 [1.12, 2.30]). Stratification revealed stronger relations of fourth quartile and both Campylobacter and infectious diarrhea in townships, the most rural community type in the study geography. Increasing extreme rainfall in the week prior to diagnosis strengthened fourth quartile Campylobacter associations. The poultry operation activity metric was largely unassociated with E. coli, Salmonella, and non-specific diarrhea. Findings suggest high-density poultry operations may be associated with campylobacteriosis and infectious diarrhea in nearby communities, highlighting additional public health concerns of industrial agriculture.

Authors' response to comments from Nachman KE et al.

Authors' response to comments letter to the editor from Nachman KE et al.

Tapping the Vast Potential of the Data Deluge in Small-scale Food-Animal Production Businesses: Challenges to Near Real-time Data Analysis and Interpretation.

Food-animal production businesses are part of a data-driven ecosystem shaped by stringent requirements for traceability along the value chain and the expanding capabilities of connected products. Within this sector, the generation of animal health intelligence, in particular, in terms of antimicrobial usage, is hindered by the lack of a centralized framework for data storage and usage. In this Perspective, we delimit the 11 processes required for evidence-based decisions and explore processes 3 (digital data acquisition) to 10 (communication to decision-makers) in more depth. We argue that small agribusinesses disproportionally face challenges related to economies of scale given the high price of equipment and services. There are two main areas of concern regarding the collection and usage of digital farm data. First, recording platforms must be developed with the needs and constraints of small businesses in mind and move away from local data storage, which hinders data accessibility and interoperability. Second, such data are unstructured and exhibit properties that can prove challenging to its near real-time preprocessing and analysis in a sector that is largely lagging behind others in terms of computing infrastructure and buying into digital technologies. To complete the digital transformation of this sector, investment in rural digital infrastructure is required alongside the development of new business models to empower small businesses to commit to near real-time data capture. This approach will deliver critical information to fill gaps in our understanding of emerging diseases and antimicrobial resistance in production animals, eventually leading to effective evidence-based policies.

Recent Research Examining Links Among Klebsiella pneumoniae from Food, Food Animals, and Human Extraintestinal Infections.

Klebsiella pneumoniae is a colonizer of livestock, a contaminant of retail meats and vegetables, and a cause of extraintestinal infections in humans. Antibiotic-resistant strains of K. pneumoniae are becoming increasingly prevalent among hospital and community-acquired infections. Antibiotics are used extensively in conventional food-animal production, where they select for antibiotic-resistant bacteria. Antibiotic-resistant K. pneumoniae has been isolated from livestock as well as from a variety of retail meats, seafood, and vegetables. Furthermore, recent phylogenetic analyses suggest close relationships between K. pneumoniae from humans and livestock. Therefore, it is essential that we quantify the contribution of foodborne K. pneumoniae to antibiotic-resistant human infections.