Evaluating the contribution of antimicrobial use in farmed animals to global antimicrobial resistance in humans

Surveillance of Antimicrobial Resistance in the Asian Seabass (Lates calcarifer) Supply Chain Using Nanopore Sequencing

Intensive fish farming worldwide has increased reliance on antibiotics to control bacterial pathogens, raising concerns about antimicrobial resistance (AMR) in aquaculture. These resistant bacteria can persist and pass through the food supply chain, from farms to consumers. Despite this risk, antimicrobial resistance genes (ARGs) in aquaculture environments and fish products have not been elucidated. This study aimed to detect ARGs found in the Asian seabass (Lates calcarifer), an economically important fish in Thailand, collected from farms, fish container vehicles, and markets, using Nanopore metagenomic sequencing. We detected multiple ARGs in all sample types. Water samples harbored the rpsL gene conferring streptomycin resistance. Container samples exhibited the highest diversity of ARGs, including multiple beta-lactamases and the rsmA gene, conferring resistance to fluoroquinolones, diaminopyrimidines, and phenicol antibiotics. Fish samples generally lacked ARGs, except for one sample harboring rsmA. Non-metric multidimensional scaling revealed distinct microbial communities in water, compared with those found in container and fish samples, indicating potential cross-contamination during handling or storage. Our findings emphasize that containers could be critical control points for minimizing AMR spread. Overall, this study highlights the interconnection between environmental, fish, and human health, highlighting the importance of integrated AMR surveillance and management in aquaculture systems.

Association between national action and trends in antibiotic resistance: an analysis of 73 countries from 2000 to 2023

The world's governments have agreed on actions to address the challenge of antibiotic resistance. This raises the question of what level of national action is associated with improved outcomes, including both slower growth and lower levels of antibiotic resistance. Answering this question is challenged by variation in data availability and quality as well as disruptive events such as the COVID-19 pandemic. We investigate the association between level of national action and temporal trends in multiple indicators related to health system capacity, antibiotic use (ABU), absolute rates of resistance (ABR) and a Drug Resistance Index (DRI). Using the Global Database for Tracking Antimicrobial Resistance (TrACSS) to construct an index of national action, we apply cross-sectional regression across 73 countries to estimate the association between the level of action in 2016 and trends in national indicators (2000-2016). We find that national action is consistently associated with improved linear or categorical trends in all groups of indicators. Reductions are associated with a relatively high action index (range 0-4) for ABU (median 2.8, 25-75% quartile 2.6-3.3), ABR (3.0, 2.4-3.4), and DRI (3.5, 3.1-3.6). These associations are robust to the inclusion of other contextual factors related to socio-economic conditions, human population density, animal production and climate. Since 2016, a majority of both Low- and Middle-Income Countries (LMICs) and High-Income Countries (HICs) report increased action on repeated questions, while one third of countries report reduced action. The main limitations in interpretation are heterogeneity in data availability and in when actions have been implemented. Our findings highlight the importance of national action to address the domestic situation related to antibiotic resistance and indicate the value of both incremental changes in reducing adversity of outcomes and the need for high levels of action in delivering reduced levels of resistance.

Piloting an Information and Communication Technology Tool to Help Addressing the Challenge of Antimicrobial Resistance in Low-Income Countries

Background/Objectives: Antimicrobial use (AMU) in livestock drives antimicrobial resistance (AMR). AMR has a significant impact on public health. While several interventions have been used to address this challenge, few have utilized Information and Communication Technology (ICT) approaches. The objective of this study was to pilot and assess an ICT system to monitor the use of veterinary drugs and disseminate information to farmers in peri-urban smallholder poultry systems in Kenya. Methods: The system was developed in collaboration with the stakeholders. It captures drug sales in veterinary pharmacies and disease incidence and treatments reported by farmers. The system was piloted from May 2023 to December 2023. Monthly follow-ups were conducted to monitor progress and address problems. Assessment was performed through focus group discussions with the users (two with farmers and two with veterinary pharmacy staff) and descriptive statistics of the data collected by the system. Results: A total of 15,725 records were obtained from veterinary pharmacies, including antibiotics (57%), dewormers (22%), and vitamins (11%). Requests for a specific product were recorded in 38% of the sales, while 63% were accompanied by some evidence (empty drug containers, old packages, old prescriptions, pictures of sick birds, and actual sick birds). A total of 91 records were obtained from the farmers. The health problems reported were mostly respiratory (40%) and digestive (30%) disorders. The percentage of customers who requested advice on animal health when visiting veterinary pharmacies ranged from 5 to 20%. Conclusions: AMU can be improved in the study area. The piloted system may help policymakers monitor the sales and usage of antibiotics, improve animal health management, and promote responsible AMU.

Early-warning signals and the role of H9N2 in the spillover of avian influenza viruses

BACKGROUND

The spillover of avian influenza viruses (AIVs) presents a significant global public health threat, leading to unpredictable and recurring pandemics. Current pandemic assessment tools suffer from deficiencies in terms of timeliness, capability for automation, and ability to generate risk estimates for multiple subtypes in the absence of documented human cases.

METHODS

To address these challenges, we created an integrated database encompassing global AIV-related data from 1981 to 2022. This database enabled us to estimate the rapid expansion of spatial range and host diversity for specific AIV subtypes, alongside their increasing prevalence in hosts that have close contact with humans. These factors were used as early-warning signals for potential AIV spillover. We analyzed spillover patterns of AIVs using machine learning models, spatial Durbin models, and phylogenetic analysis.

FINDINGS

Our results indicate a high potential for future spillover by subtypes H3N1, H4N6, H5N2, H5N3, H6N2, and H11N9. Additionally, we identified a significant risk for re-emergence by subtypes H5N1, H5N6, H5N8, and H9N2. Furthermore, our analysis highlighted 12 key strains of H9N2 as internal genetic donors for human adaptation in AIVs, demonstrating the crucial role of H9N2 in facilitating AIV spillover.

CONCLUSIONS

These findings provide a foundation for rapidly identifying high-risk subtypes, thus optimizing resource allocation in vaccine manufacture. They also underscore the potential significance of reducing the prevalence of H9N2 as a complementary strategy to mitigate chances of AIV spillovers.

FUNDING

National Key Research and Development Program of China.

Key farm characteristics associated with the level of antimicrobial use in rosé veal production - A Danish database study

Antimicrobial use (AMU) in veal production is high compared to other bovine production types and has been suggested as an area with potential for AMU reduction. High AMU is a public health concern due to its association with antimicrobial resistance (AMR). Identifying farm characteristics associated with AMU could provide valuable insights for stakeholders seeking to monitor and implement initiatives to reduce AMU. This study aimed at investigating farm characteristics associated with AMU in Danish rosé veal farms, which is the main veal production type in Denmark. The AMU and characteristics included were extracted from two Danish national databases; The Danish Central Husbandry Register (CHR) and the Danish Veterinary Medicines Statistics Program (VetStat). Characteristics included were farm size, mortality, number of suppliers, sites per farm, and farm-level composition of animals with regards to sex and breed. The 118 farms included in the study received 41 % of the total amount of antimicrobials prescribed for Danish calves and young stock in 2020 measured in Animal Daily Doses (ADD). A multivariable linear regression model with the annual average farm-level AMU as outcome was created. AMU was measured as ADD per 100 animals per day (ADD100) and square root-transformed in the model. Increasing farm size and number of suppliers and decreasing proportion of crossbred bulls were found to be significantly associated with higher AMU. However, proportion of crossbred bulls was correlated with proportion of females. Separating the effects of breed and sex was not possible, partly due to the highly summarised data structure. Mortality and number of sites were not significantly associated with AMU. Farms with the type "starter-farms" has previously been shown to have a higher AMU compared to other rosé veal farm types. An important finding in this study was that grouping multiple sites into farms by using ownership data made it possible to summarise AMU for the full line of production from arrival at the veal farm to exit for slaughter. The results and approaches from this paper present an opportunity for repeated evaluation of farm characteristics associated with AMU, which could be used to continuously adapt and target AMU monitoring and control. In addition, it is done on existing surveillance data which keeps the cost of the study low in terms of data collection and data management.

Policies and strategies to control antimicrobial resistance in livestock production: A comparative analysis of national action plans in European Union Member States

Policy strategies targeting imprudent antimicrobial use (AMU) in livestock farming have been established at the global and country levels, recognising the risks associated with antimicrobial resistance (AMR). This study evaluates the strategies addressing AMU and AMR in animal farms and the food supply chain in EU Member States using a multimethod approach. Our aim is to contribute to the debates surrounding the goals set by the EU Commission and the 'Strategic framework for collaboration on antimicrobial resistance: Together for One Health'. We first review the policies, strategies and specific legislation in the European Union (EU) and Member States about AMU/AMR in livestock production. We then evaluate the national action plans for AMU reduction in the EU using the progressive management pathway tool from the FAO. Finally, we assess the measures that affect AMU reduction by applying a system generalised method of moments to a 8-year panel of the same countries. According to our results, efforts to reduce AMU could be focused on controlling excessive AMU in the pig sector. Further veterinary training on AMU/AMR and improvements in the performance of the veterinary sector, as well as strengthening the development of multisector and One Health collaboration and coordination, can also contribute to achieving better standards in AMU reduction in the livestock sector and, consequently, for AMR control.

Natural Solutions to Antimicrobial Resistance: The Role of Essential Oils in Poultry Meat Preservation with Focus on Gram-Negative Bacteria

The increase in antimicrobial resistance (AMR) is a major global health problem with implications on human and veterinary medicine, as well as food production. In the poultry industry, the overuse and misuse of antimicrobials has led to the development of resistant or multi-drug resistant (MDR) strains of bacteria such as Salmonella spp., Escherichia coli and Campylobacter spp., which pose a serious risk to meat safety and public health. The genetic transfer of resistance elements between poultry MDR bacteria and human pathogens further exacerbates the AMR crisis and highlights the urgent need for action. Traditional methods of preserving poultry meat, often based on synthetic chemicals, are increasingly being questioned due to their potential impact on human health and the environment. This situation has led to a shift towards natural, sustainable alternatives, such as plant-derived compounds, for meat preservation. Essential oils (EOs) have emerged as promising natural preservatives in the poultry meat industry offering a potential solution to the growing AMR problem by possessing inherent antimicrobial properties making them effective against a broad spectrum of pathogens. Their use in the preservation of poultry meat not only extends shelf life, but also reduces reliance on synthetic preservatives and antibiotics, which contribute significantly to AMR. The unique chemical composition of EOs, that contains a large number of different active compounds, minimizes the risk of bacteria developing resistance. Recent advances in nano-encapsulation technology have further improved the stability, bioavailability and efficacy of EOs, making them more suitable for commercial use. Hence, in this manuscript, the recent literature on the mechanisms of AMR in the most important Gram-negative poultry pathogens and antimicrobial properties of EOs on these meat isolates was reviewed. Additionally, chemical composition, extraction methods of EOs were discussed, as well as future directions of EOs as natural food preservatives. In conclusion, by integrating EOs into poultry meat preservation strategies, the industry can adopt more sustainable and health-conscious practices and ultimately contribute to global efforts to combat AMR.

A mixed method approach to analysing patterns and drivers of antibiotic use and resistance in beef farms in Argentina

Introduction

Antimicrobial resistance is a challenge to be faced by all livestock sectors; within beef farming, antibiotic use patterns vary by country and management practices. Argentina is a country with high beef production & consumption but limited information surrounding antibiotic use. The aims of this project was to understand how antibiotics are being used across the beef industry in Argentina and exploring drivers of usage.

Methods

Quantitative and qualitative data was collected by: A survey of breeding and feedlot farms including antibiotic use (from purchase data); a detailed analysis of two feedlot farms' therapeutic antibiotic use records; a survey of vets' views on certain antibiotic practices; and a focus group of farmers and vets focusing on wider influences affecting decision making. Antibiotic use data was calculated using mg/population corrected unit (PCU) (ESVAC) and thematic analysis was used to identify drivers of antibiotic use among participants.

Results

The median use across 17 farms that supplied purchase data was 76.52  mg/kg PCU (ESVAC; IQR  =  36.81  mg/kg PCU [ESVAC]). The detailed farm records showed that the largest reason for treatment was group treatments (72.92% of treatments) followed by treatment for respiratory disease (12.75% of treatments). Macrolides accounted for 76.37% of treatments. Nearly half of farms used routine prophylactic treatment for arriving animals (n  =  7/18). The use of quarantine and 'sick pens' were seen as important by surveyed vets with antibiotic prophylaxis and in-feed antibiotics seen as contributors to antibiotic resistance. The focus group highlighted the influence of the economic and political landscape on husbandry practices and the responsibility the farming sector had towards antibiotic stewardship.

Discussion

Overall, Argentine beef feedlots resemble North American beef feedlots in terms of antibiotic practices but with considerably lower usage, with in-feed monensin representing a large proportion of total ABU. The adaptation period presents a challenge to animal health; antibiotics are administered a prophylaxis, metaphylactic and individual treatments depending on farm management practices. Further research into internationally comparable measures of ABU and detailed cost-benefit analysis of practical, on-farm interventions are needed to aid improved antimicrobial stewardship in livestock systems globally.

Improvements of weaned pigs barn hygiene to reduce the spread of antimicrobial resistance

The spread of antimicrobial resistance (AMR) in animal husbandry is usually attributed to the use of antibiotics and poor hygiene and biosecurity. We therefore conducted experimental trials to improve hygiene management in weaned pig houses and assessed the impact on the spread. For each of the two groups examined, the experimental group (EG) and the control group (CG), three replicate batches of piglets from the same pig breeder, kept in pre-cleaned flat decks, were analyzed. In the flat decks of the experimental groups, the hygiene conditions (cleaning, disinfection, dust removal and fly control) were improved, while regular hygiene measures were carried out in the control groups. The occurrence and spread of AMR were determined in Escherichia coli (E. coli; resistance indicator) using cultivation-dependent (CFU) and -independent (qPCR) methods as well as whole genome sequencing of isolates in samples of various origins, including feces, flies, feed, dust and swabs. Surprisingly, there were no significant differences (p > 0.05) in the prevalence of resistant E. coli between the flat decks managed with conventional techniques and those managed with improved techniques. Selective cultivation delivered ampicillin- and sulfonamide-resistant E. coli proportions of up to 100% and 1.2%, respectively. While 0.5% E. coli resistant to cefotaxime and no ciprofloxacin resistance were detected. There was a significant difference (p < 0.01) in the abundance of the blaTEM-1 gene in fecal samples between EG and CG groups. The colonization of piglets with resistant pathogens before arrival, the movement of flies in the barn and the treatment of bacterial infections with antibiotics obscured the effects of hygiene improvement. Biocide tolerance tests showed no development of resistance to the farm regular disinfectant. Managing hygiene alone was insufficient for reducing antimicrobial resistances in piglet rearing. We conclude that the complex factors contributing to the presence and distribution of AMR in piglet barns underscore the necessity for a comprehensive management strategy.

Multi-Criteria Evaluation Model of Management for Weaned Piglets and Its Relations with Farm Performance and Veterinary Medicine Consumption

Weaned piglets, being immature, demand careful handling to mitigate post-weaning stress in order to avoid immunosuppression and the use of antimicrobials to palliate the effects of disease outbreaks due to poor management. The objective of this work is to design a quick scan calculator or multi-criteria evaluation model of management for weaned piglets, founded on 10 critical indices covering post-weaning management aspects based on hygienic measures and management of facilities and animals. These include pre-weaning handling, batch management, biosecurity, water management, feed management, health program, stockmen training, temperature, ventilation, and floor conditions and density to relate handling and hygiene practices with farm performance and the consumption of veterinary medication. Each index carries a maximum score of ten, with evaluations derived from different management factors that make up each index (from three to eight factors were evaluated per index). Their cumulative score reflects the degree of adequacy of on-farm management. Therefore, a perfectly managed farm would achieve 100 points. The calculator underwent testing on 23 intensive farms with a total population of close to 16,000 sows and more than 400,000 weaned piglets, revealing the highest mean scores in floor conditions and density (8.03 out of 10) and pre-weaning handling and health programs (6.87 and 6.28, respectively). Conversely, the lowest scores corresponded to temperature, ventilation, water management, and stockmen training (4.08, 4.32, 4.81, and 4.93, respectively). The assessed farms averaged a global score of 56.12 out of 100 (from 37.65 to 76.76). The calculator's global score correlated with key post-weaning productivity and piglet health indicators, such as the feed conversion ratio, mortality rate, and piglet production cost, with r values of -0.442, -0.437, and -0.435, respectively (p < 0.05). Additionally, it negatively correlated with medication costs per piglet (r = -0.414; p < 0.05) and positively with annual farm productivity (r = 0.592; p < 0.01). To enhance management, hygiene, and prevention, farms should prioritize addressing indices with the lowest scores, thereby reducing medication consumption and enhancing productivity and health outcomes. Additionally, this quick scan calculator can be used for benchmarking purposes.