Antimicrobial resistance in the farm-to-plate continuum: more than a food safety issue

Mapping socioeconomic factors driving antimicrobial resistance in humans: An umbrella review

Introduction

Antimicrobial resistance (AMR) is one of the biggest public health challenges of our time. National Action Plans have failed so far to effectively address socioeconomic drivers of AMR, including the animal and environmental health dimensions of One Health.

Objective

To map what socioeconomic drivers of AMR exist in the literature with quantitative evidence.

Methods

An umbrella review was undertaken across Medline, Embase, Global Health, and Cochrane Database of Systematic Reviews, supplemented by a grey literature search on Google Scholar. Review articles demonstrating a methodological search strategy for socioeconomic drivers of AMR were included. Two authors extracted drivers from each review article which were supported by quantitative evidence. Drivers were grouped thematically and summarised narratively across the following three layers of society: People & Public, System & Environment, and Institutions & Policies.

Results

The search yielded 6300 articles after deduplication, with 23 review articles included. 27 individual thematic groups of drivers were identified. The People & Public dimensions contained the following themes: age, sex, ethnicity, migrant status, marginalisation, sexual behaviours, socioeconomic status, educational attainment, household composition, maternity, personal hygiene, lifestyle behaviours. System & Environment yielded the following themes: household transmission, healthcare occupation, urbanicity, day-care attendance, environmental hygiene, regional poverty, tourism, animal husbandry, food supply chain, water contamination, and climate. Institutions & Policies encompassed poor antibiotic quality, healthcare financing, healthcare governance, and national income. Many of these contained bidirectional quantitative evidence, hinting at conflicting pathways by which socioeconomic factors drive AMR.

Conclusion

This umbrella review maps socioeconomic drivers of AMR with quantitative evidence, providing a macroscopic view of the complex pathways driving AMR. This will help direct future research and action on socioeconomic drivers of AMR.

Tenfold multiplex PCR method for simultaneous detection of mcr-1 to mcr-10 genes and application for retrospective investigations of Salmonella and Escherichia coli isolates in China

The increasing prevalence of antimicrobial resistance has raised significant concern globally. Colistin is currently considered a last resort for treating Gram-negative bacterial infections. However, the emergence of colistin resistance has led to a difficult situation against bacterial infections. Therefore, the monitoring of colistin resistance is of great importance for the control of bacterial infections. The mobile colistin resistance (mcr) gene has been identified as a colistin resistance gene, and ten mcr genes (mcr-1 to mcr-10) have been identified to date. Hence, the detection of mcr genes can help predict bacterial colistin resistance at the molecular level. However, there have not been reported multiplex PCR methods for simultaneously detecting mcr-1 to mcr-10 until now. In this study, we established a one-step multiplex PCR method for simultaneous detection of mcr-1 to mcr-10 for the first time. Furthermore, we retrospectively investigated the prevalence of the ten mcr genes in Escherichia coli (E. coli) and Salmonella isolates in China. The results showed that the mcr detection rate of Salmonella isolated during 2004-2019 was 4.73 % (16/338), and only mcr-9 was harbored. As well, the mcr detection rate of E. coli isolated during 2012-2015 was 20.42 % (49/240) and only mcr-1 was identified. Moreover, we also investigated the relationship between mcr harboring and colistin phenotype-resistance. The broth micro-dilution assay results showed that all mcr-1-positive E. coli isolates were colistin-resistant. However, all mcr-9-positive Salmonella isolates did not represent colistin-resistance. Our findings are beneficial for the monitoring and control of colistin resistance.

Antimicrobial Resistant Staphylococcus spp., Escherichia coli, and Salmonella spp. in Food Handlers: A Global Review of Persistence, Transmission, and Mitigation Challenges

Antimicrobial resistance in foodborne pathogens represents a critical global health challenge, with food handlers serving as key contributors in their transmission. This comprehensive review synthesizes evidence on the prevalence, transmission dynamics, and antimicrobial resistance patterns of three major pathogens, Staphylococcus spp., Escherichia coli, and Salmonella spp., among food handlers worldwide. Analysis of studies across diverse geographical regions reveals considerable variation in colonization rates, with Staphylococcus spp. prevalence ranging from 19.5% to 95.0%, Escherichia coli from 2.8% to 89.3%, and Salmonella spp. from 0.07% to 9.1%. Resistance profiles demonstrate alarming trends, including widespread β-lactam resistance and emerging resistance to last-resort antibiotics like carbapenems. Particularly concerning is the high occurrence of multidrug resistant (MDR) strains and extended spectrum β-lactamase (ESBL) producers in low- and middle-income countries. This review identified inadequate handwashing, poor hygiene infrastructure, and asymptomatic carriage as critical factors facilitating the transmission of antimicrobial resistant strains. These findings underscore the urgent need for enhanced surveillance systems, targeted decolonization strategies, improved hygiene protocols, and food handler education to mitigate the spread of resistant pathogens through the food chain.

Different effects of bio/non-degradable microplastics on sewage sludge compost performance: Focusing on antibiotic resistance genes, virulence factors and key metabolic functions

Microplastics (MP) have aroused increasing concern due to the negative environmental impact. However, the impact of bio/non-biodegradable MPs on the sludge composting process has not been thoroughly investigated. This study examined antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial community functions in sludge compost with the application of polylactic acid (PLA) and polypropylene (PP), using metagenomic sequencing. The findings indicated that both types of MPs could extend the thermophilic phase, enhance microbial activity, and inhibit the formation of humic acids. Compared to CK, the subtypes of ARGs decreased 4.22 % and 13.11 % in PLA and PP groups, respectively. But new ARGs emerged, particularly in the PLA group. The proportions of ARGs related to efflux and VFs associated with the adhesion system increased 1.62 %-2.27 % and 55.56 %-60.00 %, respectively, in MPs-added composts. The relative abundance of potential bacterial hosts (e.g., Psychrobacter) carrying multiple ARGs and VFs was much higher in PLA-added compost than in the other two. Moreover, PP facilitated denitrification process and PLA enhanced dissimilatory nitrate reduction to ammonium. Both types of MPs inhibited assimilatory nitrate reduction to ammonia but promoted inorganic nitrogen assimilation. This study broadens our understanding of the potential environmental risks posed by biodegradable and non-biodegradable microplastics on sludge compost and offers valuable insights for the management and application of compost products.

Antimicrobial Resistance in Diverse Ecological Niches-One Health Perspective and Food Safety

Antimicrobial resistance (AMR) is a multi-sectoral, systemic, and global issue worldwide. Antimicrobial use (AMU) is a key factor in the selection of resistant bacteria within different ecological niches, from agriculture to food-producing animals to humans. There is a question regarding the extent to which the use of antibiotics in livestock production and the primary food production sector influences the selection and transmission of resistant bacteria and/or resistant genes throughout the food chain and thus contributes to the complexity in the development of AMR in humans. Although the trends in the prevalence of foodborne pathogens have changed over time, the burden of ecological niches with resistance genes, primarily in commensal microorganisms, is of concern. The implementation of the harmonized surveillance of AMU and AMR would provide comprehensive insights into the actual status of resistance and further interventions leading to its reduction. Tracking AMR in different ecological niches by applying advanced genome-based techniques and developing shared AMR data repositories would strengthen the One Health concept.

Antimicrobial resistance and etiological dynamics affected by tropical climate variability on year-round diagnosis of upper respiratory infections in companion rabbits with snuffles

Upper respiratory infections (URIs) in rabbits are of significant concern, presenting diagnostic challenges and necessitating targeted antimicrobial stewardship. This study aimed to evaluate the etiological bacteria causing URIs in rabbits and their antimicrobial resistance (AMR) in Thailand during 2022, while exploring potential correlations between tropical meteorological factors and URI occurrence. For year-round diagnosis, seventy-eight companion rabbits with snuffles were confirmed infection based on bacterial culture. Antimicrobial susceptibility was tested using the Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. Meteorological data were obtained from the Meteorological Department of Thailand, Ministry of Digital Economy and Society and used for analyzing the climate influences. The results showed that highest URI occurrence could be found during the rainy season (46.15%, 95% CI 35.53-57.14%), with a significant correlation between URI occurrence and precipitation (r = 0.66, p = 0.02). Gram-negative bacteria were the predominant pathogens (67.95%, 95% CI 56.96-77.25%), particularly Pseudomonas spp., Acinetobacter spp., Enterobacter spp., and Pasteurella multocida. Consequently, AMR profiles revealed high resistance to penicillin and co-trimoxazole, with multidrug resistance common among major bacterial groups. These findings highlight the influence of tropical climate on URI occurrence and the growing AMR challenge in companion rabbits, underscoring the need for region-specific monitoring and antimicrobial stewardship.

Crosslinking bacterial postbiotics for microbial and quality control of strawberries postharvest: bacteriological and 16S amplicon metagenome evidence

Introduction

Strawberries are renowned for their exceptional flavor and nutritional properties but have a short shelf life due to rapid ripening and a high vulnerability to postharvest microbial decay. Postbiotic formulations (PBFs) derived from lactic acid bacteria (LAB) can be developed into effective preservation products, extending postharvest shelf life while maintaining fruit quality.

Methods

This study aimed to assess the effects of postbiotic-based formulations (PBFs) consisting of two key components: (1) a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O, serving as the antimicrobial agent, and (2) an exopolysaccharide (EPS) from W. confusa UTNCys2-2, functioning as the biopolymer carrier. These formulations were tested against a multidrug-resistant Serratia liquefaciens P4StpC1 strain, isolated from ready-to-eat strawberries, and their potential mode of action was analyzed in vitro. Time-kill assays and electron microscopy were used to evaluate their impact on the target cells. Furthermore, the performance of PBFs was compared to a commercial disinfectant (C1) in terms of their effects on strawberry microbiota and fruit quality, employing bacteriological techniques and 16S amplicon metagenomic analysis.

Results

The selected PBFs showed bacteriolytic effect on Serratia in vitro. The target cell viability was significantly reduced upon 1 h co-cultivation by inducing several morphological and ultrastructural modifications. Dipping strawberries at the ripe stage four in PBFs indicated no increase in total cell counts, thus the microorganisms colonization was retained during storage with refrigeration. The 16S metagenome analysis showed that the treatment impacted the fruit microbiota, significantly increasing Lactobacillus abundance (p < 0.001) by day eight compared to the disinfectant control. This suggests the formulation supports beneficial microbes, enhancing antimicrobial effects. Additionally, the postbiotic coating improved shelf-life, preserved fruit quality, and delayed deterioration in strawberries. The strawberries quality attributes were not affected by the treatment. Principal Component Analysis (PCA) revealed clear sample separation based on maturity stage, independent of the treatment.

Conclusion

The results highlight the potential of crosslinking of a peptide-protein fraction with EPS to prevent the colonization of undesirable microorganisms on postharvest strawberries while enhancing their safety and quality.

Nanomaterial-Based Strategies to Combat Antibiotic Resistance: Mechanisms and Applications

The rapid rise of antibiotic resistance has become a global health crisis, necessitating the development of innovative strategies to combat multidrug-resistant (MDR) pathogens. Nanomaterials have emerged as promising tools in this fight, offering unique physicochemical properties that enhance antibiotic efficacy, overcome resistance mechanisms, and provide alternative therapeutic approaches. This review explores the diverse nanomaterial-based strategies used to combat antibiotic resistance, focusing on their mechanisms of action and practical applications. Nanomaterials such as metal nanoparticles, carbon-based nanomaterials, and polymeric nanostructures exhibit antibacterial properties through various pathways, including the generation of reactive oxygen species (ROS), disruption of bacterial membranes, and enhancement of antibiotic delivery. Additionally, the ability of nanomaterials to bypass traditional resistance mechanisms, such as biofilm formation and efflux pumps, has been demonstrated in numerous studies. This review also discusses the synergistic effects observed when nanomaterials are combined with conventional antibiotics, leading to increased bacterial susceptibility and reduced required dosages. By highlighting the recent advancements and clinical applications of nanomaterial-antibiotic combinations, this paper provides a comprehensive overview of how nanomaterials are reshaping the future of antibacterial therapies. Future research directions and challenges, including toxicity and scalability, are also addressed to guide the development of safer, more effective nanomaterial-based antibacterial treatments.

Human and Veterinary Medicine Collaboration: Synergistic Approach to Address Antimicrobial Resistance Through the Lens of Planetary Health

Antimicrobial resistance (AMR) represents a critical threat to human, animal, and environmental health, challenging global efforts to maintain sustainable ecosystems and public health systems. In this review, the complex, cross-disciplinary issues of AMR are explored within the framework of planetary health, emphasizing the interconnectedness of human and veterinary medicine with broader environmental and social systems. Specifically, it addresses the social, economic, environmental, and health dimensions of AMR under the planetary health framework. The social aspects consider how public awareness, education, and healthcare practices shape antimicrobial use (AMU) and resistance patterns. The economic impact evaluates the cost burdens of AMR, including healthcare costs, loss of productivity, and the implications for the livestock and food production industries. The environmental dimension highlights the role of pharmaceutical waste, agricultural runoff, and industrial pollution in contributing to the spread of antimicrobials and resistant pathogens in ecosystems. To illustrate these challenges, a comprehensive literature review using the PubMed and Web of Science databases was conducted, identifying 91 relevant articles on planetary health and AMR. In this review, the knowledge from these studies and additional references is integrated to provide a holistic overview of the AMR crisis. By applying the four pillars of planetary health-social, economic, environmental, and health knowledge-in this manuscript, the necessity is underscored of collaborative strategies across human and veterinary medicine to combat AMR. Ultimately, this synergistic approach aims to shape the policies and practices that safeguard public health, protect ecosystems, and promote a sustainable future by implementing antimicrobial stewardship programs and encouraging prudent AMU.

The burden of antimicrobial resistance in livestock: A framework to estimate its impact within the Global Burden of Animal Diseases programme

In addition to affecting animal health and production, antimicrobial resistance (AMR) in livestock can have far-reaching social and economic consequences, including on human health and the environment. Given the diversity of data needs and the absence of standardised methodologies, the scale of antimicrobial use (AMU) and AMR's social and economic burden on livestock is complex to gauge. Yet, quantifying this impact can be an essential input for farm-level decision-making and, more widely, for policy development, public awareness, resource allocation to interventions and research and development prioritisation, particularly in a One Health context. This work proposes a conceptual framework to guide the assessment of the burden of AMU and AMR in livestock using the Global Burden of Animal Diseases (GBADs) approach. Its development identified and mapped critical socio-economic concepts in AMU and AMR in livestock and their relationships. The Animal Health Loss Envelope (AHLE), a monetary metric that sets a boundary for overall losses from health hazards and allows an understanding of the relative importance of health problems in livestock, was used as the metric in which the concepts and data needs for the AMU and AMR assessment were anchored. The proposed framework identifies pathways for losses and data inputs needed to estimate the burden of AMU and AMR within this wider envelope of losses. These include information on health expenditure and mortality and morbidity effects related to AMR in livestock. This work highlights the need for improved health and production data collection in livestock production as an essential stepping stone to accurately producing AMU and AMR burden estimates.

Knowledge, Attitudes, Practices on Antimicrobial Use in Animals Among Livestock Sector Stakeholders in Kenya

Background: Antimicrobials are used on farms to manage livestock diseases. In many developing countries, antimicrobial use (AMU) is insufficiently controlled, and antimicrobials are prone to misuse and abuse, thereby fostering the emergence of antimicrobial resistance (AMR). AMR remains a challenge in Kenya, and the extent remains unknown. This study assessed the knowledge, attitudes, and practices (KAP) regarding AMU among multisectoral stakeholders in Kenya. Methods: The cross-sectional survey was conducted in August 2021 among 381 livestock farmers in Busia, Nakuru, and Isiolo Counties, while 47 animal health service providers (AHSPs) and 32 One Health practitioners (OHPs) were enrolled across Kenya. The data collection tool uploaded on KoBoCollect software was used to collect information on demographics, farming systems, KAP on AMR and AMU, and sources of information. Descriptive statistics were performed. Knowledge was either correct or incorrect, while practices were assigned as desirable or undesirable. Bivariable analysis to assess factors associated with KAP using odds ratio (OR) at 95% confidence level (CL). The Pearson correlation test was conducted to test the correlation between demographic independent variables and farmers' KAP, p < 0.05. Results: Most farmers, 234 (61.4%), were young adults between 30 and 49 years old. Additionally, 48.9% of the farmers had less than 5 years of experience in farming. Among the AHSPs, 76.6% were male, with 21 (44.7%) having 2-5 years of experience. All (32) OHPs had over 15 years of experience. Correct knowledge in AMR/AMU was observed in 52.6% of the farmers, 88.2% of AHSPs, and all OHPs. Desirable practices were observed in 133 (34.9%) of farmers, 22 (45.1%) of AHSPs, and 25 (76.4%) of OHPs. Among the farmers, having basic education was associated with correct knowledge (OR 4.07, p=0.0007); however, being male (OR 1.584, p=0.0456) and having a higher education level (OR 1.582, p=0.0165) were associated with desirable practices. There was a significant positive correlation between having correct knowledge and level of education (p < 0.0001), years of farming, and correct knowledge (p < 0.0001). However, years of farming negatively correlated with the desirable practices (p < 0.0001). Farmers' preferred sources of information regarding AMR/AMU were friends 130 (33.9%), farmer meetings/workshops 99 (25.9%), and radio 41 (10.7%). AHSPs obtain information from scientific conferences/trainings (17) (65.4%), workshops (13) (50.0%), and TV and radio (12) (46.2%), while OHSPs mostly get information through college training (14) (58.3%) and workshops (8) (33.3%). Conclusion: Correct knowledge of AMR/AMU did not result in adopting the desirable practices. A better understanding of the socioeconomic aspects of welfare, good livestock production measures, and AMU stewardship will be desired. This study provides a foundation for developing effective antimicrobial stewardship, best farm practices, and intervention programs to reduce inappropriate AMU. Public Implication: Farmers' AHSP practices are likely to promote the emergence of AMR, a health challenge for animals and humans.

Investigation into the supplementation of a ferric sillen core-linked polymer on the health and physiological performance of broiler chickens

Poultry is a ubiquitous and highly sought-after protein source valued for its accessibility, notable protein content, and lack of religious constraints. However, the demand for poultry has resulted in a surge in intensive production practices. The transition from subsistence agricultural practices to intensive food production resulted in the widespread adoption of antibiotics for both therapeutic and economic purposes. These interventions were intended to enhance meat yield, promote bird health, and enhance cost-effectiveness of production. However, this inadvertently contributed to the rise of antimicrobial resistance (AMR). Therefore, the need to explore alternative approaches to mitigate the problems associated with AMR has become increasingly pressing. In response, metal-based compounds have emerged as a promising substitute to conventional antibiotics. In this study, the effects of a water soluble metallo-antimicrobial supplement, ferric sillen core-linked polymer (FSCLP), on body weight gain, feed conversion, water intake, volatile fatty acid (VFA) production, cecal microbiome and intestinal morphology in broilers was examined. The findings of this study suggested that the addition of the FSCLP resulted in better bird performance, even during a period of heat stress. Volatile fatty acids analysis of cecal contents indicated that there were significantly higher levels (p < 0.05) of butyric and valeric acids. Cecal microbiome analysis confirmed significantly lower abundance (p < 0.05) of Proteobacteria (e.g., E. coli) and a significantly greater abundance of VFA-producing bacteria such as Intestinimonas butyriciproducens, Blautia and Lachnospiraceae. The intestinal morphology data showed supplementation with the FSCLP at 80 ppm resulted in a significantly higher (p < 0.05) villus height of the jejunum. This study emphasises the potential of FSCLP as a feasible solution to the issues faced by AMR in chicken production, providing insights into its beneficial impacts on performance, microbial composition, and intestinal health.

Controlling of foodborne pathogen biofilms on stainless steel by bacteriophages: A systematic review and meta-analysis

This study investigates the potential of using bacteriophages to control foodborne pathogen biofilms on stainless steel surfaces in the food industry. Biofilm-forming bacteria can attach to stainless steel surfaces, rendering them difficult to eradicate even after a thorough cleaning and sanitizing procedures. Bacteriophages have been proposed as a possible solution, as they can penetrate biofilms and destroy bacterial cells within, reducing the number of viable bacteria and preventing the growth and spread of biofilms. This systematic review and meta-analysis evaluates the potential of bacteriophages against different biofilm-forming foodborne bacteria, including Cronobacter sakazakii, Escherichia coli, Staphylococcus aureus, Pseudomonas fluorescens, Pseudomonas aeruginosa and Listeria monocytogenes. Bacteriophage treatment generally causes a significant average reduction of 38 % in biofilm formation of foodborne pathogens on stainless steel. Subgroup analyses revealed that phages are more efficient in long-duration treatment. Also, applying a cocktail of phages is 1.26-fold more effective than applying individual phages. Phages at concentrations exceeding 107 PFU/ml are significantly more efficacious in eradicating bacteria within a biofilm. The antibacterial phage activity decreases substantially by 3.54-fold when applied at 4 °C compared to temperatures above 25 °C. This analysis suggests that bacteriophages can be a promising solution for controlling biofilms in the food industry.

The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface

Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.

Rapid testing of antibiotic residues to increase food safety awareness of animal origin

Background and Aim

Antibiotics are used to improve growth, reduce disease, and decrease mortality in animals grown for food. The government regulates and prohibits the use of antibiotics, in particular, the use of antibiotic growth promoter (AGP) in livestock; however, it is not yet known whether the use of antibiotics is in accordance with regulations so that there are no antibiotic residues in food of animal origin. To ensure food safety of animal origin and to raise awareness of food safety, it is necessary to detect antibiotic residues in fish, eggs, and chicken meat from Yogyakarta Special Province through monitoring and monitoring. To ensure food safety and regulatory compliance in food samples, antibiotic residue screening techniques are essential. A number of methods, such as time-consuming and costly chromatographic and spectroscopic methods, have been developed for the detection of antibiotic residues in food samples; however, not all laboratories have these facilities. Therefore, a rapid diagnosis of food of animal origin is required. The purpose of this study was to rapidly test antibiotic residues by using Premi®test kits (R-Biopharm AG, Germany) to increase awareness of food safety of animal origin.

Materials and Methods

We tested 345 animal-based food samples from traditional markets, supermarkets, and central markets in five districts of Yogyakarta Special Province for antibiotic residues using rapid test kits and observation questionnaires to identify risk factors.

Results

The presence of antibiotic residues in food-animal origin samples from the Yogyakarta region had an antibiotic residue level of 9.28% (32/345), consisting of fish samples 11.3% (18/97), eggs 15.65% (1/114), and chicken meat samples 0.87% (13/102). The highest percentage of samples positive for residual antibiotics was 21.9% (7/32) from supermarket meat samples. The highest amounts of antibiotic residues were found in fish samples collected from Sleman Regency, up to 25% (8/32), whereas in supermarket fish samples, there were as high as 18.8% (6/32).

Conclusion

Antibiotic residues in animal-based food can be attributed to various factors, including product source, transportation conditions, and environmental conditions. The widespread distribution of antibiotic residues in fish comes from environmental conditions during maintenance, distribution, and retailing. Monitoring antibiotic residue prevalence in food-animal origins, particularly chicken meat, eggs, and fish, is crucial for improving animal food quality and safety.

Characterising proximal and distal drivers of antimicrobial resistance: An umbrella review

INTRODUCTION

Antimicrobial resistance (AMR) is a multifactorial challenge driven by a complex interplay of proximal drivers, such as the overuse and misuse of antimicrobials and the high burden of infectious diseases, and distal factors, encompassing broader societal conditions such as poverty, inadequate sanitation, and healthcare system deficiencies. However, distinguishing between proximal and distal drivers remains a conceptual challenge.

OBJECTIVES

We conducted an umbrella review, aiming to systematically map current evidence about proximal and distal drivers of AMR and to investigate their relationships.

METHODS

Forty-seven reviews were analysed, and unique causal links were retained to construct a causality network of AMR. To distinguish between proximal and distal drivers, we calculated a 'driver distalness index (Di)', defined as an average relative position of a driver in its causal pathways to AMR.

RESULTS

The primary emphasis of the literature remained on proximal drivers, with fragmented existing evidence about distal drivers. The network analysis showed that proximal drivers of AMR are associated with risks of resistance transmission (Di = 0.49, SD = 0.14) and antibiotic use (Di = 0.58, SD = 0.2), which are worsened by intermediate drivers linked with challenges of antibiotic discovery (Di = 0.62, SD = 0.07), infection prevention (Di = 0.67, SD = 0.14) and surveillance (Di = 0.69, SD = 0.16). Distal drivers, such as living conditions, access to sanitation infrastructure, population growth and urbanisation, and gaps in policy implementation were development and governance challenges, acting as deep leverage points in the system in addressing AMR.

CONCLUSIONS

Comprehensive AMR strategies aiming to address multiple chronic AMR challenges must take advantage of opportunities for upstream interventions that specifically address distal drivers.

Low temperatures do not impair the bacterial plasmid conjugation on poultry meat

Conjugation plays an important role in the dissemination of antimicrobial resistance genes. Besides, this process is influenced by many biotic and abiotic factors, especially temperature. This study aimed to investigate the effect of different conditions of temperature and storage (time and recipient) of poultry meat, intended for the final consumer, affect the plasmid transfer between pathogenic (harboring the IncB/O-plasmid) and non-pathogenic Escherichia coli organisms. The determination of minimal inhibitory concentrations (MIC) of ampicillin, cephalexin, cefotaxime, and ceftazidime was performed before and after the conjugation assay. It was possible to recover transconjugants in the poultry meat at all the treatments, also these bacteria showed a significant increase of the MIC for all antimicrobials tested. Our results show that a non-pathogenic E. coli can acquire an IncB/O-plasmid through a conjugation process in poultry meat, even stored at low temperatures. Once acquired, the resistance genes endanger public health especially when it is about critically and highly important antimicrobials to human medicine.

Antimicrobial use and resistance in food animal production: food safety and associated concerns in Sub-Saharan Africa

The use of antimicrobials in food animal (FA) production is a common practice all over the world, with even greater usage and dependence in the developing world, including Sub-Saharan Africa (SSA). However, this practice which serves obvious economic benefits to producers has raised public health concerns over the last decades, thus driving the selection and dissemination of antimicrobial resistance and adversely impacting food safety and environmental health. This review presents the current and comprehensive antimicrobial usage practices in food animal production across SSA. We further highlighted the overall regional drivers as well as the public health, environmental, and economic impact of antimicrobial use in the production of food animals. Antimicrobial use is likely to increase with even exacerbated outcomes unless cost-effective, safe, and sustainable alternatives to antibiotics, especially probiotics, prebiotics, bacteriocins, antimicrobial peptides, bacteriophages, vaccines, etc. are urgently advocated for and used in food animal production in SSA. These, in addition to the implementation of strong legislation on antimicrobial use, and improved hygiene will help mitigate the public health concerns associated with antimicrobial use in food animals and improve the well-being and safety of food animals and their products.

Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

BACKGROUND

Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches.

RESULTS

We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome.

CONCLUSIONS

This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.

Potential Causes of Spread of Antimicrobial Resistance and Preventive Measures in One Health Perspective-A Review

Antimicrobial resistance, referring to microorganisms' capability to subsist and proliferate even when there are antimicrobials is a foremost threat to public health globally. The appearance of antimicrobial resistance can be ascribed to anthropological, animal, and environmental factors. Human-related causes include antimicrobial overuse and misuse in medicine, antibiotic-containing cosmetics and biocides utilization, and inadequate sanitation and hygiene in public settings. Prophylactic and therapeutic antimicrobial misuse and overuse, using antimicrobials as feed additives, microbes resistant to antibiotics and resistance genes in animal excreta, and antimicrobial residue found in animal-origin food and excreta are animals related contributive factors for the antibiotic resistance emergence and spread. Environmental factors including naturally existing resistance genes, improper disposal of unused antimicrobials, contamination from waste in public settings, animal farms, and pharmaceutical industries, and the use of agricultural and sanitation chemicals facilitatet its emergence and spread. Wildlife has a plausible role in the antimicrobial resistance spread. Adopting a one-health approach involving using antimicrobials properly in animals and humans, improving sanitation in public spaces and farms, and implementing coordinated governmental regulations is crucial for combating antimicrobial resistance. Collaborative and cooperative involvement of stakeholders in public, veterinary and ecological health sectors is foremost to circumvent the problem effectively.

Circular Health: exploiting the SDG roadmap to fight AMR

Circular Health is a novel approach to address complex health issues that is based on the expansion of the One Health Paradigm. Circular health recognizes the need for a multidisciplinary convergence effort to complement the biomedical dimension of health. Antimicrobial resistance (AMR) is one of the greatest global concerns for public health that is likely on the rise, given the extensive use of antibiotics during the early Covid-19 years. Prior to the Covid-19 pandemic, an expert group chaired by Jim O'Neill published "The Review on Antimicrobial Resistance", which contains a final report and recommendations on how to tackle AMR. The report, for the first time, considers AMR from a multi-perspective viewpoint highlighting how it cannot be successfully addressed unless there is a converging approach encompassing many dimensions of the problem. In this perspective, we propose to include the recommendations from that seminal report and other more recent reviews which include the lessons learnt from the Covid-19 pandemic, into the operational framework of the sustainable development goals (SDGs). AMR represents a perfect case study to explore how the SDG roadmap has the potential of becoming the driving force and implementation tool to address complex health issues by pursuing the optimization of resources and actions via a convergent and multi-stakeholder approach. The implementation of health-related policies through the whole spectrum of the SDGs could be both a novel and a well-established framework to inform multi-dimensional policies for more sustainable health in the future.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

Food matrix design can influence the antimicrobial activity in the food systems: A narrative review

Antimicrobial agents are safe preservatives having the ability to protect foods from microbial spoilage and extend their shelf life. Many factors, including antimicrobials' chemical features, storage environments, delivery methods, and diffusion in foods, can affect their antimicrobial activities. The physical-chemical characteristics of the food itself play an important role in determining the efficacy of antimicrobial agents in foods; however the mechanisms behind it have not been fully explored. This review provides new insights and comprehensive knowledge regarding the impacts of the food matrix, including the food components and food (micro)structures, on the activities of antimicrobial agents. Studies of the last 10 years regarding the influences of the food structure on the effects of antimicrobial agents against the microorganisms' growth were summarized. The mechanisms underpinning the loss of the antimicrobial agents' activity in foods are proposed. Finally, some strategies/technologies to improve the protection of antimicrobial agents in specific food categories are discussed.

Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments

Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.

Antimicrobial Susceptibility Profile of Pathogenic and Commensal Bacteria Recovered from Cattle and Goat Farms

The use of antibiotics in food animals results to antimicrobial resistant bacteria that complicates the ability to treat infections. The purpose of this study was to investigate the prevalence of pathogenic and commensal bacteria in soil, water, manure, and milk from cattle and goat farms. A total of 285 environmental and 81 milk samples were analyzed for Enterobacteriaceae by using biochemical and PCR techniques. Susceptibility to antibiotics was determined by the Kirby-Bauer disk diffusion technique. A total of 15 different Enterobacteriaceae species were identified from goat and cattle farms. Manure had significantly higher (p < 0.05) Enterobacteriaceae (52.0%) than soil (37.2%), trough water (5.4%), and runoff water (5.4%). There was a significant difference (p < 0.05) in Enterobacteriaceae in goat milk (53.9%) and cow milk (46.2%). Enterobacteriaceae from environment showed 100% resistance to novobiocin, erythromycin, and vancomycin E. coli O157:H7, Salmonella spp., Enterococcus spp., and Listeria monocytogenes displayed three, five, six, and ten. AMR patterns, respectively. NOV-TET-ERY-VAN was the most common phenotype observed in all isolates. Our study suggest that cattle and goat farms are reservoirs of multidrug-resistant bacteria. Food animal producers should be informed on the prudent use of antimicrobials, good agricultural practices, and biosecurity measures.

Antimicrobial resistance dissemination associated with intensive animal production practices in Argentina: A systematic review and meta-analysis

Abuse and misuse of antimicrobial agents has accelerated the spread of antimicrobial-resistant bacteria. The association between antimicrobial-resistant infections in humans and antimicrobial use in agriculture is complex, but well-documented. This study provides a systematic review and meta-analysis of the dissemination of antimicrobial resistance (AMR) to antimicrobials defined as critically important by the WHO, in swine, chicken, and cattle from intensive and extensive production systems in Argentina. We conducted searches in electronic databases (MEDLINE-PubMed, Web of Science, SciELO, the National System of Digital Repositories from Argentina) as well as in the gray literature. Inclusion criteria were epidemiological studies on AMR in the main food-transmitted bacteria, Salmonella spp., Campylobacter spp., Escherichia coli and Enterococcus spp., and mastitis-causing bacteria, isolated from swine, chicken, dairy and beef cattle from Argentina. This study gives evidence for supporting the hypothesis that AMR of common food-transmitted bacteria in Argentina is reaching alarming levels. Meta-analyses followed by subgroup analyses confirmed the association between the prevalence of AMR and (a) animal species (p<0.01) for streptomycin, ampicillin and tetracycline or (b) the animal production system (p<0.05) for streptomycin, cefotaxime, nalidixic acid, ampicillin and tetracycline. Moreover, swine (0.47 [0.29; 0.66]) and intensive production (0.62 [0.34; 0.83]) showed the highest pooled prevalence of multidrug resistance while dairy (0.056 [0.003; 0.524]) and extensive production (0.107 [0.043; 0.240]) showed the lowest. A research gap regarding beef-cattle from feedlot was identified. Finally, there is an urgent need for political measures meant to coordinate and harmonize AMR surveillance and regulate antimicrobial use in animal production.

Composition and distribution of bacterial communities and antibiotic resistance genes in fish of four mariculture systems

Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10^-3 - 6.30 × 10^-2 copies per 16 S rRNA gene. Transposase gene (tnpA-04) was detected in all samples with the abundance of 3.57 × 10^-3 - 3.59 × 10^-2 copies per 16 S rRNA gene, and was strongly correlated with multiple ARGs (e.g., aphA1, tet(34), mphA-02). Proteobacteria, Deinococcus-Thermus, Firmicutes, and Bacteroidetes were the dominant phyla in the four mariculture systems, accounting for 65.1%-96.2% of the total bacterial community. Notably, the high relative abundance of Stenotrophomonas, a potential human pathogen, was elevated by 20.5% in the hybrid grouper gut in the monoculture system. In addition, variation partitioning analysis (VPA) showed that the difference in bacterial communities between mariculture systems was the main driving factor of ARGs distribution differences in hybrid groupers. This study provides a new comprehensive understanding of the characterization of fish-related ARGs contamination in different mariculture systems and facilitates the assessment of potential risks of ARGs and pathogen taxa to human health.

Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs

The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL-Ec isolates were subjected to WGS. The prediction of antibiotic resistance genes, virulence factors (VFs) and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively. Diverse sequence types (STs) were detected with ST2144 and ST88 being predominant and bla_CTX-M-15 (55%) being the principal ESBL gene. All except two isolates harboured various aminoglycoside resistance genes, including aph(3″)-Ib (6/11, 55%) and aph(6)-1d (6/11, 55%), while the qnrS1 gene was identified in four of the isolates. The ESBL-Ec isolates showed a 93.6% score of being human pathogens. The fim, ehaB, ibeB/C were the leading virulence factors detected. All isolates harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs, with one isolate harbouring up to 18 ExPEC VFs. Five isolates (45.45%) harboured the plasmid incompatibility group IncF (FII, FIB, FIC, FIA). The study revealed that there is an urgent need to implement effective strategies to contain the dissemination of resistant and virulent ESBL-Ec through the food chain in Cameroon and South Africa.

Contamination of Fresh Produce with Antibiotic-Resistant Bacteria and Associated Risks to Human Health: A Scoping Review

Fresh produce, when consumed raw, can be a source of exposure to antimicrobial residues, antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) of clinical importance. This review aims to determine: (1) the presence and abundance of antimicrobial residues, ARB and ARGs in fresh agricultural products sold in retail markets and consumed raw; (2) associated health risks in humans; and (3) pathways through which fresh produce becomes contaminated with ARB/ARGs. We searched the Ovid Medline, Web of Science and Hinari databases as well as grey literature, and identified 40 articles for inclusion. All studies investigated the occurrence of multidrug-resistant bacteria, and ten studies focused on ARGs in fresh produce, while none investigated antimicrobial residues. The most commonly observed ARB were E. coli (42.5%) followed by Klebsiella spp. (22.5%), and Salmonella spp. (20%), mainly detected on lettuce. Twenty-five articles mentioned health risks from consuming fresh produce but none quantified the risk. About half of the articles stated produce contamination occurred during pre- and post-harvest processes. Our review indicates that good agricultural and manufacturing practices, behavioural change communication and awareness-raising programs are required for all stakeholders along the food production and consumption supply chain to prevent ARB/ARG exposure through produce.

Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota

Antibiotic resistance in bacteria has become a major global health problem. One of the main reservoirs of antibiotic resistance genes is the human gut microbiota. To characterise these genes, a metagenomic approach was used. In this study, a comprehensive antibiotic resistome catalog was established using fecal samples from 246 healthy individuals from world's longevity township in Jiaoling, China. In total, 606 antibiotic resistance genes were detected. Our results indicated that antibiotic resistance genes in the human gut microbiota accumulate and become more complex with age as older groups harbour the highest abundance of these genes. Tetracycline resistance gene type tetQ was the most abundant group of antibiotic resistance genes in gut microbiota, and the main carrier of antibiotic resistance genes was Bacteroides. Antibiotic efflux, inactivation, and target alteration were found to be the dominant antimicrobial resistance mechanisms. This research may help to establish a comprehensive antibiotic resistance catalog that includes extremely long-lived healthy people such as centenarians, and may provide potential recommendations for controlling the use of antibiotics.