Use Of Antimicrobials In Livestock Research Articles

Antimicrobial use and resistance data in human and animal sectors in the Lao PDR: evidence to inform policy

ObjectivesTo review the scientific evidence base on antimicrobial use (AMU) and antimicrobial resistance (AMR) in human and animal sectors in the Lao PDR (Laos).MethodsWe reviewed all publications from July 1994...

Creating an innovation ecosystem for rapid diagnostic tests for livestock to support sustainable antibiotic use

ABSTRACT Antimicrobial resistance (AMR) is one of today’s greatest public health threats and reducing antimicrobial use in livestock is essential to prevent its spread, requiring rapid diagnostic tests (RDTs) to ensure that the drug prescribed matches the sensitivity of the disease organism. However, despite decades of research on RDTs and a relatively permissive regulatory environment in the UK, few devices are in commercial use. Challenges discussed by RDT developers included identifying commercially-viable targets, and management of the innovation ecosystem, e.g. to create clear pathways to market supporting positive interactions between farmers, vets, and other actors along the value chain. Future support for RDT development could be provided through incorporation in: assured food systems; business service packages provided by centralised laboratories; or animal health monitoring packages related to the spread of AMR. Breeding stock sales could require an accompanying health package including RDTs, vaccines and/or antibiotics, linking to precision agriculture approaches. Unlike the example of RDT development for COVID-19, it seems that the urgency of the issue and the clarity of links between animal and human health outcomes are not yet sufficient to support a fast-tracking programme for the development of RDTs to combat AMR.

Veterinary Herd Health Consultancy and Antimicrobial Use in Dairy Herds.

The globally increasing level of antimicrobial resistance affects both human and animal health, why it is necessary to identify ways to change our current use of antimicrobials. The veterinary herd health collaboration between veterinarians and dairy farmers provides a useful setting for changing antimicrobial use in livestock. However, farmers and veterinarians work in a complex agricultural setting influenced by socio-economic factors, which complicates their choices regarding antimicrobial usage. It is therefore necessary to be aware of the range of potential influencing factors and to integrate this knowledge in the relevant local settings. This manuscript presents a literature review of relevant factors relating to antimicrobial use within the veterinary herd health consultancy setting, including knowledge gaps of relevance for changing the use of antimicrobials. An enriched version of the framework of the Theory of Planned Behaviour was used to organise the literature review. We identified diverging attitudes on correct treatment practices and perceptions of antimicrobial resistance among veterinarians and farmers, influenced by individual risk perception as well as social norms. Furthermore, disagreements in terms of goal setting and in the frequency of herd visits in relation to herd health consultancy can negatively influence the collaboration and the intention to change antimicrobial use. Farmers and veterinarians emphasise the importance of legislation and the role of the dairy industry in changing antimicrobial use, but the relevance of specific factors depends on the country-specific context. Overall, farmers and veterinarians must communicate better to understand each other's perspectives and establish common goals within the collaboration if they are to work efficiently to reduce antimicrobial use. Farmers and veterinarians both requested changes in individual behaviour; however, they also called for national and structural solutions in terms of balanced legislation and the availability of better diagnostics to facilitate a change in antimicrobial use practices. These various paths to achieving the desired changes in antimicrobial use illustrate the need to bridge methodological research approaches of veterinary science and social sciences for a better understanding of our potential to change antimicrobial use within the dairy farm animal sector.

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

BackgroundAntimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.ResultsMicrobial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.ConclusionsAntimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.

Pilot Monitoring of Antimicrobial Residues in Chicken and Porkin Vietnam

Antibiotic residues in consumer foods pose a threat to human health and contribute to increasing antimicrobial resistance. The study was conducted from January to July 2019 in six provinces in Vietnam. In total, 360 pork samples and 360 chicken samples were collected for analysis. The samples were first screened with an enzyme-linked immunosorbent assay test kit for residues in the beta-lactam, tetracycline, and sulfonamide groups. All positive and suspected positive samples were confirmed by liquid chromatography-tandem mass spectrometry to determine the concentration of ampicillin, amoxicillin, sulfamethazine, sulfaquinoxaline, oxytetracycline, and doxycycline residues. The final confirmed result showed that 13 (3.6%), 99 (27.5%), and 16 (4.4%) chicken samples and 13 (3.6%), 29 (8.1%), and 29 (8.1%) pork samples were positive or suspected positive with beta-lactam, tetracycline, and sulfonamide residues, respectively. The liquid chromatography-tandem mass spectrometry method detected amoxicillin (8.1 to 151.6 ng/g), ampicillin (1.9 to 7.5 ng/g), doxycycline (1.1 to 491.1 ng/g), oxytetracycline (1.1 to 12.9 ng/g), sulfaquinoxaline (1.1 to 7.3 ng/g), and sulfamethazine (1.0 to 1,556.5 ng/g) in positive or suspected positive pork and chicken samples. Tetracycline (18%) was the most frequently found residue, followed by sulfonamide (6%). The proportion of chicken samples with a residue level higher than the maximum residue limit (3%) and the level of tetracycline residue were significantly higher than pork (1%). A significantly higher proportion of samples with residue levels higher than MRL (4%) and the highest levels of tetracycline residue were observed in north Vietnam. This data can help motivate decision-making toward lowering the use of antimicrobials in livestock and antibiotic residue in livestock products.

Data on antimicrobial use in livestock: Lessons from Uganda

In 2016, the General Assembly of the United Nations recognised inappropriate Antimicrobial Use (AMU) in livestock as one of the leading causes of increasing Antimicrobial Resistance (AMR). This is happening at a time when livestock production is expected to increase dramatically particularly in Africa, in response to the large rise in aggregate demand due to population growth, urbanisation and increasing income levels. Therefore, understanding the characteristics and appropriateness of AMU in livestock in this region is of utmost importance, yet data is seldom available. We propose to collect information on AMU in livestock by including related questions in nationally representative agricultural surveys that are carried out regularly (annually or every 2–3 years) by National Statistical Offices. This approach, with its limitation though, is a viable and cost-effective way to gather essential information on AMU in livestock farming. The Uganda Bureau of Statistics (UBOS) in collaboration with the Food and Agriculture Organization of the United Nations (FAO) piloted the introduction of key AMU questions in the Annual Agricultural Survey (AAS), gathering data from 6 thousand agricultural households nation-wide. Results show that AMU is considerable among livestock keeping households (35%), who use antibiotics not only for curative treatment (~58%) but also for disease prevention (~44%) and growth promotion (~5%). Data from the AAS also allows users to explore linkages between antibiotics use, livestock production practices (e.g. herd composition and size, feeding, breeding techniques, etc.) and other household / farm characteristics (e.g. location, education, household size, etc.), thereby effectively informing policy decisions.

Update on Streptococcus suis Research and Prevention in the Era of Antimicrobial Restriction: 4th International Workshop on S. suis.

Streptococcus suis is a swine pathogen and a zoonotic agent afflicting people in close contact with infected pigs or pork meat. Sporadic cases of human infections have been reported worldwide. In addition, S. suis outbreaks emerged in Asia, making this bacterium a primary health concern in this part of the globe. In pigs, S. suis disease results in decreased performance and increased mortality, which have a significant economic impact on swine production worldwide. Facing the new regulations in preventive use of antimicrobials in livestock and lack of effective vaccines, control of S. suis infections is worrisome. Increasing and sharing of knowledge on this pathogen is of utmost importance. As such, the pathogenesis and epidemiology of the infection, antimicrobial resistance, progress on diagnosis, prevention, and control were among the topics discussed during the 4th International Workshop on Streptococcus suis (held in Montreal, Canada, June 2019). This review gathers together recent findings on this important pathogen from lectures performed by lead researchers from several countries including Australia, Canada, France, Germany, Japan, Spain, Thailand, The Netherlands, UK, and USA. Finally, policies and recommendations for the manufacture, quality control, and use of inactivated autogenous vaccines are addressed to advance this important field in veterinary medicine.

The Costs, Benefits and Human Behaviours for Antimicrobial Use in Small Commercial Broiler Chicken Systems in Indonesia.

There are growing concerns over the threat to human health from the unregulated use of antimicrobials in livestock. Broiler production is of great economic and social importance in Indonesia. This study used a structured questionnaire approach to explore the human behaviours and economic drivers associated with antimicrobial use in small commercial broiler systems in Indonesia (n = 509). The study showed that antimicrobial use was high with farmers easily able to access antimicrobials through local animal medicine, however, it was difficult for farmers to access veterinary advice on responsible antimicrobial use. The most significant finding was that the relative cost of antimicrobials was low, and farmers observed improvements in productivity rates from routine antimicrobial administration. However, farmers seldom kept detailed records on farm productivity or economic costs; this is a hurdle to undertaking a more detailed economic analysis of antimicrobial use. There is a need for further research on the cost-effectiveness of alternative methods of preventing disease and ensuring that feasible alternatives are easily available. Farm-level economics and securing the food supply chain need to be central to any future policy interventions to reduce antimicrobial use in broiler systems in Indonesia and this observation is relevant at a regional and global level.

Investigation of a Reduction in Tylosin on the Prevalence of Liver Abscesses and Antimicrobial Resistance in Enterococci in Feedlot Cattle.

Recent concerns over linkages between antimicrobial resistance in human pathogens and antimicrobial use in livestock have prompted researchers to investigate management strategies that reduce the current reliance on in-feed tylosin to control liver abscesses in feedlot cattle. A total of 7,576 crossbred yearlings were allocated to the study (~253 animals/pen, 10 replicate pens per treatment) and individually randomized to one of three treatments. Tylosin phosphate (11 ppm) was included in-feed (1) for the first 125 days on feed (DOF) (FIRST-78%), (2) for DOF 41 to 161 (LAST-75%), or (3) for the entire feeding period (CON; day 0–161). Fecal composites were collected from the pen floor on days 0, 81, and 160 of the finishing period. Serial dilutions were spread plated for enumeration of enterococci on Bile Esculin Azide (BEA) agar and BEA amended with 8 μg/ml erythromycin. Results indicated that although the proportion of EryR enterococci increased with DOF (P < 0.01), neither treatment (P = 0.34) or treatment × DOF (P = 0.37) affected antimicrobial resistance. Of the 538 isolates, 97% were enterococci, with mixed species isolated early in the feeding period and only Enterococcus hirae isolated at the end. Isolates were most frequently resistant to tylosin (86%), erythromycin (84%), and doxycycline (31%). Macrolide and tetracycline resistant isolates harbored erm(B), msrC, and tet(L), tet(M), tet(O) genes, respectively. Overall, the proportion of EryR enterococci increased (P < 0.05) in all three treatments over the feeding period. Compared to the control cattle, FIRST-78% cattle had more severe (P < 0.05) liver abscesses, while there was a trend (P < 0.08) for this response in LAST-75% cattle. There was no difference (P > 0.05) in total liver abscesses, growth performance, carcass traits, morbidity, or mortality among treatments. These results support the potential to reduce the duration and therefore quantity of tylosin administered to feedlot cattle during the feeding period without impacting animal productivity.

Manure Compost Is a Potential Source of Tetracycline-Resistant Escherichia coli and Tetracycline Resistance Genes in Japanese Farms.

Manure compost has been thought of as a potential important route of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) from livestock to humans. To clarify the abundance of ARB and ARGs, ARB and ARGs were quantitatively determined in tetracycline-resistant Escherichia coli (harboring the tetA gene)-spiked feces in simulated composts. In the simulated composts, the concentration of spiked E. coli decreased below the detection limit at day 7. The tetA gene remained in manure compost for 20 days, although the levels of the gene decreased. Next, to clarify the field conditions of manure compost in Japan, the quantities of tetracycline-resistant bacteria, tetracycline resistance genes, and residual tetracyclines were determined using field-manure-matured composts in livestock farms. Tetracycline-resistant bacteria were detected in 54.5% of tested matured compost (6/11 farms). The copy number of the tetA gene and the concentrations of residual tetracyclines in field manure compost were significantly correlated. These results suggest that the use of antimicrobials in livestock constitutes a selective pressure, not only in livestock feces but also in manure compost. The appropriate use of antimicrobials in livestock and treatment of manure compost are important for avoiding the spread of ARB and ARGs.

Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves.

The increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), a single treatment of enrofloxacin, or a single treatment of tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sequencing was conducted. The effect of antibiotic treatment on each taxon and genetic functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher relative abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other study groups. The SEED database was used for genetic functional analyses, which showed that calves in the enrofloxacin group started with a higher relative abundance of “Resistance to antibiotics and toxic compounds” function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. “Resistance to Fluoroquinolones” and “Erythromycin resistance”, of relevance given the study groups, were not statistically different in relative abundance between study groups. “Resistance to fluoroquinolones” increased during the study period regardless of study group. Despite small differences over the first weeks between study groups, at Day 112 the microbiota composition and genetic functional profile was similar among all study groups. In our study, enrofloxacin or tulathromycin had minimal impacts on the microbial composition and genetic functional microbiota of calves over the study period.

External Societal Costs of Antimicrobial Resistance in Humans Attributable to Antimicrobial Use in Livestock.

Antimicrobial use (AMU) in animal agriculture contributes to antimicrobial resistance (AMR) in humans, which imposes significant health and economic costs on society. Economists call these costs negative externalities, societal costs that are not properly reflected in market prices. We review the relevant literature and develop a model to quantify the external costs of AMU in animal agriculture on AMR in humans. Parameters required for this estimate include (a) the health and economic burden of AMR in humans,(b) the impact of AMU in animal agriculture on AMR in animals, (c) the fraction of AMR in humans attributable to animal agriculture, and (d) AMU in animals. We use a well-documented historic case to estimate an externality cost of about US$1,500 per kilogram of fluoroquinolones administered in US broiler chicken production. Enhanced data collection, particularly on the third and fourth parameters, is urgently needed to quantify more fully the externalities of AMU in animal agriculture.

Exploring Perspectives on Antimicrobial Use in Livestock: A Mixed-Methods Study of UK Pig Farmers.

Increasing levels of antimicrobial resistance in human and veterinary medicine have raised concerns over the irresponsible use of antimicrobials. The role of administering antimicrobials in food producing animals most frequently falls to the farmer, therefore it is essential that their use of antimicrobials is both optimal and responsible. This study sought in-depth information on the drivers behind antimicrobial use behaviors and farmer attitudes to responsible use using a mixed-methodological approach. Initially, in-depth semi-structured interviews were conducted with a purposively selected sample of farmers (n = 22). A thematic analysis approach was taken to identify key themes from these qualitative data. The generalizability and variation of these themes was then tested on a larger randomly selected sample of pig farmers through a questionnaire study (n = 261). The influences behind antimicrobial use were complex with multiple drivers motivating decisions. There was no consensual opinion on what farming systems resulted in either a low or high antimicrobial requirement however, farmers reported that good management practices, low stocking densities, and a high health status were associated with low antimicrobial use. Farmers expressed desire to avoid the long-term use of in-feed antimicrobials, but identified barriers to discontinuing such behaviors, such as pig morbidity, mortality, and economic losses. The high cost of antimicrobials was described as a motivation toward seeking alternative methods of controlling disease to prophylactic use; however, this expense was balanced against the losses from an increased burden of disease. The high financial costs involved in pig production alongside the economic uncertainty of production and pressure from retailers, were identified as limiting the scope for improvements in pig accommodation and facilities which could reduce the antimicrobial requirements on farm. Long-term, sustainable and economically stable relationships between retailers and farmers may allow farmers to make necessary investments in improving management and housing in order to reduce antimicrobial use. Greater use and more widespread deployment of effective vaccinations were highlighted by farmers as being a feasible alternative to antimicrobial use in preventing disease.

Developing Canadian Defined Daily Doses for Animals: A Metric to Quantify Antimicrobial Use.

Antimicrobial use surveillance data need to be analyzed and reported in a standardized and harmonized way. In veterinary medicine, one approach is to use defined daily doses (DDD) for animals. DDD for animals are technical standards used in various measures or metrics that quantify antimicrobial use. The European Medicines Agency published principles for assigning DDDvet values based on information on dosing obtained from nine European countries. For measuring antimicrobial use in livestock within Canada, DDDs for animals reflective of Canadian veterinary antimicrobial use (DDDvetCAs) were needed. Our objectives were (1) to describe the development of DDDvetCA standards for pigs and poultry (broiler chickens and turkeys) for authorized and compounded antimicrobial active ingredients used in Canada, including those used extra-label; and (2) to compare the DDDvetCAs with EMA's DDDvets, where possible. Species-specific DDDvetCAs were assigned based on the average of unique antimicrobial daily doses obtained from product information, stratified by route of administration and age indication (where applicable). The feed, water and bolus DDDvetCAs were compared to oral DDDvets, and injectable DDDvetCAs to parenteral DDDvets, that matched by antimicrobial active ingredient. Seventy-five DDDvetCAs were assigned for pigs; 51 for poultry. Seventeen injectable DDDvetCAs could be compared to 14 EMA's parenteral DDDvets and 53 feed, water, and bolus DDDvetCAs could be compared to 40 oral DDDvets. Feed and water DDDvetCAs were generally lower than EMA's oral DDDvets, although differences in methodology between Canada and Europe make comparisons challenging. The assignment of DDDvetCAs was a resource intensive and iterative process. EMA's published principles for assigning DDDvets were an invaluable source of information. The use of DDDvetCAs will reflect exposure of Canadian animals to antimicrobials, be useful for evaluating associations between use and resistance within Canada and provide information for risk assessment and stewardship policies. However, when reporting antimicrobial use data internationally, using the same DDD standards as other reporting countries will facilitate between country comparisons, although differences in which antimicrobial active ingredients are licensed between countries may create challenges. Future steps include assigning DDDvetCAs for other food animal species, such as cattle, veal, and farmed fish.

Multidrug-Resistant Bacteria from Raw Meat of Buffalo and Chicken, Nepal.

Antimicrobial resistance is a major global issue for human and animals. Increased use of antimicrobials in livestock and poultry has become one of the causes of antimicrobial resistance development in microorganisms. The aim of the study was to characterize antimicrobial resistant bacteria from raw buffalo and chicken meat in standard in vitro condition. A total of 140 raw meat samples were collected from different retail shops of Bhaktapur Metropolitan City, Nepal. Among them, 70 were raw buffalo meat and 70 were raw chicken meat samples. Bacterial growth, identification, and antimicrobial susceptibility test were performed according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Out of 140 samples, bacterial growth was seen in 67 raw buffalo meat and 59 raw chicken meat samples, i.e., bacterial growth was observed in 90.0% of the samples. A total of 161 bacterial isolates were detected. Escherichia coli (35.4%) and Klebsiella spp. (30.4%) were found to be the most prevalent bacteria followed by Citrobacter spp. (11.8%), Staphylococcus aureus (9.3%), Salmonella spp. (7.4%), and Proteus spp. (5.5%). Chicken meat isolates showed higher antimicrobial resistance rates in comparison to buffalo meat isolates, particularly against antimicrobials like Amoxicillin, Tetracycline, Cotrimoxazole and Nalidixic acid, p value<0.05 when compared between buffalo and chicken meat. Overall, 32.7% Multidrug-Resistant (MDR) isolates were found, in which 50.0% MDR isolates were found from chicken raw meat and 21.9% were found from buffalo raw meat. MDR isolates of Escherichia coli, Proteus spp. and Staphylococcus aureus constituted 52.5%, 77.7% and 40.0%, respectively, of both buffalo and chicken raw meat. This study indicates antimicrobials resistant bacteria existing at an alarming rate, higher in chicken meat than in buffalo meat.

Ultrasensitive and Rapid-Response Sensor for the Electrochemical Detection of Antibiotic Residues within Meat Samples.

Antimicrobial use in livestock has emerged as a pressing global issue because of the rise of antimicrobial-resistant bacteria. Regulatory authorities across the globe have taken steps to discourage the misuse of these antibiotics by banning or limiting the use of medically important antibiotics in food animals. However, to ensure that food animals are not being administered antibiotics inappropriately, there is a need for a reliable, raid-response biosensor that can detect the presence of these antibiotic residuals in meat products. We have developed an affinity-based electrochemical biosensor for the label-free detection of ceftiofur residues in meat samples. The sensor uses a self-assembled immunoassay to target the ceftiofur biomarker by employing electrochemical impedance spectroscopy to probe the interfacial capacitive changes as ceftiofur binds to the sensor surface. We have demonstrated a platform that can detect ceftiofur within 15 min of introducing the sample at concentrations down to 0.01 ng/mL in 1× phosphate-buffered saline and 10 ng/mL in 220 mg ground turkey meat samples.

Characterizing Antimicrobial Use in the Livestock Sector in Three South East Asian Countries (Indonesia, Thailand, and Vietnam).

A framework was developed to characterize the antimicrobial use/antimicrobial resistance complex in livestock systems in Indonesia, Vietnam, and Thailand. Farm profitability, disease prevention, and mortality rate reduction were identified as drivers toward antimicrobial use in livestock systems. It revealed that antimicrobial use was high in all sectors studied, and that routine preventative use was of particular importance to broiler production systems. Misleading feed labeling was identified as a hurdle to the collection of accurate antimicrobial use data, with farmers being unaware of the antimicrobials contained in some commercial feed. Economic analysis found that the cost of antimicrobials was low relative to other farm inputs, and that farm profitability was precariously balanced. High disease and poor prices were identified as potential drivers toward economic loss. The research indicates that antimicrobial use in small-scale poultry production systems improves feed conversion ratios and overall productivity. However, data were limited to quantify adequately these potential gains and their impacts on the food supply. During the study, all countries embraced and implemented policies on better management of antimicrobial use in livestock and surveillance of antimicrobial resistance. Future policies need to consider farm-level economics and livestock food supply issues when developing further antimicrobial use interventions in the region.

Antimicrobial use monitoring

Antimicrobial use in livestock is under increasing scrutiny by various regulatory, industry, and consumer groups. It is likely that in the future, production systems will be required to document antimicrobial use in order to have access to some supply chains. Regardless of from what direction this requirement comes, the veterinarian is in a unique position to help guide the formation and the application of this "documentation". There are clearly many ways to define, measure, and document antimicrobial use. This project focuses on differentiating measures that would be useful tools for managing antimicrobial use for infectious disease from those that are suitable only for monitoring macrotrends related to use reduction.

Microbial Resistance Due to the Use of Antimicrobials in Livestock and Agriculture

Antimicrobials are widely used in agriculture and livestock, nevertheless their large-scale and indiscriminate use contributes considerably to the development of microbial resistance. The intense commercialization of agricultural products accelerates the dissemination of pathogens that present resistance profiles, which characterize them as extremely harmful to plants and animals. Thus, there is an urgent need to control the use of antimicrobials in animal and vegetable food products in order to find new agents that are less able to develop resistance. It is essential the guidance of the professionals and the population about the rational use of antimicrobials in agriculture and livestock for the maintenance and protection of the human healthy and environment.

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.