Agriculture and Agri-Food Canada's research program on antimicrobial resistance

An epidemiological framework for improving the accuracy of whole-genome sequence-based antimicrobial resistance surveillance in Salmonella

Whole-genome sequence-based surveillance of bacteria for determinants of antimicrobial resistance (AMR) promises many advantages over traditional, wet-lab approaches. However, adjustments to parameters used to identify genetic determinants from sequencing data can affect results and interpretation of the important determinants in circulation. Using a dataset of whole-genome sequences from 1633 isolates of Salmonella Heidelberg and S. Kentucky collected from surveillance of Canadian poultry production, we queried the genomic data using an in silico AMR detection tool, StarAMR, applying a range of parameter values required for the detection pipeline to test for differences in detection accuracy. We compared the results from each iteration to phenotypic antimicrobial susceptibility results, and generated estimates of sensitivity and specificity using regression models that controlled for the effects of multiple sampling events and variables, and interactions between covariates. Results from our analyses revealed small, yet significant effects of the input parameters on the sensitivity and specificity of the AMR detection tool, and these effects differed based on the serovar and drug class in question. Findings from this study may have implications for the incorporation of whole-genome sequence-based approaches to the surveillance of AMR determinants in bacteria sampled from food products and animals related to food production.

A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort

Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.

Joining Forces against Antibiotic Resistance: The One Health Solution

Antibiotic resistance is a significant global health concern that affects both human and animal populations. The One Health approach acknowledges the interconnectedness of human health, animal health, and the environment. It emphasizes the importance of collaboration and coordination across these sectors to tackle complex health challenges such as antibiotic resistance. In the context of One Health, antibiotic resistance refers to the ability of bacteria to withstand the efficacy of antibiotics, rendering them less effective or completely ineffective in treating infections. The emergence and spread of antibiotic-resistant bacteria pose a threat to human and animal health, as well as to the effectiveness of medical treatments and veterinary interventions. In particular, One Health recognizes that antibiotic use in human medicine, animal agriculture, and the environment are interconnected factors contributing to the development and spread of antibiotic resistance. For example, the misuse and overuse of antibiotics in human healthcare, including inappropriate prescribing and patient non-compliance, can contribute to the selection and spread of resistant bacteria. Similarly, the use of antibiotics in livestock production for growth promotion and disease prevention can contribute to the development of antibiotic resistance in animals and subsequent transmission to humans through the food chain. Addressing antibiotic resistance requires a collaborative One Health approach that involves multiple participants, including healthcare professionals, veterinarians, researchers, and policymakers.

Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg

Antimicrobial resistance (AMR) has become a critical threat to public health worldwide. The use of antimicrobials in food and livestock agriculture, including the production of poultry, is thought to contribute to the dissemination of antibiotic resistant bacteria (ARB) and the genes and plasmids that confer the resistant phenotype (ARG). However, the relative contribution of each of these processes to the emergence of resistant pathogens in poultry production and their potential role in the transmission of resistant pathogens in human infections, requires a deeper understanding of the dynamics of ARB and ARG in food production and the factors involved in the increased risk of transmission.

How Universal Health Coverage can curb the escalating antimicrobial resistance in Pakistan: a call to action for the country's healthcare system

Antimicrobial resistance (AMR) has emerged as a major threat to the global healthcare economy during Coronavirus disease 2019 (COVID-19), especially in developing countries like Pakistan where the healthcare facilities are already substandard. To combat AMR, the World Health Organization (WHO) has taken several initiatives including the establishment of a sustainable Universal Health Coverage (UHC) system. The implementation of UHC could eliminate various factors that contribute to a high AMR rate including self-medication. Our commentary explores in depth the current UHC system in Pakistan and how UHC could be the answer to Pakistan's AMR crisis.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) colonisation and infection among livestock workers and veterinarians: a systematic review and meta-analysis

OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing public health concern worldwide. The objective of this study was to calculate a summary odds ratio (OR) of livestock-associated MRSA colonisation and infection in humans, and to determine specific risk factors in livestock production contributing to MRSA colonisation.

METHODS

We screened PubMed and Embase for studies published from 2005 to 2019 inclusive, reporting livestock-associated (LA)-MRSA colonisation and infection among livestock workers/veterinarians, their families, and community members not regularly exposed to livestock. The primary outcome of interest was the OR of LA-MRSA colonisation comparing exposed and control groups. Quality was assessed according to the Newcastle-Ottawa quality assessment scale. A meta-analysis using a random-effects model was conducted to calculate a pooled OR. The heterogeneity in the meta-analysis was assessed using the I² method, and publication bias was evaluated using funnel plots.

RESULTS

A total of 3490 studies were identified by the search, with 37 studies including 53 matched exposed-control groups and 14 038 participants eligible for the meta-analysis. The pooled OR for LA-MRSA among livestock workers and veterinarians is 9.80 (95% CI 6.89 to 13.95; p=0.000; I2 =73.4), with no significant publication bias (Egger's p=0.66). The OR for swine workers was highest at 15.41 (95% CI 9.24 to 25.69), followed by cattle workers (11.62, 95% CI 4.60 to 29.36), veterinarians (7.63, 95% CI 3.10 to 18.74), horse workers (7.45, 95% CI 2.39 to 23.25), livestock workers (5.86, 95% CI 1.14 to 30.16), poultry workers (5.70, 95% CI 1.70 19.11), and industrial slaughterhouse workers (4.69, 95% CI 1.10 to 20.0).

CONCLUSIONS

Livestock workers, particularly swine farmers, are at significantly higher risk for LA-MRSA colonisation and subsequent infection. These results support the need for preventive practices to reduce LA-MRSA risk among those who handle and treat livestock.

TRIAL REGISTRATION NUMBER

CRD42019120403.

Prevalence of Multidrug-Resistant Foodborne Pathogens and Indicator Bacteria from Edible Offal and Muscle Meats in Nashville, Tennessee

This study investigated the prevalence of antimicrobial-resistant bacteria in retail edible offal and muscle meats in Nashville, Tennessee. A total of 348 retail meats (160 edible offal and 188 muscle) were analyzed for Salmonella enterica serovar, Campylobacter, Escherichia coli, E. coli O157:H7, and enterococci. Bacteria was identified using biochemical and PCR methods. Salmonella enterica serovar (4.4% and 4.3%), Campylobacter (1.9% and 1.1%), E. coli (79.4% and 89.4%), and enterococci (88.1% and 95.7%) was detected in offal and muscle meats, respectively. Chicken liver (9.7%) was most frequently contaminated with Salmonella enterica serovar, followed by ground chicken (6.9%) and chicken wings (4.2%). No Salmonella enterica serovar was detected in beef liver, beef tripe, and ground beef. The prevalence of Campylobacter was 6.9%, 2.3%, and 1.4% in beef liver, ground beef, and ground chicken, respectively. None of the meats were positive for E. coli O157:H7. Resistance of isolates was significantly (p < 0.05) highest in erythromycin (98.3%; 99.1%), followed by tetracycline (94%; 98.3%), vancomycin (88.8%; 92.2%) as compared to chloramphenicol (43.1%; 53.9%), amoxicillin/clavulanic (43.5%; 45.7%), and ciprofloxacin (45.7%; 55.7%) in offal and muscle meats, respectively. Imipenem showed the lowest resistance (0%; 0.9%). A total of 41 multidrug-resistant patterns were displayed. Edible offal could be a source of antibiotic-resistant bacteria.

Non-viable chicken embryos: an overlooked niche harbouring a significant source of multidrug resistant bacteria in the poultry production

Antimicrobial resistance (AMR) is a global issue, posing a grave threat to the public, animal, and environmental health. The AMR surveillance at the level of the hatchery is crucial to develop an AMR control strategy in the poultry industry. The objective of this study was to investigate the AMR profiles of bacteria isolated from yolk material of non-viable broiler chicken embryos at hatch from commercial hatcheries in western Canada. Antimicrobial susceptibility testing was done using the Kirby–Bauer disk diffusion method focusing on Escherichia coli (n = 170) and Enterococcus (n = 256) species, which are commonly used as indicators of AMR evolution. E. coli isolates were resistant to tetracycline, ampicillin, amoxycillin-clavulanic acid, triple sulpha, ceftiofur, gentamycin, and spectinomycin at the rate of 52.9%, 50.6%, 40.0% 31.8%, 29.4%, 29.4%, 21.8% respectively. Among those, 37.1% of E. coli were multidrug resistant. The descending order of antimicrobial resistance of E. faecalis was; tetracycline (61.9%), ceftiofur (46.2%), bacitracin (43.9%), erythromycin (31.4%) and tylosin (27.4%). Multidrug resistance was detected in 40.4% of E. faecalis isolates, and 85.7% of E. faecium isolates. To the best of our knowledge, this is the first report on AMR surveillance of non-viable chicken embryos. Overall, the present study revealed that non-viable chicken embryos, an overlooked niche for AMR surveillance, harbour multidrug-resistant E. coli, and enterococci that can be a substantial source of superbugs in the environment. Our data also highlight the urgency of including non-viable chicken embryos in AMR surveillance programme to understand AMR dissemination and its control.

Veterinary peer study groups as a method of continuous education-A new approach to identify and address factors associated with antimicrobial prescribing

Within the dairy industry, most antimicrobials are used for dry-cow therapy or mastitis treatment. To reduce antimicrobial usage in dairy cows, increasing awareness and behaviour change is necessary. As veterinarians are known to be influenced by their peers, peer study groups as a continuous education might contribute to this. Therefore, the objective of this study was to analyse written records of veterinary peer study group meetings to identify factors associated with antimicrobial prescribing decisions, and to analyse veterinarians' attitude towards the benefits of this continuous education method. Twenty-three participating Swiss cattle practitioners were divided into three groups. Each group met every two to five months, together with a facilitator and an expert on the topic to be discussed. Written records from every meeting were taken and analysed qualitatively to identify factors influencing veterinarians' decisions on antimicrobial prescribing and mastitis therapy. In addition, focus group discussions were conducted after the last meeting, to assess the veterinarians' learning achievements gained during the peer study group meetings. Extrinsic factors such as external pressure, competition, farmer, individual animal, farm and diagnostics as well as intrinsic factors such as own experience/attitude, knowledge and change of mindset during career could be shown to influence veterinarians' decisions on antimicrobial prescribing. In the focus group discussions, the veterinarians stated that they gained new knowledge, received new stimuli, exchanged with their peers and felt supported in their relationship to their farmers. Since the identified factors are partly interrelated, it is not sufficient to change a single factor to achieve a change in the antimicrobial prescription behaviour of veterinarians. Veterinary peer study groups could contribute to the intention to change, because veterinarians experienced multiple benefits from this method of continuous education. In order to quantify this, the prescription data of the veterinarians are analysed in a next step.