A proposed analytic framework for determining the impact of an antimicrobial resistance intervention

Early evaluation of the Food and Drug Administration (FDA) guidance on antimicrobial use in food animals on antimicrobial resistance trends reported by the National Antimicrobial Resistance Monitoring System (2012-2019)

Antimicrobial resistance (AMR) is one of the biggest challenges to global public health. To address this issue in the US, governmental agencies have implemented system-wide guidance frameworks and recommendations aimed at reducing antimicrobial use. In particular, the Food and Drug Administration (FDA) prohibited the extra-label use of cephalosporins in food animals in 2012 and issued the guidance for industry (GFI) #213 about establishing a framework to phase out the use of all medically relevant drugs for growth promotion in 2012. Also in 2015, the FDA implemented veterinary feed directive (VFD) drug regulations (GFI# 120) to control the use of certain antimicrobials. To assess the potential early effects of these FDA actions and other concurrent antimicrobial stewardship actions on AMR in the food chain, we compared the patterns of the phenotypic (minimum inhibitory concentration (MIC) and percentage of resistance) and genotypic resistances for selected antimicrobials before and after 2016 across different enteric pathogen species, as reported by the National Antimicrobial Resistance Monitoring System (NARMS). Most of the antimicrobials analyzed at the phenotypic level followed a downward trend in MIC after implementing the guidance. Although, most of those changes were less than one 1-fold dilution. On the other hand, compared to MIC results, the results based on phenotypic resistance prevalence evidenced higher differences in both directions between the pre- and post-guidance implementation period. Also, we did not find relevant differences in the presence of AMR genes between pre- and post-VFD drug regulations. We concluded that the FDA guidance on antimicrobial use has not led to substantial reductions in antimicrobial drug resistance yet.

Drivers of ESBL-producing Escherichia coli dynamics in calf fattening farms: A modelling study

The contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producing Escherichia coli (ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics on arrival had a strong effect on average ESBL-EC prevalence (relative reduction of 77.0%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.3%).

High biosecurity and welfare standards in fattening pig farms are associated with reduced antimicrobial use

In order to reduce antimicrobial use in pig production, the consequences of insufficient biosecurity and welfare problems need to be known. This study aimed to investigate associations between the number of antimicrobial treatments per fattening pig, and biosecurity, indicators for animal welfare as well as the prevalence of lesions at slaughter. The data used in this study were extracted from the pig health and welfare classification system (Sikava), which gathers data on medicine usage, meat inspection, animal welfare and the condition of farm buildings from over 95% of pig production in Finland. The data were registered during years from 2011 to 2013. Upon antimicrobial prescription, information on the number of fattening pigs treated and the main reason for treatment was recorded. In addition, at least 4 times per year, pig farms registered in Sikava were visited by the farm veterinarian who assessed, among other things, biosecurity and indicators for animal welfare (air quality, condition of facilities, cleanliness, enrichment and stocking density). Finally, data from slaughterhouse inspections were collected (number of carcasses with joint infection, abscesses, lung lesions, pleurisy and liver lesions). For analysis, these datasets were aggregated at the farm level to a quarter of a year. During the studied period, the mean number of antimicrobial treatments per fattening pig per 3 months was equal to 0.09. The main reasons for antimicrobial treatments were musculoskeletal diseases, tail biting and respiratory disorders (42, 33 and 12% of diagnoses, respectively). The meat inspection scoring indicated that as much as 14.7% of all pigs had pleurisy, 5.3% liver lesions and 4.1% abscesses. A standard zero-inflated negative binomial model was used to identify factors associated with the number of antimicrobial treatments per pig. The count of antimicrobial treatments per pig increased with the size of a farm. Regardless of prevalence of lesions, farms with poor drinking equipment, insufficient enrichment and a combination of poor condition of pens and high stocking density were associated with an increased number of antimicrobial treatments for musculoskeletal diseases per pig. Problems with stocking density and enrichment were associated with the number of antimicrobial treatments for tail biting, although these results depended on prevalence of joint infections. Problems with air quality and the combination of poor cleanliness and poor condition of facilities were associated with increased number of antimicrobial treatments due to respiratory diseases. This study suggests that by improving biosecurity and welfare at pig farms, antimicrobial use can be reduced.