Pilot testing the EARS-Vet surveillance network for antibiotic resistance in bacterial pathogens from animals in the EU/EEA.

Introduction: As part of the EU Joint Action on Antimicrobial Resistance (AMR) and Healthcare-Associated Infections, an initiative has been launched to build the European AMR Surveillance network in veterinary medicine (EARS-Vet). So far, activities included mapping national systems for AMR surveillance in animal bacterial pathogens, and defining the EARS-Vet objectives, scope, and standards. Drawing on these milestones, this study aimed to pilot test EARS-Vet surveillance, namely to (i) assess available data, (ii) perform cross-country analyses, and (iii) identify potential challenges and develop recommendations to improve future data collection and analysis. Methods: Eleven partners from nine EU/EEA countries participated and shared available data for the period 2016-2020, representing a total of 140,110 bacterial isolates and 1,302,389 entries (isolate-antibiotic agent combinations). Results: Collected data were highly diverse and fragmented. Using a standardized approach and interpretation with epidemiological cut-offs, we were able to jointly analyze AMR trends of 53 combinations of animal host-bacteria-antibiotic categories of interest to EARS-Vet. This work demonstrated substantial variations of resistance levels, both among and within countries (e.g., between animal host species). Discussion: Key issues at this stage include the lack of harmonization of antimicrobial susceptibility testing methods used in European surveillance systems and veterinary diagnostic laboratories, the absence of interpretation criteria for many bacteria-antibiotic combinations of interest, and the lack of data from a lot of EU/EEA countries where little or even surveillance currently exists. Still, this pilot study provides a proof-of-concept of what EARS-Vet can achieve. Results form an important basis to shape future systematic data collection and analysis.

Evolution of the proportion of colistin-resistant isolates in animal clinical Escherichia coli over time - A hierarchical mixture model approach.

Colistin resistance has been the subject of much attention since mcr genes encoding plasmid-mediated colistin resistance description in 2015. To date, surveillance data about resistance levels encountered in food-producing animals are scarce. In France, the Resapath dataset, consisting in a large collection of disk diffusion antibiogram results transmitted by a network of laboratories. It offers a unique opportunity to study the evolution of resistance towards colistin over the past 15 years in Escherichia coli isolated from diseased food-producing animals. This study used a Bayesian hierarchical Gaussian mixture model to estimate the resistant proportions from those data. This non-classical approach deals with the colistin-specific problem of overlapping distributions of diameters measured for susceptible and resistant isolates that makes the definition of epidemiological cut-off very hard. This model also considers the variability observed between the measurements performed by different laboratories. Proportion of resistant isolates has been calculated for several food-producing animals and most encountered diseases. From those estimations, a marked evolution of the proportions of resistant isolates is noticeable, for swine suffering from digestive disorders. In this group, an increase over the 2006-2011 period from 0.1% [ 0.0%, 1.2%] in 2006-28.6% [25.1%, 32.3%] in 2011 was followed by a decrease to reach 3.6% [2.3%;5.3%] in 2018. For isolates related to digestive disorders in calves, percentages increased and reached 7% in 2009 then decreased as for swine. In contrast, for poultry productions, estimated proportions and credibility intervals were constantly very close to zero.

Trends in antimicrobial resistance among Escherichia coli from defined infections in humans and animals.

OBJECTIVES: To characterize and compare resistance trends in clinical Escherichia coli isolates from humans, food-producing animals (poultry, cattle and swine) and pets (dogs and cats). METHODS: Antibiogram results collected between January 2014 and December 2017 by MedQual [the French surveillance network for antimicrobial resistance (AMR) in bacteria isolated from the community] and RESAPATH (the French surveillance network for AMR in bacteria from diseased animals) were analysed, focusing on resistance to antibiotics of common interest to human and veterinary medicine. Resistance dynamics were investigated using generalized additive models. RESULTS: In total, 743 637 antibiograms from humans, 48 170 from food-producing animals and 7750 from pets were analysed. For each antibiotic investigated, the resistance proportions of isolates collected from humans were of the same order of magnitude as those from food-producing animals or pets. However, resistance trends in humans differed from those observed in pets and food-producing animals over the period studied. For example, resistance to third-generation cephalosporins and fluoroquinolones was almost always below 10% for both humans and animals. However, in contrast to the notable decreases in resistance observed in both food-producing animals and pets, resistance in humans decreased only slightly. CONCLUSIONS: Despite several potential biases in the data, the resistance trends remain meaningful. The strength of the parallel is based on similar data collection in humans and animals and on a similar statistical methodology. Resistance dynamics seemed specific to each species, reflecting different antibiotic-use practices. These results advocate applying the efforts already being made to reduce antibiotic use to all sectors and all species, both in human and veterinary medicine.

Co-resistance to Amoxicillin and Tetracycline as an Indicator of Multidrug Resistance in Escherichia coli Isolates From Animals.

OBJECTIVES: To examine the relevance of co-resistance to amoxicillin and tetracycline as an indicator of multidrug resistance (MDR) in animal health. METHODS: Escherichia coli isolates collected between 2012 and 2016 by the French surveillance network for antimicrobial resistance in diseased animals (RESAPATH) were analyzed. The proportions of MDR isolates and the proportions of isolates presenting co-resistance to amoxicillin and tetracycline were calculated for seven animal species (cattle, horse, dog, swine, poultry, duck, and turkey). The degree of agreement between these two proportions was estimated by calculating the kappa value. RESULTS: In total, 55,904 isolates were analyzed. MDR proportions were variable among animal species, ranging from 21.9% [20.2; 23.7] in horses to 56.0% [55.4; 56.7] in cattle. A similar situation was observed for proportions of isolates with co-resistance to amoxicillin and tetracycline, with the highest value for cattle 65.0% [64.3; 65.6]. This co-resistance was also most often associated with resistance to other antibiotics, regardless of the animal species considered. Comparative analysis showed substantial agreement between MDR and this co-resistance, with a kappa value of 0.75, all animal species considered. CONCLUSION: Given the widespread use of penicillins and tetracyclines in animal health, co-resistance to amoxicillin and tetracycline could be an efficient indicator of MDR in E. coli isolates. Based on a specific resistance profile and not an arbitrary number of resistances compared with MDR, this potential indicator is also precise, convenient and suitable for routine use.

Antimicrobial resistance of Pasteurella multocida isolated from diseased food-producing animals and pets.

Surveillance of Pasteurella multocida resistance in food-producing animals is essential to guide the first-line treatment of respiratory diseases and to limit economic losses. Since Pasteurella are the most common bacteria isolated from dog and cat bites, this surveillance is also needed to guide treatment in humans in case of bites. The aim of this study was to characterize the phenotypic resistance of P. multocida strains isolated from respiratory infections in animals, including both food-producing animals and pets. Data collected between 2012 and 2017 by the French national surveillance network for antimicrobial resistance referred to as RESAPATH were analyzed. The proportions of resistance to antimicrobials of relevance in veterinary and human medicines were estimated for each animal species. For cattle, resistance trends over the period were investigated using non-linear analysis applied to time-series. In total, 5356 P. multocida isolates were analyzed. Proportions of resistance of P. multocida were almost all below 20% over the period, and, more precisely, all resistance proportions were below 10% for rabbits, sheep and dogs. The highest resistance proportions to enrofloxacin were identified for cattle (4.5%) and dogs (5.2%). Despite its frequent use in livestock, resistance to florfenicol was less than 1% in P. multocida strains, regardless of the animal species considered. Time series analyses revealed continuous increases in resistance to tetracycline, tilmicosin, flumequine and fluoroquinolones in P. multocida strains isolated from cattle. These trends contrast with the decrease in use of antibiotics in cattle in France and with the decrease in resistance observed in E. coli isolated from diseased cattle.

Antimicrobial Usages and Antimicrobial Resistance in Commensal Escherichia coli From Veal Calves in France: Evolution During the Fattening Process.

Extended-Spectrum-Cephalosporin (ESC)-resistant Enterobacteriaceae have widely spread in all settings worldwide. In animals, Extended-Spectrum Beta-Lactamase (ESBL) producers have been frequently identified in veal calves. The objectives of this study were to investigate the trends in the ESBL load and antimicrobial resistance (AMR) proportions, and antimicrobial usages (AMU) in veal calves during the fattening process. Ten fattening farms were selected and 50 animals per farm were sampled. AMR was assessed in bacteria from the dominant flora (collected on non-selective MacConckey agar) and in ESBL/AmpC-carrying bacteria from the subdominant flora (selected on ChromID ESBL selective plates) upon arrival and 5-6 months later before slaughter. The number and types of treatments during fattening were also collected. Rates of ESBL-producing E. coli from the subdominant flora significantly decreased in all farms (arrival: 67.7%; departure: 20.4%) whereas rates of multidrug-resistant E. coli from the dominant flora have significantly increased (arrival: 60.2%; departure: 67.2%; p = 0.025). CTX-M-1 was the most frequently identified ESBL enzyme (arrival: 59.3%; departure: 52.0%). The plasmid-mediated mcr-1 gene was also identified occasionally. In parallel, levels of resistances to non-critically important antimicrobials were already high upon arrival but have still further increased over time until slaughter. Our study also highlighted that if only ESBL-producing isolates were monitored, it might have led to a partial (and partly false) picture of AMR rates globally decreasing during the fattening period. The mean number of antimicrobial treatments per calf (NTPC) was 8.75 but no association between AMU and AMR was evidenced. Most ESBL producers were clonally unrelated suggesting multiple sources and not cross-contaminations among calves during transportation. Feeding milk containing antimicrobial residues to veal calves is hypothesized to explain the high ESBL loads in animals at the entrance on farms.

Comparative epidemiology of E. coli resistance to third-generation cephalosporins in diseased food-producing animals.

Categorized by WHO as critically important antibiotics, third-generation cephalosporins (3GCs) are one of the latest therapeutic alternatives to fight severe infectious diseases in humans. Some antibiotics belonging to this class are prescribed to treat food-producing animals in specific pathological contexts. Preserving the effectiveness of 3GCs requires characterization and careful monitoring of 3GCs resistance and the identification and implementation of measures that can limit this antimicrobial resistance (AMR). Here, we characterized the 3GCs resistance in Escherichia coli isolated from diseased animals. Using data collected from broilers, hens, calves, piglets, sows, turkeys and ducks between 2006 and 2016 by the French surveillance network of AMR in pathogenic bacteria of animal origin (called RESAPATH), we investigated the dynamics of resistance to 3GCs. Our non-linear analysis applied to time series showed that the evolution of E. coli resistance to 3GCs is specific to each animal category. From 2006 to 2010, resistance to 3GCs increased for most animal categories. We observed peaks of high-level of resistance for hens (21.5% in 2010) and broilers (26.7% in 2011), whereas trends stayed below 10% for the other animal categories throughout the study period. Resistance later decreased and, since 2014, 3GCs resistance has dropped below 10% for all animal categories. The parallel between trends and measures to limit AMR over the period shed lights on the impact of practices changes, public policies (EcoAntibio Plan) and sector-led initiatives (moratorium in swine sector). Finally, they highlight the usefulness and importance of AMR surveillance networks in animal health, such as RESAPATH.

Antimicrobial resistance in bacteria isolated from mastitis in dairy cattle in France, 2006-2016.

In dairy cattle, mastitis is the most frequent bacterial disease, and the routine use of antibiotics for treatment and prevention can drive antimicrobial resistance (AMR). The aim of our study was to estimate the levels of AMR of the 3 main bacteria isolated from dairy cattle with mastitis in France (Streptococcus uberis, Escherichia coli, and coagulase-positive staphylococci) and to investigate their changes over time. Data collected between 2006 and 2016 by the French surveillance network for AMR in pathogenic bacteria of animal origin (called RESAPATH) were analyzed. The proportions of mono- and multidrug resistance were calculated and the trends were investigated using nonlinear analyses applied to time series. Over the whole period, the lowest proportions of resistance in S. uberis isolates were observed for oxacillin (2.2%) and gentamicin (2.4%) and most resistance levels were below 20%. The trends in resistance showed some significant variation, mainly for S. uberis, but without a common pattern across the various antibiotics examined. For only 2 combinations of bacteria-antibiotic the trend in resistance showed a continuous increase from 2006 to 2016: tetracycline resistance in S. uberis isolates and third-generation cephalosporin resistance in E. coli isolates. In E. coli, the highest proportions of resistance were observed for amoxicillin (28.1%) and tetracycline (23.1%). Resistance to third-generation cephalosporins in E. coli from dairy cattle was almost nil in 2006, but reached 2.4% in December 2016. This increase is particularly concerning because these antibiotics constitute one of the latest therapeutic alternatives to fight severe infectious diseases in humans. Except for penicillin (33.9%), the proportions of resistance in coagulase-positive staphylococci were below 11% during the whole study period. Multidrug resistance (isolates with acquired resistance to at least one antibiotic in 3 or more antibiotic classes) ranged from 2.4% for coagulase-positive staphylococci to 9.9% for S. uberis. These findings can serve as guidelines for practitioners in the choice of the most appropriate antibiotic according to the prevailing epidemiological context. Ultimately, our results contribute to risk assessment of AMR and provide a baseline for setting up and evaluating control measures and designing strategies to limit AMR.

Bovine spongiform encephalopathy and spatial analysis of the feed industry.

In France, despite the ban of meat-and-bone meal (MBM) in cattle feed, bovine spongiform encephalopathy (BSE) was detected in hundreds of cattle born after the ban. To study the role of MBM, animal fat, and dicalcium phosphate on the risk for BSE after the feed ban, we conducted a spatial analysis of the feed industry. We used data from 629 BSE cases as well as data on use of each byproduct and market area of the feed factories. We mapped risk for BSE in 951 areas supplied by the same factories and connection with use of byproducts. A disease map of BSE with covariates was built with the hierarchical Bayesian modeling methods, based on Poisson distribution with spatial smoothing. Only use of MBM was spatially linked to risk for BSE, which highlights cross-contamination as the most probable source of infection after the feed ban.

Case-control study on feed risk factors for BSE cases born after the feed ban in France.

In France, after the ban on meat and bone meal (MBM) in cattle feeding in June 1990, cases of Bovine Spongiform Encephalopathy (BSE) have continued to be detected in bovines born after that ban (called BAB cases). A case-control study was therefore carried out to determine the way these cases were contaminated. A multivariate conditional model was built adjusting for the production type of the animals and taking into account the herd size. The results confirmed that feeding cattle with proprietary concentrates was at risk for BSE, with an adjusted odds ratio of 6.8 (2.5; 18.7) for the consumption of less or three different proprietary concentrates and 17.6 (5.7; 54.8) for more than three, when comparing with no consumption of proprietary concentrates, considering feeding of bovines before the age of two. The results suggest that cross-contaminations by MBM in bovine concentrates have occurred after 1990. To a lesser extent, on-farm cross-contaminations, i.e. consumption by cattle of feedstuffs initially dedicated to other animals and which could legally contain MBM, have probably also existed, since the presence on farms of poultry fed purchased feed involved an increased risk of BSE with an odds ratio of 1.8 (1.1; 3.0). The use of milk replacers, which often incorporates animal fats, was also at risk with an odds ratio of 1.8 (1.0; 3.1).

Sheep feed and scrapie, France.

Scrapie is a small ruminant, transmissible spongiform encephalopathy (TSE). Although in the past scrapie has not been considered a zoonosis, the emergence of bovine spongiform encephalopathy, transmissible to humans and experimentally to sheep, indicates that risk exists for small ruminant TSEs in humans. To identify the risk factors for introducing scrapie into sheep flocks, a case-control study was conducted in France from 1999 to 2000. Ninety-four case and 350 control flocks were matched by location and main breed. Three main hypotheses were tested: direct contact between flocks, indirect environmental contact, and foodborne risk. Statistical analysis was performed by using adjusted generalized linear models with the complementary log-log link function, considering flock size as an offset. A notable effect of using proprietary concentrates and milk replacers was observed. The risk was heterogeneous among feed factories. Contacts between flocks were not shown to be a risk factor.

Poultry, pig and the risk of BSE following the feed ban in France--a spatial analysis.

A spatial analysis was carried out in order to analyse the reason why the risk of Bovine Spongiform Encephalopathy (BSE) was spatially heterogeneous in France, during the period following the feed ban of Meat and Bone Meal to cattle. The hypothesis of cross-contamination between cattle feedstuff and monogastric feedstuff, which was strongly suggested from previous investigations, was assessed, with the assumption that the higher the pig or poultry density is in a given area, the higher the risk of cross-contamination and cattle infection might be. The data concerned the 467 BSE cases born in France after the ban of meat and bone meal (July 1990) and detected between July 1st, 2001 and December 31, 2003, when the surveillance system was optimal and not spatially biased. The disease mapping models were elaborated with the Bayesian graphical modelling methods and based on a Poisson distribution with spatial smoothing (hierarchical approach) and covariates. The parameters were estimated by a Markov Chain Monte Carlo simulation method. The main result was that the poultry density did not significantly influence the risk of BSE whereas the pig density was significantly associated with an increase in the risk of 2.4% per 10 000 pigs. The areas with a significant pig effect were located in regions with a high pig density as well as a high ratio of pigs to cattle. Despite the absence of a global effect of poultry density on the BSE risk, some areas had a significant poultry effect and the risk was better explained in some others when considering both pig and poultry densities. These findings were in agreement with the hypothesis of cross-contamination, which could take place at the feedstuff factory, during the shipment of food or on the farm. Further studies are needed to more precisely explore how the cross-contamination happened.

Spatial heterogeneity of the risk of BSE in France following the ban of meat and bone meal in cattle feed.

In France, meat-and-bone meal (MBM) has been prohibited for cattle feeding since 1990, but bovine spongiform encephalopathy (BSE) cases, called 'NAIF', appeared in animals born after this feed ban. Furthermore, in 1996 a new measure was taken: removal of cadavers and specified risk materials (SRM) from the processing of MBM dedicated to animal feed. Nevertheless, BSE cases (called 'super-NAIF') appeared in cattle born after this measure was in force. We analysed the spatial distribution of 445 'NAIF' and 58 'super-NAIF' cases detected in France from July 1, 2001 to July 31, 2003. The detection of BSE was based both on the mandatory reporting system (MRS) and the systematic test screening of cattle at the abattoir and at the fallen-animal plant with rapid tests. The background population was based on the adult-cow census. The disease mapping of the BSE risk was based on the standardised incidence ratio (stochastic Poisson process). A spatial component, which takes into account the spatial dependence between the geographical units by a notion of adjacency was used to eliminate the over-dispersion in the risk assessment. The geographical units were defined by hexagons with a side of 23km (France had 1264 hexagons). The parameters were estimated by a Metropolis Gibbs sampling algorithm using the Markov-chain Monte Carlo methods. The BSE cases were not randomly distributed. Furthermore, the areas at risk for the 'super-NAIF' matched part of the areas at risk for the 'NAIF' cases-which suggests that it might be a common source of contamination.