Pan-European resistance monitoring programmes encompassing food-borne bacteria and target pathogens of food-producing and companion animals

O-Antigen decorations in Salmonella enterica play a key role in eliciting functional immune responses against heterologous serovars in animal models

Introduction

Different serovars of Salmonella enterica cause systemic diseases in humans including enteric fever, caused by S. Typhi and S. Paratyphi A, and invasive nontyphoidal salmonellosis (iNTS), caused mainly by S. Typhimurium and S. Enteritidis. No vaccines are yet available against paratyphoid fever and iNTS but different strategies, based on the immunodominant O-Antigen component of the lipopolysaccharide, are currently being tested. The O-Antigens of S. enterica serovars share structural features including the backbone comprising mannose, rhamnose and galactose as well as further modifications such as O-acetylation and glucosylation. The importance of these O-Antigen decorations for the induced immunogenicity and cross-reactivity has been poorly characterized.

Methods

These immunological aspects were investigated in this study using Generalized Modules for Membrane Antigens (GMMA) as delivery systems for the different O-Antigen variants. This platform allowed the rapid generation and in vivo testing of defined and controlled polysaccharide structures through genetic manipulation of the O-Antigen biosynthetic genes.

Results

Results from mice and rabbit immunization experiments highlighted the important role played by secondary O-Antigen decorations in the induced immunogenicity. Moreover, molecular modeling of O-Antigen conformations corroborated the likelihood of cross-protection between S. enterica serovars.

Discussion

Such results, if confirmed in humans, could have a great impact on the design of a simplified vaccine composition able to maximize functional immune responses against clinically relevant Salmonella enterica serovars.

Wild-type distributions of minimum inhibitory concentrations and epidemiological cut-off values-laboratory and clinical utility

The characterization of wild-type minimum inhibitory concentration (MIC) and zone diameter distributions with the setting of epidemiological cut-off values (ECOFFs or ECVs) provides a reference for the otherwise relative MIC values in the international system for antimicrobial susceptibility testing. Distributions of MIC values for a species and an agent follow a log-normal distribution, which in the absence of resistance mechanisms is monomodal and designated wild type (WT). The upper end of the WT distribution, the ECOFF, can be identified with statistical methods. In the presence of phenotypically detectable resistance, the distribution has at least one more mode (the non-WT), but despite this, the WT is most often identifiable using the same methods. The ECOFF provides the most sensitive measure of resistance development in a species against an agent. The WT and non-WT modes are independent of the organism´s response to treatment, but when the European Committee on Antimicrobial Susceptibility Testing (EUCAST) determines the clinical breakpoints, the committee avoids breakpoints that split WT distributions of target species. This is to avoid the poorer reproducibility of susceptibility categorization when breakpoints split major populations but also because the EUCAST has failed to identify different clinical outcomes for isolates with different MIC values inside the wild-type distribution. In laboratory practice, the ECOFF is used to screen for and exclude resistance and allows the comparison of resistance between systems with different breakpoints from different breakpoint organizations, breakpoints evolving over time, and different breakpoints between human and animal medicine. The EUCAST actively encourages colleagues to question MIC distributions as presented on the website (https://www.eucast.org/mic_and_zone_distributions_and_ecoffs) and to contribute MIC and inhibition zone diameter data.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Antimicrobial resistance of Escherichia coli in the UK: comparison of single vs. pooled samples from healthy pigs

This study compared the antimicrobial resistance (AMR) of Escherichia coli detected from single samples vs. pooled samples at herd level. The national monitoring dataset included isolates from one sample per pig holding, whereas the research study included isolates from pooled samples of 10 pigs per holding. In both datasets, caecal samples were collected from healthy pigs randomly selected at slaughterhouses and plated on non-selective and antibiotic selective media. Resistance against a panel of nine antibiotics was compared between datasets by generalized linear mixed effects models (GLMMs) and by bootstrapped generalized linear model (GLM) to account for pooling. The highest proportion of resistant E. coli was observed against tetracycline and ampicillin in both datasets. In non-selective media, single and pooled samples showed similar results, but the bootstrapped GLM detected significantly lower resistance to ciprofloxacin and nalidixic acid in the national dataset. In selective media, a significantly greater proportion of resistant isolates was observed in the research dataset for ceftazidime (OR: 0.05, 95%CI = 0.01-0.42) and nalidixic acid (OR: 0.15, 95%CI = 0.05-0.51). The results suggest that one sample per holding provides similar information on AMR at herd level as pooled samples for most of the tested antibiotics, although less resistance to ciprofloxacin, ceftazidime, and nalidixic acid was detected.

Genome analysis of third-generation cephalosporin-resistant Escherichia coli and Salmonella species recovered from healthy and diseased food-producing animals in Europe

The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.

Antimicrobial susceptibility among respiratory tract pathogens isolated from diseased cattle and pigs from different parts of Europe

AIMS

To survey antibiotic susceptibility of bacteria causing cattle and pig respiratory infections in 10 European countries.

METHODS AND RESULTS

Non-replicate nasopharyngeal/nasal or lung swabs were collected from animals with acute respiratory signs during 2015-2016. Pasteurella multocida, Mannheimia haemolytica, Histophilus somni from cattle (n = 281), and P. multocida, Actinobacillus pleuropneumoniae, Glaesserella parasuis, Bordetella bronchiseptica, and Streptococcus suis from pigs (n = 593) were isolated. MICs were assessed following CLSI standards and interpreted using veterinary breakpoints where available. Histophilus somni isolates were fully antibiotic susceptible. Bovine P. multocida and M. haemolytica were susceptible to all antibiotics, except tetracycline (11.6%-17.6% resistance). Low macrolide and spectinomycin resistance was observed for P. multocida and M. haemolytica (1.3%-8.8%). Similar susceptibility was observed in pigs, where breakpoints are available. Resistance in P. multocida, A. pleuropneumoniae, and S. suis to ceftiofur, enrofloxacin, and florfenicol was absent or <5%. Tetracycline resistance varied from 10.6% to 21.3%, but was 82.4% in S. suis. Overall multidrug-resistance was low. Antibiotic resistance in 2015-2016 remained similar as in 2009-2012.

CONCLUSIONS

Low antibiotic resistance was observed among respiratory tract pathogens, except for tetracycline.

European-wide antimicrobial resistance monitoring in commensal Escherichia coli isolated from healthy food animals between 2004 and 2018

OBJECTIVES

To describe the susceptibility of Escherichia coli to medically important antibiotics, collected over four periods (2004-2006, 2008-2009, 2013-2014, 2017-2018), from food-producing animals at slaughter.

METHODS

Intestinal contents from cattle, pigs and broilers were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; one sample/animal/farm) for isolation of Escherichia coli; antimicrobial susceptibilities were centrally determined by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation.

RESULTS

In total, 10 613 E. coli strains were recovered. In broilers, resistance percentages were the lowest (P ≤ 0.01) in the latest time period. A significant decrease in MDR over time was also observed for broilers and a tendency for a decrease for pigs. Resistance to meropenem and tigecycline was absent, and resistance to azithromycin was 0.2%-2.0%. Also, low resistance to third-generation cephalosporins (1.1%-7.4%) was detected in broilers. Resistance to colistin varied between 0.1%-4.8%. E. coli from broilers showed high resistance to ciprofloxacin (7.3%-23.3%), whereas for cattle and pigs this was 0.2%-2.5%. Low/moderate resistance to chloramphenicol (9.3%-21.3%) and gentamicin (0.9%-7.0%) was observed in pigs and broilers. The highest resistance was noted for ampicillin (32.7%-65.3%), tetracycline (41.3%-67.5%), trimethoprim (32.0%-35.7%) and trimethoprim/sulfamethoxazole (27.5%-49.7%) from pigs and broilers, with marked country differences. MDR peaked in pigs and broilers with 24 and 26 phenotypes, with 21.9%-26.2% and 18.7%-34.1% resistance, respectively.

CONCLUSIONS

In this pan-EU survey antibiotic susceptibility of commensal E. coli varied largely between antibiotics, animal species and countries. Resistance to critically important antibiotics for human medicine was absent or low, except for ciprofloxacin in broilers and ampicillin in pigs and broilers.

Global prevalence and molecular characterization of extended-spectrum β-lactamase producing-Escherichia coli in dogs and cats - A scoping review and meta-analysis

Antimicrobial resistance (AMR) represents a major threat to human and animal health. Part of the AMR dimension is the circulation of extended-spectrum β-lactamases producing-Escherichia coli (ESBL-E. coli), which is now commonly reported among companion animals. However, the global perspective of the prevalence and population structure of ESBL-E. coli circulating in dogs and cats has not been estimated limiting our understanding of their role in the dissemination of ESBL-E. coli. The aim of this study was to compare the prevalence of ESBL-E. coli between dogs and cats and across countries through meta-analysis. We also performed a scoping review to summarize the current knowledge on ESBL genes and E. coli clones circulating among companion animals. A total of 128 studies published in PubMed, Web of Science, and Scopus up to April 2020 were selected and contained information on prevalence and/or molecular characterization of ESBL genes and ESBL-E. coli clones. Our review shows an increase in the number of publications between 2000 and 2019, concentrated mainly in Europe. Prevalence varied across continents, ranging from 0.63% (Oceania) to 16.56% (Africa) in dogs and from 0% (Oceania) to 16.82% (Asia) in cats. Although there were twice as many studies reporting prevalence on dogs (n = 61) than on cats (n = 32), and only 9 studies focused exclusively on cats, our meta-analysis showed no difference in the global prevalence of ESBL-E. coli between dogs (6.87% [95% CI: 4.46-10.45%]) and cats (5.04% [95% CI: 2.42-10.22%]). A considerable diversity of ESBL genes (n = 60) and sequence types (ST) (n = 171) were recovered from companion animals. ESBL-E. coli encoded by CTX-M-15 (67.5%, 77/114) and SHV-12 (21.9%, 25/114), along with resistant strains of ST38 (22.7%, 15/66) and ST131 (50%, 33/66) were widespread and detected in all continents. While presence of ESBL-E. coli is widespread, the drivers influencing the observed ESBL-E. coli prevalence and the clinical relevance in veterinary medicine and public health along with economic impact of ESBL-E. coli infections among companion animals need to be further investigated.

ESBL-Producing Escherichia coli Carrying CTX-M Genes Circulating among Livestock, Dogs, and Wild Mammals in Small-Scale Farms of Central Chile

Antibiotic-resistant bacteria of critical importance for global health such as extended-spectrum beta-lactamases-producing (ESBL)-Escherichia coli have been detected in livestock, dogs, and wildlife worldwide. However, the dynamics of ESBL-E. coli between these animals remains poorly understood, particularly in small-scale farms of low and middle-income countries where contact between species can be frequent. We compared the prevalence of fecal carriage of ESBL-E. coli among 332 livestock (207 cows, 15 pigs, 60 horses, 40 sheep, 6 goats, 4 chickens), 82 dogs, and wildlife including 131 European rabbits, 30 rodents, and 12 Andean foxes sharing territory in peri-urban localities of central Chile. The prevalence was lower in livestock (3.0%) and wildlife (0.5%) compared to dogs (24%). Among 47 ESBL-E. coli isolates recovered, CTX-M-group 1 was the main ESBL genotype identified, followed by CTX-M-groups 2, 9, 8, and 25. ERIC-PCR showed no cluster of E. coli clones by either host species nor locality. To our knowledge, this is the first report of ESBL-E. coli among sheep, cattle, dogs, and rodents of Chile, confirming their fecal carriage among domestic and wild animals in small-scale farms. The high prevalence of ESBL-E. coli in dogs encourages further investigation on their role as potential reservoirs of this bacteria in agricultural settings.

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe

The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed bla_SHV–12 (32.3%), bla_CTX–M–1 (24.2%), and bla_CMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were bla_SHV–2 (1.0%), bla_{CTX–M–2/–14/–15} (1.0/6.1/1.0%), and bla_TEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The bla_TEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.

A history of antimicrobial drugs in animals: Evolution and revolution

The evolutionary process of antimicrobial drug (AMD) uses in animals over a mere eight decades (1940-2020) has led to a revolutionary outcome, and both evolution and revolution are ongoing, with reports on a range of uses, misuses and abuses escalating logarithmically. As well as veterinary therapeutic perspectives (efficacy, safety, host toxicity, residues, selection of drug, determination of dose and measurement of outcome in treating animal diseases), there are also broader, nontherapeutic uses, some of which have been abandoned, whilst others hopefully will soon be discontinued, at least in more developed countries. Although AMD uses for treatment of animal diseases will continue, it must: (a) be sustainable within the One Health paradigm; and (b) devolve into more prudent, rationally based therapeutic uses. As this review on AMDs is published in a Journal of Pharmacology and Therapeutics, its scope has been made broader than most recent reviews in this field. Many reviews have focused on negative aspects of AMD actions and uses, especially on the question of antimicrobial resistance. This review recognizes these concerns but also emphasizes the many positive aspects deriving from the use of AMDs, including the major research-based advances underlying both the prudent and rational use of AMDs. It is structured in seven sections: (1) Introduction; (2) Sulfonamide history; (3) Nontherapeutic and empirical uses of AMDs (roles of agronomists and veterinarians); (4) Rational uses of AMDs (roles of pharmacologists, clinicians, industry and regulatory controls); (5) Prudent use (residue monitoring, antimicrobial resistance); (6) International and inter-disciplinary actions; and (7) Conclusions.

A proposed scheme for the monitoring of antibiotic resistance in veterinary pathogens of food animals in the UK

BACKGROUND

Antibiotic resistance in bacteria is a global threat to both animal and public health, and detecting its occurrence is an important component of control strategies. Monitoring programmes for antibiotic resistance are currently in place in food-producing animals in the European Union covering the zoonotic bacteria Salmonella enterica, Campylobacter coli and Campylobacter jejuni and the indicator bacteria Escherichia coli, Enterococcus faecalis and Enterococcus faecium. However, there is no equivalent pan-European statutory monitoring programme covering the antibiotic susceptibility of veterinary bacterial pathogens in food animals. This paper considers that issue and aims to facilitate and stimulate further discussion.

METHODS

Recommendations, proposed by the authors from the scientific literature and following expert discussion at international meetings, are presented for monitoring the susceptibility of key veterinary pathogens.

RESULTS

The selected veterinary pathogens comprise Actinobacillus pleuropneumoniae, Bordetella bronchiseptica, E. coli, Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, Staphylococcus aureus and Streptococcus spp. from the major food animal species cattle, pigs and poultry. The organisms are tested using harmonised panels of antibiotics over specified dilution ranges in a broth microdilution method.

CONCLUSION

The selected antibiotics and their respective dilution ranges are presented together with the underlying rationale for inclusion; the ranges chosen are suitable for incorporation into three microtitre plates, with each organism tested using a single plate. The recommendations are being implemented in 2020 in the UK for monitoring of the susceptibility of veterinary bacterial pathogens.

ANTIBIOTIC RESISTANCE IN ESCHERICHIA COLI AND ENTEROCOCCUS SPP. ISOLATED FROM UNGULATES AT A ZOOLOGICAL COLLECTION IN THE UNITED KINGDOM

Increase of antimicrobial resistance (AMR) is a global threat to health. The AMR profile of bacteria isolated from domesticated animals and free-ranging wildlife has been studied, but there are relatively few studies of bacteria isolated from captive wild animals. Understanding the dynamics of AMR in different populations is key to minimizing emergence of resistance and to preserve the efficacy of antimicrobials. In this study, fecal samples were collected from 17 species of healthy ungulates from a zoological collection in southeast England, which yielded 39 Escherichia coli and 55 Enterococcus spp. isolates for further analysis. Antibiotic sensitivity was investigated using agar disk diffusion. Escherichia coli isolates were resistant to a range of antibiotics, with resistance to ampicillin being the most common (28%). All E. coli isolates were susceptible to apramycin, enrofloxacin, chloramphenicol, and florfenicol. None tested positive for extended-spectrum beta-lactamase or AmpC activity. Seven of 39 (18%) E. coli isolates were resistant to three or more antibiotic classes. The E. coli isolates were further analyzed using multilocus sequence typing, which identified four pairs of identical sequence type isolates and 27 diverse strains. The Enterococcus spp. isolates were resistant to a range of antibiotics, with resistance to cefpodoxime seen in 95% of isolates. All Enterococcus spp. isolates were susceptible to ampicillin, gentamicin, chloramphenicol, and vancomycin. This study identified multidrug-resistant phenotypes in enterobacterial isolates that were like those commonly found in domestic ungulates. There was no apparent spatial clustering of the resistance profiles within the zoo. Review of the medical records of individual animals showed no direct relation to the AMR profiles observed. Observed resistance to antibiotics rarely or never used may have been due to coselection or directly acquired from other sources.

Minimal inhibitory concentration of seven antimicrobials to Mycoplasma gallisepticum and Mycoplasma synoviae isolates from six European countries

Mycoplasma gallisepticum and Mycoplasma synoviae are bacterial pathogens that cause disease in poultry, adversely affecting their health and welfare, and are a financial burden on producers. This manuscript describes the results of the MycoPath project that is the first international antimicrobial susceptibility programme for mycoplasma pathogens isolated from poultry. Improved comparative analysis of minimal inhibitory concentration (MIC) results from participating countries was facilitated by using one laboratory determining all MICs. Chicken and turkey isolates were obtained from France, Germany, Great Britain, Hungary, Italy and Spain during 2014-2016. One isolate per farm was retained. The MIC of seven antimicrobial agents was determined using a broth microdilution method, with Friis Medium (M. gallisepticum) or Modified Chanock's Medium (M. synoviae). Of the 222 isolates recovered, 82 were M. gallisepticum and 130 were M. synoviae. M. gallisepticum MIC_50/90 values were 0.12/0.5, 2/8, 0.5/4, 0.12/>64, 0.008/0.062, 0.008/32, 0.062/4 mg/l for doxycycline, enrofloxacin, oxytetracycline, spiramycin, tiamulin, tilmicosin and tylosin, respectively. For M. synoviae, the values were 0.5/1, 8/16, 0.5/1, 0.5/8, 0.25/0.5, 0.062/2 and 0.062/16 mg/l respectively. A bimodal MIC distribution for the fluoroquinolone (enrofloxacin) and the macrolides (spiramycin, tilmicosin and tylosin) indicate that both species have sub-populations that are less susceptible in vitro to those antimicrobials. Some differences in susceptibilities were observed according to host species, Mycoplasma species, and country of origin. This study provides a baseline of novel data for future monitoring of antimicrobial resistance in poultry Mycoplasma species. Additionally, this information will facilitate the selection of the antimicrobial agents most likely to be effective, thus ensuring their minimal use with targeted and correct therapeutic treatments.Highlights First large-scale pan-European collection of representative Mg and Ms isolates.MIC values assessed in central laboratory for Mg and Ms from chickens and turkeys.Range of MIC values for 82 Mg and 130 Ms isolates to seven licenced antibiotics shown.Data can be used to help determine Mg and Ms veterinary-specific breakpoints.

Building the European Antimicrobial Resistance Surveillance network in veterinary medicine (EARS-Vet)

Antimicrobial resistance (AMR) should be tackled through a One Health approach, as stated in the World Health Organization Global Action Plan on AMR. We describe the landscape of AMR surveillance in the European Union/European Economic Area (EU/EEA) and underline a gap regarding veterinary medicine. Current AMR surveillance efforts are of limited help to veterinary practitioners and policymakers seeking to improve antimicrobial stewardship in animal health. We propose to establish the European Antimicrobial Resistance Surveillance network in Veterinary medicine (EARS-Vet) to report on the AMR situation, follow AMR trends and detect emerging AMR in selected bacterial pathogens of animals. This information could be useful to advise policymakers, explore efficacy of interventions, support antimicrobial stewardship initiatives, (re-)evaluate marketing authorisations of antimicrobials, generate epidemiological cut-off values, assess risk of zoonotic AMR transmission and evaluate the burden of AMR in animal health. EARS-Vet could be integrated with other AMR monitoring systems in the animal and medical sectors to ensure a One Health approach. Herein, we present a strategy to establish EARS-Vet as a network of national surveillance systems and highlight challenges of data harmonisation and bias. Strong political commitment at national and EU/EEA levels is required for the success of EARS-Vet.

Building the European Antimicrobial Resistance Surveillance network in veterinary medicine (EARS-Vet)

Antimicrobial resistance (AMR) should be tackled through a One Health approach, as stated in the World Health Organization Global Action Plan on AMR. We describe the landscape of AMR surveillance in the European Union/European Economic Area (EU/EEA) and underline a gap regarding veterinary medicine. Current AMR surveillance efforts are of limited help to veterinary practitioners and policymakers seeking to improve antimicrobial stewardship in animal health. We propose to establish the European Antimicrobial Resistance Surveillance network in Veterinary medicine (EARS-Vet) to report on the AMR situation, follow AMR trends and detect emerging AMR in selected bacterial pathogens of animals. This information could be useful to advise policymakers, explore efficacy of interventions, support antimicrobial stewardship initiatives, (re-)evaluate marketing authorisations of antimicrobials, generate epidemiological cut-off values, assess risk of zoonotic AMR transmission and evaluate the burden of AMR in animal health. EARS-Vet could be integrated with other AMR monitoring systems in the animal and medical sectors to ensure a One Health approach. Herein, we present a strategy to establish EARS-Vet as a network of national surveillance systems and highlight challenges of data harmonisation and bias. Strong political commitment at national and EU/EEA levels is required for the success of EARS-Vet.

Antimicrobial susceptibility monitoring of Mycoplasma hyopneumoniae isolated from seven European countries during 2015-2016

Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia, a chronic respiratory disease, causing significant economic losses. Results from the 2015-2016 MycoPath pan-European antimicrobial susceptibility monitoring survey of M. hyopneumoniae are presented. In total, 147 M. hyopneumoniae porcine isolates from Belgium, France, Germany, Great Britain, Hungary, Italy, and Spain were tested. One isolate per farm was retained from pigs that had not been recently treated with antimicrobial agents. The minimal inhibitory concentration (MIC) of 13 antimicrobial agents was determined in a central laboratory using a broth microdilution method, with Friis Medium, incubated at 35 ± 1 °C for 5-12 days. M. hyopneumoniae NCTC 10110 was used as Quality Control. MIC₅₀/MIC₉₀ (mg/L) values were: enrofloxacin 0.06/1; marbofloxacin 0.06/2; spiramycin 0.06/0.25; tulathromycin ≤0.001/0.004; gamithromycin 0.06/0.5; tylosin 0.016/0.06; tilmicosin 0.06/0.5; florfenicol 0.5/1; doxycycline 0.25/1; oxytetracycline 0.25/2; lincomycin 0.06/0.25; tiamulin 0.016/0.06 and valnemulin ≤0.001/0.004. Compared with the data from 2010 to 2012 MycoPath study (50 isolates), MIC_50/90 results were similar and the majority were within ± two dilution steps, except for the MIC₅₀ of oxytetracycline which is more than two dilution steps higher in the present study. Between-country comparisons show some differences in the MIC values for the fluoroquinolones, tulathromycin and tylosin, but the limited sample size per country precludes performing meaningful country comparisons for several countries. Standardized laboratory methods and interpretive criteria for MIC testing of veterinary mycoplasmas are clearly needed; there are currently no clinical breakpoints available to facilitate data interpretation and correlation of MICs with in vivo efficacy.

Antimicrobial susceptibility monitoring of canine and feline skin and ear pathogens isolated from European veterinary clinics: results of the ComPath Surveillance programme

BACKGROUND

The ComPath project is a pan-European programme dedicated to the monitoring of antimicrobial susceptibility of canine and feline pathogens using standardized methods and centralized minimal inhibitory concentration (MIC) determination.

OBJECTIVES

To report antimicrobial susceptibilities of major pathogens isolated from nontreated animals with acute clinical signs of skin, wound or ear infections in 2013-2014.

METHODS AND MATERIALS

MICs were determined by agar dilution for commonly used drugs and interpreted using Clinical and Laboratory Standards Institute (CLSI) breakpoints, if available.

RESULTS

Of 1,676 isolates recovered, the main species isolated from dogs were Staphylococcus pseudintermedius, followed by Streptococcus spp., Pseudomonas aeruginosa and Escherichia coli. In cats, Pasteurella multocida, coagulase-negative staphylococci (CoNS) and Staphylococcus aureus were isolated most frequently. Resistance rates observed for S. pseudintermedius were <26.7% for penicillin, clindamycin and chloramphenicol, and ≤11.5% for ampicillin, amoxicillin/clavulanate, cefalexin, cefovecin, gentamicin and fluoroquinolones. For S. aureus, resistance rates ranged up to 90.9% for β-lactams, and were 19.7% for clindamycin, 27% for fluoroquinolones and 0.0-6.1% for other drugs. The mecA gene was confirmed by PCR in 10.6% of S. pseudintermedius, 11.6% of CoNS and 31.4% of S. aureus isolates. In streptococci/enterococci, resistance to penicillin, ampicillin and chloramphenicol ranged from 0.0% to 11.3%, whereas fluoroquinolone resistance ranged from 0.0% to 8.5%. For E. coli, resistance ranged from 13.8 to 15.9% for fluoroquinolones and from 86.2% to 100.0% for β-lactams. Low rates of resistance (0.0-6.3%) were observed in P. multocida, and for P. aeruginosa resistance to gentamicin was 10.3%.

CONCLUSION

Overall, antimicrobial resistance of cutaneous/otic pathogens isolated from dogs and cats was low (1-10%) to moderate (10-20%). For several pathogens, the paucity of CLSI recommended breakpoints for veterinary use is a bottleneck.

Antimicrobial susceptibility of nine udder pathogens recovered from bovine clinical mastitis milk in Europe 2015-2016: VetPath results

VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-duplicate isolates (n = 1244) were obtained from cows with acute clinical mastitis in eight countries during 2015-2016 for centrally antimicrobial susceptibility testing according CLSI standards. Among Escherichia coli (n = 225), resistance was high to ampicillin and tetracycline, moderate to kanamycin and low to amoxicillin/clavulanic acid and cefazolin. The MIC_50/90 of danofloxacin, enrofloxacin and marbofloxacin were 0.03 and 0.06 μg/mL. For Klebsiella spp. (n = 70), similar results were noted, except for ampicillin and kanamycin. We detected 3.7 % (11/295) Enterobacteriaceae isolates carrying an ESBL/AmpC gene. Staphylococcus aureus (n = 247) and coagulase-negative staphylococci (CoNS; n = 189) isolates were susceptible to most antimicrobials tested except to penicillin (25.1 and 29.1 % resistance). Two S. aureus and thirteen CoNS isolates harboured mecA gene. Streptococcus uberis isolates (n = 208) were susceptible to β-lactam antibiotics (87.1-94.7 % susceptibility), 23.9 % were resistant to erythromycin and 37.5 % to tetracycline. Resistance to pirlimycin was moderate. For Streptococcus dysgalactiae (n = 132) the latter figures were 10.6 and 43.2 %; pirlimycin resistance was low. MIC values for Streptococcus agalactiae, Trueperella pyogenes and Corynebacterium spp. were generally low. This current VetPath study shows that mastitis pathogens were susceptible to most antimicrobials with exceptions of staphylococci against penicillin and streptococci against erythromycin or tetracycline. For most antimicrobials, the percentage resistance and MIC_50/90 values among the major pathogens were comparable to that of the preceeding VetPath surveys. This work highlights the high need to set additional clinical breakpoints for antimicrobials frequently used to treat mastitis.

Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems

Antimicrobial resistance (AMR) is a significant threat to both human and animal health. The spread of AMR bacteria and genes across systems can occur through a myriad of pathways, both related and unrelated to agriculture, including via wastewater, soils, manure applications, direct exchange between humans and animals, and food exposure. Tracing origins and drivers of AMR bacteria and genes is challenging due to the array of contexts and the complexity of interactions overlapping health practice, microbiology, genetics, applied science and engineering, as well as social and human factors. Critically assessing the diverse and sometimes contradictory AMR literature is a valuable step in identifying tractable mitigation options to stem AMR spread. In this article we review research on the nonfoodborne spread of AMR, with a focus on domesticated animals and the environment and possible exposures to humans. Attention is especially placed on delineating possible sources and causes of AMR bacterial phenotypes, including underpinning the genetics important to human and animal health.

Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe

BACKGROUND

Extended-spectrum-β-lactamases (ESBL) and plasmid-mediated cephalosporinases (pAmpC)-producing Enterobacteriaceae isolates are now reported worldwide in humans, animals, and in the environment. We identified the determinants of resistance to β-lactams and associated resistance genes as well as phylogenetic diversity of 53 ESBL- or pAmpC-producing Enterobacteriaceae isolated from dogs and cats in Europe.

MATERIALS/METHODS

Of a collection of 842 Enterobacteriaceae isolates that were recovered in 2013 and 2014 from 842 diseased and untreated dogs and cats, for 242 ampicillin or amoxicillin resistant isolates (MIC ≥ 16 mg/L), cefotaxime (CTX) and ceftazidime (CAZ) MICs were determined. Isolates with CTX and/or CAZ MIC ≥ 1 mg/L (n = 63) were selected, and their genomes were fully sequenced using Illumina Technology. Genomic data were explored to identify the resistance determinants, the plasmid incompatibility groups, and the sequence types (STs). Plasmid location of bla_ESBL and bla_AmpC was evaluated for all isolates based on the co-localization of resistance and plasmid incompatibility group genes on the same contig. Phylogenetic trees were constructed using core-genome MLST.

RESULTS

Of the 63 sequenced isolates, 53 isolates harbored a bla_ESBL or bla_AmpC gene. Ten CTX and/or CAZ non-wild type isolates had neither bla_ESBL nor bla_AmpC. Among the 63 isolates, 44 (69.8 %) were Escherichia coli, 11 (17.5 %) were Klebsiella pneumoniae, and 8 (12.7 %) were Proteus mirabilis. Fifty-one (80.9 %) isolates originated from dogs and 12 (19.1 %) from cats. Isolates were sampled from urinary tract (n = 36), skin and soft tissue (n = 22) and respiratory tract infections (n = 5). Thirty-two isolates (32/53, 60.4 %) carried bla_ESBL genes, including bla_CTX-M-15 (n = 12), bla_CTX-M-14 (n = 6), bla_CTX-M-1 (n = 5), bla_CTX-M-2 (n = 3), bla_CTX-M-27 (n = 3), bla_SHV-28 (n = 4), bla_SHV-12 (n = 2), and bla_VEB-6 (n = 1). Four isolates of K. pneumoniae had both bla_CTX-M-15 and bla_SHV-28. Twenty-one isolates (21/53, 39.6 %) carried genes encoding pAmpC, including bla_CMY-2 (n = 19) and bla_DHA-1 (n = 2). Thirteen E. coli isolates harbored both bla_ESBL or bla_AmpC genes and plasmids of incompatibility groups IncIB (9/13), IncI1 (8/13), and IncFII (6/13). In addition to the reduced susceptibility to CTX and/or CAZ, reduced susceptibility or evidence of acquired resistance to at least one other relevant class of antibiotics was observed for all 63 isolates. E. COLI: isolates clustered in 23 STs, including B2 virulent clones from humans such as ST131 (n = 5), K. pneumoniae isolates mostly clustered in 3 STs: ST11 (n = 4), ST307 (n = 3), and ST16 (n = 2). Phylogenetic analysis identified the spread of E. coli ST131 bla_CTX-M-27, and of K. pneumoniae ST307 harboring bla_CTX-M-15 and bla_SHV-28 or ST11 bla_CTX-M-15.

CONCLUSIONS

We report here a 6.3 % prevalence of ESBL/pAmpC producing Enterobacteriaceae in diseased dogs and cats. This EU survey confirms that dogs and cats can be infected with epidemic multidrug resistant clones that may also spread in humans.

New antimicrobial susceptibility data from monitoring of Mycoplasma bovis isolated in Europe

Mycoplasma bovis is an important respiratory pathogen of cattle across Europe and is included in the MycoPath pan-European antimicrobial susceptibility monitoring programme. M. bovis strains (232) were isolated from cattle, not recently treated with antimicrobials, at diverse geographical locations in France, Great Britain, Hungary, Italy and Spain during 2014 to 2016. Only one isolate per farm and per outbreak was retained. For each isolate, the MICs of ten antimicrobials were determined in a central laboratory using a broth microdilution method with modified Eaton's medium and incubation at 35 °C ± 1 °C for 24 ± 6 h. MIC₅₀/MIC₉₀ (mg/L) values for the 232 strains were: danofloxacin 0.25/1; enrofloxacin 0.5/8; marbofloxacin 1/4; gamithromycin >64/>64; spiramycin 8/16; tilmicosin >64/>64; tulathromycin >64/>64; tylosin 64/>64; florfenicol 4/8; oxytetracycline 8/32. Minor between-country differences in the MIC₉₀ values were observed for the fluoroquinolones, spiramycin and oxytetracycline, whilst the MIC values for the other compounds were similar. Spain and Italy had the higher MIC₉₀ values for the fluoroquinolones. Compared with the 2010-2012 study (156 isolates) results are similar, with an overall MIC₅₀ increase of at most one doubling dilution for enrofloxacin, spiramycin, tylosin, florfenicol and oxytetracycline. In contrast, the MIC₉₀ value for oxytetracycline decreased from >64 to 32 mg/L. Standardized laboratory methods and interpretive criteria for MIC testing of veterinary mycoplasmas are clearly needed; there are currently no clinical breakpoints available to facilitate data interpretation and correlation of MICs with in vivo efficacy.

Survey of antimicrobial susceptibility of bacterial pathogens isolated from dogs and cats with respiratory tract infections in Europe: ComPath results

AIMS

To present antimicrobial susceptibilities for bacteria from dogs and cats with respiratory tract infection (RTI) across Europe in 2013-2014 and compare with data from 2008-2010.

METHODS AND RESULTS

Minimal inhibitory concentrations were determined for 464 isolates following Clinical and Laboratory Standards Institute standards using antibiotics approved for RTI treatment. Where possible, susceptibility was calculated using predominantly human-derived breakpoints whilst some antibiotics had no breakpoints. The main pathogen from dogs was Staphylococcus pseudintermedius which was > 90% susceptible to fluoroquinolones and oxacillin (92·5%; six isolates confirmed mecA-positive) and 53·8, 80·0 and 88·8% susceptible to tetracycline, penicillin and trimethoprim/sulfamethoxazole. Streptococci, Escherichia coli, Bordetella bronchiseptica, Staphylococcus aureus and Pseudomonas aeruginosa were also present in dog RTI. Streptococci were fully susceptible to penicillin, ampicillin and pradofloxacin. None were enrofloxacin-resistant but 31·4% had intermediate susceptibility. The least active agent against streptococci was tetracycline (51·4% susceptible). For E. coli, 90·9% were amoxicillin/clavulanic acid-susceptible; susceptibility to other compounds ranged from 63·6 to 81·8%. There are no breakpoints for B. bronchiseptica and Ps. aeruginosa. For Staph. aureus, penicillin susceptibility was low (34·8%); for other compounds 87·0-100%. The main RTI pathogen from cats was Pasteurella multocida, where only pradofloxacin has breakpoints (100% susceptible). Susceptibility of coagulase-negative staphylococci ranged from 66·7% (penicillin) to 97·2% (pradofloxacin). Streptococci from cats were 100% susceptible to all antibiotics except enrofloxacin and tetracycline (both 65·2% susceptible).

CONCLUSIONS

Overall, antimicrobial resistance was low to medium in RTI in dogs and cats, although susceptibility varied widely among pathogens studied.

SIGNIFICANCE AND IMPACT OF THE STUDY

Responsible use of antibiotics is crucial to maintain susceptibility and continued resistance monitoring is important to support this goal. These findings support the need for the setting of RTI-specific breakpoints for pathogens of dogs and cats.

Antimicrobial Resistance in Streptococcus spp

The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.

Prevalence and Emergence of Extended-Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram Negative Bacteria of Animal Origin in the Mediterranean Basin

In recent years, extended ESBL and carbapenemase producing Gram negative bacteria have become widespread in hospitals, community settings and the environment. This has been triggered by the few therapeutic options left when infections with these multi-drug resistant organisms occur. The emergence of resistance to colistin, the last therapeutic option against carbapenem-resistant bacteria, worsened the situation. Recently, animals were regarded as potent antimicrobial reservoir and a possible source of infection to humans. Enteric Gram negative bacteria in animals can be easily transmitted to humans by direct contact or indirectly through the handling and consumption of undercooked/uncooked animal products. In the Mediterranean basin, little is known about the current overall epidemiology of multi-drug resistant bacteria in livestock, companion, and domestic animals. This review describes the current epidemiology of ESBL, carbapenemase producers and colistin resistant bacteria of animal origin in this region of the world. The CTX-M group 1 seems to prevail in animals in this area, followed by SHV-12 and CTX-M group 9. The dissemination of carbapenemase producers and colistin resistance remains low. Isolated multi-drug resistant bacteria were often co-resistant to non-beta-lactam antibiotics, frequently used in veterinary medicine as treatment, growth promoters, prophylaxis and in human medicine for therapeutic purposes. Antibiotics used in veterinary medicine in this area include mainly tetracycline, aminoglycosides, fluoroquinolones, and polymyxins. Indeed, it appears that the emergence of ESBL and carbapenemase producers in animals is not related to the use of beta-lactam antibiotics but is, rather, due to the co-selective pressure applied by the over usage of non-beta-lactams. The level of antibiotic consumption in animals should be, therefore, re-considered in the Mediterranean area especially in North Africa and western Asia where no accurate data are available about the level of antibiotic consumption in animals.

Antimicrobial susceptibility of enterococci recovered from healthy cattle, pigs and chickens in nine EU countries (EASSA Study) to critically important antibiotics

The European Antimicrobial Susceptibility Surveillance in Animals (EASSA) program collects zoonotic and commensal bacteria from food-producing animals at slaughter and tracks their susceptibility to medically important antibiotics. Results of commensal enterococci species (2013-2014) are presented here. Intestinal content from cattle, pigs and chickens were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; 1 sample/animal/farm) for isolation of enterococci, MICs of 9 antibiotics were assessed by CLSI agar dilution in a central laboratory. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation. In total 960 Enterococcus faecium and 779 Enterococcus faecalis strains were recovered. Seven porcine E. faecium/faecalis strains of Spanish origin were resistant to linezolid. One avian E. faecalis and one porcine E. faecium strain were non-wild type (MICs 8 mg/L) to daptomycin. Clinical vancomycin resistance was absent; 2 poultry E. faecium and 1 bovine E. faecalis strains were non-wild type, all with MICs of 8 mg/L. None of the strains tested were clinically resistant to tigecycline. Little clinical resistance to ampicillin or gentamicin was observed. Clinical resistance of E. faecium to quinupristin/dalfopristin was slightly higher (2.2-12.0%) but 61.9-83.2% of the strains were classified as non-wild type. Very high percentages resistance to tetracycline (67.4-78.3%) and to erythromycin (27.1-57.0%) were noted for both E. faecium and E. faecalis in pigs and chickens compared to cattle (5.2-30.4 and 9.0-10.4%, respectively). Similar non-wild type results were observed for E. hirae (n = 557), E. durans (n = 218) and E. casseliflavus (n = 55) including percentage non-wild type for daptomycin, linezolid, tigecycline being absent and for vancomycin low. For these species percentage non-wild type to erythromycin was lower as compared to E. faecalis/faecium. This pan-EU survey shows high variability in antibiotic susceptibility of commensal enterococci from healthy food animals. Clinical resistance to critically important antibiotics for human medicine was absent or low, except for erythromycin.

Antimicrobial Resistance: Its Surveillance, Impact, and Alternative Management Strategies in Dairy Animals

Antimicrobial resistance (AMR), one among the most common priority areas identified by both national and international agencies, is mushrooming as a silent pandemic. The advancement in public health care through introduction of antibiotics against infectious agents is now being threatened by global development of multidrug-resistant strains. These strains are product of both continuous evolution and un-checked antimicrobial usage (AMU). Though antibiotic application in livestock has largely contributed toward health and productivity, it has also played significant role in evolution of resistant strains. Although, a significant emphasis has been given to AMR in humans, trends in animals, on other hand, are not much emphasized. Dairy farming involves surplus use of antibiotics as prophylactic and growth promoting agents. This non-therapeutic application of antibiotics, their dosage, and withdrawal period needs to be re-evaluated and rationally defined. A dairy animal also poses a serious risk of transmission of resistant strains to humans and environment. Outlining the scope of the problem is necessary for formulating and monitoring an active response to AMR. Effective and commendably connected surveillance programs at multidisciplinary level can contribute to better understand and minimize the emergence of resistance. Besides, it requires a renewed emphasis on investments into research for finding alternate, safe, cost effective, and innovative strategies, parallel to discovery of new antibiotics. Nevertheless, numerous direct or indirect novel approaches based on host-microbial interaction and molecular mechanisms of pathogens are also being developed and corroborated by researchers to combat the threat of resistance. This review places a concerted effort to club the current outline of AMU and AMR in dairy animals; ongoing global surveillance and monitoring programs; its impact at animal human interface; and strategies for combating resistance with an extensive overview on possible alternates to current day antibiotics that could be implemented in livestock sector.

Monitoring of antimicrobial susceptibility of udder pathogens recovered from cases of clinical mastitis in dairy cows across Europe: VetPath results

VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-duplicate milk samples were collected from cows with acute clinical mastitis in nine countries and 934 isolates were obtained during 2009-2012 for subsequent antimicrobial susceptibility testing in a central laboratory. CLSI broth microdilution methodology was used, and where available, MICs were interpreted using CLSI approved veterinary-specific (ceftiofur) otherwise human clinical breakpoints. Among Escherichia coli (n=207) and Klebsiella spp., (n=87), resistance was moderate to tetracycline and high to cephapirin (E. coli only) whereas resistance to other β-lactam antibiotics was very low (ceftiofur) to low (amoxicillin/clavulanic acid, cephalexin, cephalonium). The MIC₉₀ of enrofloxacin and marbofloxacin was 0.03 and 0.06μg/mL respectively (E. coli) with 0.5% strains displaying higher MICs. Staphylococcus aureus (n=192) and coagulase-negative staphylococci (CNS; n=165) strains were susceptible to most antibiotics tested except to penicillin (25.0 and 29.1% resistance), respectively. Three S. aureus and seven CNS strains were oxacillin-resistant and harboured mecA. Streptococcus uberis strains (n=188) were susceptible to the β-lactam antibiotics although 35.6% were penicillin intermediately susceptible, and 20.2% were resistant to erythromycin, 36.7% to tetracycline. For Streptococcus dysgalactiae (n=95) the latter figures were 13.7 and 56.8%, respectively. For most antibiotics, the percentage resistance among E. coli, S. aureus and S. uberis was comparable to that of the VetPath 2002-2006 survey. This current, expanded VetPath study shows that mastitis pathogens were susceptible to most antibiotics with exceptions of staphylococci tested against penicillin and streptococci against erythromycin or tetracycline. This work highlights the high need to set additional clinical breakpoints for antibiotics frequently used to treat mastitis.

Review of antimicrobial resistance surveillance programmes in livestock and meat in EU with focus on humans

OBJECTIVES

In this review, we describe surveillance programmes reporting antimicrobial resistance (AMR) and resistance genes in bacterial isolates from livestock and meat and compare them with those relevant for human health.

METHODS

Publications on AMR in European countries were assessed. PubMed was reviewed and AMR monitoring programmes were identified from reports retrieved by Internet searches and by contacting national authorities in EU/European Economic Area (EEA) member states.

RESULTS

Three types of systems were identified: EU programmes, industry-funded supranational programmes and national surveillance systems. The mandatory EU-financed programme has led to some harmonization in national monitoring and provides relevant information on AMR and extended-spectrum β-lactamase/AmpC- and carbapenemase-producing bacteria. At the national level, AMR surveillance systems in livestock apply heterogeneous sampling, testing and reporting modalities, resulting in results that cannot be compared. Most reports are not publicly available or are written in a local language. The industry-funded monitoring systems undertaken by the Centre Européen d'Etudes pour la Santé Animale (CEESA) examines AMR in bacteria in food-producing animals.

CONCLUSIONS

Characterization of AMR genes in livestock is applied heterogeneously among countries. Most antibiotics of human interest are included in animal surveillance, although results are difficult to compare as a result of lack of representativeness of animal samples. We suggest that EU/EEA countries provide better uniform AMR monitoring and reporting in livestock and link them better to surveillance systems in humans. Reducing the delay between data collection and publication is also important to allow prompt identification of new resistance patterns.

Prudent use and regulatory guidelines for veterinary antibiotics-politics or science?

Regulatory guidelines are in place across the world to ensure that approval of antibiotics is consistent with current scientific understanding of quality, efficacy and safety including minimizing the risk of the development of antibiotic resistance. We suggest the regulatory process is fit for purpose and does indeed approve products that are safe for use with regard to development of antibiotic resistance. However, we maintain that in order to preserve the longevity of antibiotics, treatment should be based on an established diagnosis and normally only antibiotics authorized for the diagnosed indication and indicated bacteria are used. Furthermore, susceptibility testing should be carried out whenever possible. Despite a general acceptance that antibiotic resistance is a significant issue, antibiotics can still receive a marketing authorization without a sponsor having to generate a clinical breakpoint. The consequence of this is that for many antibiotics we have no measure of what is resistant and what is susceptible at the approved dose. We argue that the time is right for all approvals of new or existing antibiotics to have independently agreed clinical breakpoints, as part of the regulatory process, without which talk of resistance is somewhat meaningless. This is relevant not only for novel antibiotics but also for generic compounds.

Immunogenicity of a Bivalent Adjuvanted Glycoconjugate Vaccine against Salmonella Typhimurium and Salmonella Enteritidis

Salmonella enterica serovars Typhimurium and Enteritidis are the predominant causes of invasive non-typhoidal Salmonella (iNTS) disease. Considering the co-endemicity of S. Typhimurium and S. Enteritidis, a bivalent vaccine formulation against both pathogens is necessary for protection against iNTS disease, thus investigation of glycoconjugate combination is required. In the present work, we investigated the immune responses induced by S. Typhimurium and S. Enteritidis monovalent and bivalent glycoconjugate vaccines adjuvanted with aluminum hydroxide (alum) only or in combination with cytosine-phosphorothioate-guanine oligodeoxynucleotide (CpG). Humoral and cellular, systemic and local, immune responses were characterized in two different mouse strains. All conjugate vaccines elicited high levels of serum IgG against the respective O-antigens (OAg) with bactericidal activity. The bivalent conjugate vaccine induced systemic production of antibodies against both S. Typhimurium and S. Enteritidis OAg. The presence of alum or alum + CpG adjuvants in vaccine formulations significantly increased the serum antigen-specific antibody production. The alum + CpG bivalent vaccine formulation triggered the highest systemic anti-OAg antibodies and also a significant increase of anti-OAg IgG in intestinal washes and fecal samples, with a positive correlation with serum levels. These data demonstrate the ability of monovalent and bivalent conjugate vaccines against S. Typhimurium and S. Enteritidis to induce systemic and local immune responses in different mouse strains, and highlight the suitability of a bivalent glycoconjugate formulation, especially when adjuvanted with alum + CpG, as a promising candidate vaccine against iNTS disease.

EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA)

EFSA and EMA have jointly reviewed measures taken in the EU to reduce the need for and use of antimicrobials in food-producing animals, and the resultant impacts on antimicrobial resistance (AMR). Reduction strategies have been implemented successfully in some Member States. Such strategies include national reduction targets, benchmarking of antimicrobial use, controls on prescribing and restrictions on use of specific critically important antimicrobials, together with improvements to animal husbandry and disease prevention and control measures. Due to the multiplicity of factors contributing to AMR, the impact of any single measure is difficult to quantify, although there is evidence of an association between reduction in antimicrobial use and reduced AMR. To minimise antimicrobial use, a multifaceted integrated approach should be implemented, adapted to local circumstances. Recommended options (non-prioritised) include: development of national strategies; harmonised systems for monitoring antimicrobial use and AMR development; establishing national targets for antimicrobial use reduction; use of on-farm health plans; increasing the responsibility of veterinarians for antimicrobial prescribing; training, education and raising public awareness; increasing the availability of rapid and reliable diagnostics; improving husbandry and management procedures for disease prevention and control; rethinking livestock production systems to reduce inherent disease risk. A limited number of studies provide robust evidence of alternatives to antimicrobials that positively influence health parameters. Possible alternatives include probiotics and prebiotics, competitive exclusion, bacteriophages, immunomodulators, organic acids and teat sealants. Development of a legislative framework that permits the use of specific products as alternatives should be considered. Further research to evaluate the potential of alternative farming systems on reducing AMR is also recommended. Animals suffering from bacterial infections should only be treated with antimicrobials based on veterinary diagnosis and prescription. Options should be reviewed to phase out most preventive use of antimicrobials and to reduce and refine metaphylaxis by applying recognised alternative measures.

Detection of mcr-1 colistin resistance gene in polyclonal Escherichia coli isolates in Barcelona, Spain, 2012 to 2015

Colistin resistance was detected in 53 of 10,011 Escherichia coli (0.5%) by prospective phenotypic testing of consecutive clinical isolates in a single hospital in Barcelona, Spain (2012-15). The mcr-1 gene was retrospectively identified by PCR and sequencing in 15 of 50 available isolates. Each isolate had a unique PFGE pattern except for two. This clonal diversity supports the hypothesis of horizontal dissemination of the mcr-1 gene in the local study population.

Antimicrobial Susceptibility Monitoring of Bacterial Pathogens Isolated from Urinary Tract Infections in Dogs and Cats Across Europe: ComPath Results

ComPath is a pan-European antimicrobial surveillance program collecting bacterial pathogens from dogs and cats not recently exposed to antimicrobials. We present minimum inhibitory concentration data obtained using Clinical and Laboratory Standards Institute methodology for 616 urinary tract infection (UTI) isolates collected between 2008 and 2010. In both dogs and cats, the most common pathogen was Escherichia coli (59.8% and 46.7%, respectively). Antimicrobial activity against E. coli in dogs and cats was similar with fluoroquinolone and trimethoprim/sulfamethoxazole susceptibility >90%. Ampicillin susceptibility was ∼80%. Staphylococcus intermedius Group isolates from dogs (67/437, 15.3%) had high antimicrobial susceptibility (>90%) toward beta-lactams, fluoroquinolones, and trimethoprim/sulfamethoxazole. Four canine isolates (6%) were oxacillin resistant, and harbored mecA. Proteus mirabilis from dogs (48/437, 11.0%) had high antimicrobial susceptibility (∼90%) to amoxicillin/clavulanic acid, enrofloxacin, and marbofloxacin and slightly lower susceptibility (∼80-85%) to ampicillin and orbifloxacin. Streptococcus canis isolates (35/437, 8.0%) from dogs were all susceptible to ampicillin and amoxicillin/clavulanic acid and >90% susceptible to marbofloxacin. Although resistance was not observed, high intermediate susceptibility was seen for both enrofloxacin (28.6%) and orbifloxacin (85.7%). Overall, antimicrobial in vitro activity appears to be high in UTI pathogens from dogs and cats with low multidrug resistance, although a lack of specific dog and cat breakpoints for important antimicrobials such as cefovecin, cephalexin, and ibafloxacin prevents analysis of susceptibility for these agents.

Strain Selection for Generation of O-Antigen-Based Glycoconjugate Vaccines against Invasive Nontyphoidal Salmonella Disease

Nontyphoidal Salmonellae, principally S. Typhimurium and S. Enteritidis, are a major cause of invasive bloodstream infections in sub-Saharan Africa with no vaccine currently available. Conjugation of lipopolysaccharide O-antigen to a carrier protein constitutes a promising vaccination strategy. Here we describe a rational process to select the most appropriate isolates of Salmonella as source of O-antigen for developing a bivalent glycoconjugate vaccine. We screened a library of 30 S. Typhimurium and 21 S. Enteritidis in order to identify the most suitable strains for large scale O-antigen production and generation of conjugate vaccines. Initial screening was based on growth characteristics, safety profile of the isolates, O-antigen production, and O-antigen characteristics in terms of molecular size, O-acetylation and glucosylation level and position, as determined by phenol sulfuric assay, NMR, HPLC-SEC and HPAEC-PAD. Three animal isolates for each serovar were identified and used to synthesize candidate glycoconjugate vaccines, using CRM₁₉₇ as carrier protein. The immunogenicity of these conjugates and the functional activity of the induced antibodies was investigated by ELISA, serum bactericidal assay and flow cytometry. S. Typhimurium O-antigen showed high structural diversity, including O-acetylation of rhamnose in a Malawian invasive strain generating a specific immunodominant epitope. S. Typhimurium conjugates provoked an anti-O-antigen response primarily against the O:5 determinant. O-antigen from S. Enteritidis was structurally more homogeneous than from S. Typhimurium, and no idiosyncratic antibody responses were detected for the S. Enteritidis conjugates. Of the three initially selected isolates, two S. Typhimurium (1418 and 2189) and two S. Enteritidis (502 and 618) strains generated glycoconjugates able to induce high specific antibody levels with high breadth of serovar-specific strain coverage, and were selected for use in vaccine production. The strain selection approach described is potentially applicable to the development of glycoconjugate vaccines against other bacterial pathogens.

Characterization of ESBL- and AmpC-Producing Enterobacteriaceae from Diseased Companion Animals in Europe

The study aimed to characterize beta-lactam resistance mechanisms of Enterobacteriaceae isolates recovered from diseased dogs and cats between 2008 and 2010 in a European surveillance program (ComPath I) for the antibiotic susceptibility of bacterial pathogens. A total of 608 non-duplicated Enterobacteriaceae isolates were obtained prior antibiotic treatment from diseased dogs (n=464) and cats (n=144). Among the 608 Enterobacteriaceae isolates, 22 presented a minimal inhibitory concentration against cefotaxime above EUCAST breakpoints of susceptibility. All the 22 isolates remained susceptible to carbapenems. Ten isolates were confirmed as extended-spectrum-beta-lactamase (ESBL) producers by PCR-sequencing of bla coding genes including 9 blaCTX-M (CTX-M-1, 14, 15, 32,…) and 1 blaTEM-52 and 12 were AmpC-producing isolates (10 plasmidic CMY-2 group and 2 isolates overexpressing their chromosomal AmpC). ESBLs and plasmid-mediated AmpC (pAmpC)-producing isolates were mainly recovered from dogs (n=17) suffering from urinary tract infections (n=13) and originated from eight different countries. ESBL-bearing plasmids were mostly associated with IncFII incompatibility groups while CMY-2 was predominantly associated with plasmid of the IncI1 group. ESBL/pAmpC-producing Escherichia coli belonged to phylogroup A (n=5), B2 (n=4), and D (n=5). Multilocus sequence typing analysis revealed that among three CTX-M-15-producing E. coli, two belong to sequence type (ST) 131 and one to ST405. The presence of CTX-M-15 including on IncFII plasmids in E. coli ST131-B2 has also been described in isolates of human origin. This suggests the possibility of exchanges of these isolates from humans to companion animals or vice-versa.

Antimicrobial susceptibility monitoring of mastitis pathogens isolated from acute cases of clinical mastitis in dairy cows across Europe: VetPath results

VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-replicate milk samples were collected from cows with acute clinical mastitis in eight countries. Escherichia coli, Staphylococcus aureus and Streptococcus uberis were isolated by standardised methods. Antimicrobial susceptibility was determined in a central laboratory by CLSI broth microdilution methodology; results were interpreted using clinical breakpoints where available. Among E. coli (n=280), resistance to tetracycline (14.3%) and cefapirin (11.1%) were most common. Resistance to other β-lactam antibiotics was absent (ceftiofur) or very low (cefalexin, amoxicillin/clavulanic acid). The MIC90 of enrofloxacin and marbofloxacin was 0.03 and 0.06μg/mL, respectively, with 0.7% of strains displaying a deviating high MIC. Staphylococcus aureus (n=250) were susceptible to most antibiotics tested, although 36.0% were resistant to penicillin G. For other β-lactam antibiotics where a CLSI breakpoint was available, no resistance was detected. Tetracycline resistance was low (5.2%). Streptococcus uberis (n=282) were susceptible to all β-lactam antibiotics, although 29.8% were intermediately susceptible to penicillin G; 18.8% of strains were resistant to erythromycin and 28.7% to tetracycline. This European study shows that bacteria associated with acute clinical mastitis are susceptible to most antibiotics with the exception of penicillin G against S. aureus, and erythromycin and tetracycline against S. uberis. The results of this study should serve as a reference baseline. This work also highlights the urgent need to set additional clinical breakpoints for antibiotics frequently used to treat mastitis.

Tackling antibiotic resistance: the environmental framework

Antibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.