OBJECTIVES: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. METHODS: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. RESULTS: mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. CONCLUSIONS: Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Animal and Plant Health Agency Weybridge UK

Austrian Agency for Health and Food Safety Graz Austria

Bacteriology Serology Laboratory Veterinary Services Cyprus

Central Veterinary Research Laboratory Kildare Ireland

Croatian Veterinary Institute Zagreb Croatia

Danish Veterinary and Food Administration Ringsted Denmark

Department of Biological Sciences Texas Tech University Lubbock TX USA

Department of Pathobiology Ghent University Merelbeke Belgium

DIANA Lab Dept of Computer Science and Biomedical Informatics University of Thessaly Lamia Greece

European Food Safety Authority Parma Italy

European Union Reference Laboratory for Antimicrobial Resistance Research Group for Global Capacity Building Technical University of Denmark Kongens Lyngby Denmark

French Agency for Food Environmental and Occupational Health and Safety Maisons Alfort France

German Federal Institute for Risk Assessment Berlin Germany

Institute for Diagnosis and Animal Health Bucharest Romania

Institute for Hygiene and Veterinary Public Health Bucharest Romania

Institute for Microbiology and Parasitology Ljubljana Slovenia

Institute of Food Safety Animal Health and Environment BIOR Riga Latvia

Instituto Nacional de Investigação Agrária e Veterinária Oeiras Portugal

Istituto Zooprofilattico Sperimentale del Lazio e della Toscana 'M Aleandri' Rome Italy

Jockey Club College of Veterinary Medicine and Life Sciences Kowloon Hong Kong

Laboratoire de Médecine Vétérinaire de l'État Dudelange Luxembourg

National Diagnostic and Research Veterinary Institute Sofia Bulgaria

National Food and Veterinary Risk Assessment Institute Vilnius Lithuania

National Food Chain Safety Office Veterinary Diagnostic Directorate Budapest Hungary

National Veterinary Research Institute Pulawy Poland

Public Health Laboratory Valletta Malta

Research Group for Genomic Epidemiology Technical University of Denmark Kongens Lyngby Denmark

School of Veterinary Medicine Texas Tech University Amarillo TX USA

Sciensano Brussels Belgium

Spanish Agency for Food Safety and Nutrition Madrid Spain

State Veterinary and Food Institute Dolny Kubin Slovakia

State Veterinary Institute Prague Czech Republic

Statens Serum Institut Copenhagen Denmark

Veterinary Laboratory of Chalkis Chalkis Greece

Vetsuisse Faculty Institute of Veterinary Bacteriology University of Bern Bern Switzerland

Wageningen Bioveterinary Research Part of Wageningen University and Research Lelystad Netherlands

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