Azithromycin Resistance in Escherichia coli and Salmonella from Food-Producing Animals and Meat in Europe
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 2014-2018 and the Danish AMR surveillance programme in 2016-2019. Methods  WGS data of 1,042 E. coli (170 azithromycin non-wild-type (non-WT) (MIC > 16 mg/L) and 872 WT) and 274 Salmonella (28 azithromycin non-WT and 246 WT) were screened for macrolide resistance genes and mutations in rplV and rplD genes using ResFinder v4.0 and custom scripts. Genotype-phenotype concordance and MLST were determined for all isolates. mef(C)-mph(G)-harbouring plasmids were characterised by conjugation and sequencing. Results  Genes 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. Presence of macrolide resistance genes, alone or in combinations, was concordant with azithromycin non-WT phenotype in 69% of isolates. Distinct mph(A) operon structures in azithromycin WT (n=50) and non-WT (n=141) isolates were observed. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine S. Derby and S. 4,(5),12:i:-, flanked downstream by IS91-family element ISVsa3 or TnAs1 and associated with IncI1-a, IncI1-? and IncFII plasmids. Conclusions  High diversity of azithromycin resistance genes was detected in E. coli and Salmonella from food-producing animals and meat in Europe. The genes mef(C)-mph(G) and erm(42) detected on mobile genetic elements appear to be emerging azithromycin resistance determinants primarily in porcine E. coli isolates. The finding of specific mph(A) operon structures in azithromycin WT and non-WT isolates increases the accuracy of WGS-based detection of azithromycin resistance.