Antimicrobial resistance genes and mutations were detected by whole genome sequencing of the E. coli and salmonella isolates selected for confirmatory testing at the EURL-AR by EFSA, with regard to the EU surveillance of AMR for 2019. The isolates derived from 30 European countries and 332 E. coli and 4 Salmonella isolates were included. The list presents the antimicrobial resistance genes and mutations as detected by use of ResFinder 4.0 in relation to the antimicrobial panels used for the phenotypic AST surveillance.
The full list presenting the prevalence of resistance genes and mutations can be found below.
The prevalence of a resistance gene or mutation is presented as a percentage of the total number of genes/mutations detected for the specific antimicrobial, unless other is specified.
AMPICILLIN (cephalosporin resistance genes/mutations not included). 174 isolates harbored a total of 210 resistance genes conferring resistance to only ampicillin: TEM-genes (91.9 %), OXA-genes (5.7 %), LAP-2 (1.9 %), CARB-2 (0.5 %). The TEM-genes were dominated by TEM-1B (70 %), TEM-1A (8 %) and TEM-30 (5 %), and the OXA-genes were OXA-1 (75 %) and OXA-10 (25 %).
AZITHROMYCIN. 63 isolates harbored a total of 64 azithromycin resistance genes: mphA (78.1 %), mefB (10.9 %), mefC-mphG (9.4 %), msrE (1.6 %).
CARBAPENEMS. No resistance genes or mutations were detected for ertapenem, imipenem or meropenem.
CEPHALOSPORINS. 286 isolates were detected with cephalosporin resistance genes or mutations. For isolates with the so called ampC-profiles (i.e. resistant to betalactamase inhibitors), 65 % of the isolates had ampC promotor mutations, while 35 % carried the CMY-2 genes. For isolates with other profiles, like true ESBLs, the resistance was explained by CTX-M genes (93.7 % of the isolates), SHV-12 (5.3 % of the isolates) and TEM-genes (1.0 % of the isolates). The detected CTX-M genes were dominated by CTX-M-1 (48 %), CTX-M-15 (15 %), CTX-M-32 (15 %), CTX-M-14 (8 %) and CTX-M-55 (5 %).
CHLORAMPHENICOL. 110 isolates harbored a total of 152 chloramphenicol resistance genes: floR (54.6 %), catA1 (33.6 %), cmlA1 (8.6 %), catB3 (2.6 %), catA2 (0.7 %).
CIPROFLOXACIN. 154 isolates were detected with fluoroquinolon resistance genes and/or mutations. For 11 % of the isolates a combination of genes and mutations were detected, whereas mutations alone were detected for 45 % of the isolates, and genes alone were detected for 44 % of the isolates. The genes observed were qnr-genes (94 %) and the aac(6’)-lb-cr gene (6 %). The qnr-genes observed were qnrS1 (84 %), qnrB19 (10 %), qnrS2 (5 %) and qnrA1 (1 %). As for nalidixic acid, the mutations were all gyrA mutations, except for a few parC (p.A56T) mutations. The gyrA mutations were dominated by gyrA (p.S83L) (92 %), in combination with gyrA (p.D87N) in 75 % of the cases.
COLISTIN. 97 isolates harbored a total of 97 colistin resistance genes: mcr-1.1 (94.8%), mcr-1.12 (1.0 %), mcr-3.2 (1.0 %), mcr-4.2 (1.0 %), mcr-4.6 (1.0 %), mcr-9 (1.0 %).
GENTAMICIN. 67 isolates harbored a total of 72 gentamicin resistance genes: aac3-genes (95.8 %), ant2”-gener (2.8 %), rmtB (1.4 %). The majority of the aac3-genes were aac3-IV (41 %) and aac3-IId (35%).
NALIDIXIC ACID. 91 isolates were detected with mutations conferring resistance to nalidixic acid. All mutations were gyrA mutations, except for 2 isolates with a parC (p.A56T) mutation. The gyrA mutations were dominated by gyrA (p.S83L) (86 % of the isolates), in combination with gyrA (p.D87N) in 50 % of the cases.
SULFAMETHOXAZOLE. 216 isolates harbored a total of 304 sulfonamide genes: sul2 (51.0 %), sul3 (26.6 %), sul1 (22.4 %).
TEMOCILLIN. No resistance genes or mutations were detected.
TETRACYCLINE. 222 isolates harbored a total of 281 tetracycline resistance genes: tetA (61.2 %), tetB (19.9 %), tetM (17.1 %), tetY (1.1 %), tetD (0.7 %).
TIGECYCLINE. No resistance genes or mutations were detected.
TRIMETHOPRIM. 174 isolates harbored a total of 192 trimethoprim genes: dfrA12 (32.3 %), dfrA1 (27.1 %), dfrA14 (13.0 %), dfrA17 (13.0 %), dfrA5 (8.9 %), dfrA8 (1.6 %), dfrA36 (1.6 %), dfrA7 (1.0 %), dfrA19 (0.5 %).