56 Chapter 4 Table 1. BD Phoenix System susceptibility of 84 E. coli strains in the training set Cefoxitin (R>8 mg/L)a Ceftriaxone (S ≤1 mg/L; R >4 mg/L)b Ceftazidime (S ≤1 mg/L; R >4 mg/L)b n Percentage R S S 20 23.81 R S I 13 15.48 R S R 8 9.52 R R S 1 1.19 R I I 1 1.19 R R I 1 1.19 R I R 4 4.76 R R R 36 42.86 total=84 total=100.00 R, resistant; S, susceptible; I, intermediate. a MIC cut-off adapted from EUCAST guideline on detection of resistance mechanisms v2.0. b MIC breakpoints according to EUCAST clinical breakpoints for bacteria v.9.0. Validation sets 1 and 2 Validation set 1 consisted of 47 clinical E. coli strains. WGS results showed that 72.3% (n=34) of the strains were hyperproducers and 12.8% (n=6) were pampC and hyperproduction negative. Two pampC variants were found, 12.8% (n=6) blaCMY-2 and 2.1% (n=1) blaDHA-1 (Figure S1B). To cope with the low number of pampC-positive strains in validation set 1, validation set 2 (n=41) consisted of pampC-positive strains with mainly blaCMY-2 (97.6%) (Figure S1C). Genomic composition In total, the 172 E. coli strains represented 75 different MLST STs, of which ST131 (8.14%, n=14), ST38 (6.98%, n=12) and ST73 (6.98%, n=12) were the most prevalent. Furthermore, the STs of 13 strains were unknown (see Table S1). For the identification of pampC genes we found that there was 100% concordance between the tools abricate and KMA, which supports the accurate detection of pampC genes from WGS data.
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