Table 3 Comparison of AMR phenotype vs genotype.

From: Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

Antimicrobial

Resistant phenotype N (%)

Major error N (%)

Very major error N (%)

Determinants (% of resistance explained)

Ceftriaxone

47 (16.3%)

2 (0.8%)

5 (11%)

blaCTX-M-15 (71%), blaCTX-M-14 (13%)

Meropenem

4 (1.4%)

1 (0.3%)

0 (0%)

blaIMP-4 (50%), blaOXA-48 (50%)

Ciprofloxacin

42 (15.0%)

15 (6.0%)

6 (14%)

qnrB1 (61%), qnrS1 (7%), GyrA-83 (32%), GyrA-87 (16%), ParC-80 (23%) *

Gentamicin

11 (3.7%)

0 (0%)

1 (9%)

aac(6’)-Ib-cr (79%), rmtB (15%), aac3-IIa (15%), aac3-IId (12%), aadA2 (9%), ant(2”)-Ia (9%), aac(6’)-Ib4 (6%)

Tobramycin

32 (10.8%)

1 (0.4%)

1 (3%)

Amikacin

7 (2.4%)

\({\!}^{\S}\)0 (0%)

\({\!}^{\S}\)2 (29%)

Trimethoprim

70 (23.8%)

2 (0.9%)

14 (20%)

dfrA14 (51%), dfrA12 (6%); +sul2 (89%), +sul1 (29%)

+Sulfamethoxazole

54 (18.4%)

4 (1.7%)

4 (7%)

  1. Based on most resistant isolate per infection episode (n = 294). Major error = number (%) of susceptible isolates in which a resistance determinant was identified; very major error = number (%) of resistant isolates in which a resistance determinant was not identified (i.e., unexplained resistance). Genetic determinants explaining ≥5% of resistance to the given drug or class are listed. *Note aac(6’)-Ib-cr reduces susceptibility to fluoroquinolones (Machuca et al.) but does not on its own raise the MIC above the breakpoint for clinical resistance; it was present in 60% of ciprofloxacin resistant strains, but these all carried qnr genes and/or gyrA+ parC mutations that could explain resistance; hence aac(6’)-Ib-cr is not included in the list of genetic determinants explaining ciprofloxacin resistance. §Errors for amikacin resistance prediction (MIC ≥ 16 mg/L) shown in the table are based on excluding aac(6’)-Ib-cr as a determinant, as we could not find any evidence that this specific allele confers resistance in Klebsiella (causative genes detected were rmtB and aac(6’)-Ib4); including aac(6’)-Ib-cr removes the two very major errors but results in 24 major errors due to isolates carrying the gene but which have low MIC for amikacin (MIC 8 (n = 2), 4 (n = 7) or <2 (n = 15)).
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