Abstract:
Klebsiella pneumoniae is a Gram-negative rod, mostly known for causing nosocomial
infections in the immunocompromised, the elderly, and the neonates. In the last decade,
the emergence and spread of both extensively drug resistant (XDR) and hypervirulent K.
pneumoniae (hvKP) clones have rendered the species a major public health concern.
Whole-genome sequencing (WGS) was used for the molecular characterization of 32
carbapenem-resistant K. pneumoniae (CRKP) and two carbapenem-resistant K.
quasipneumoniae. Resistance was assessed by performing antibiotic susceptibility
testing (AST) and PCRs for the most common extended-spectrum β-lactamase and
carbapenemase encoding genes. Virulence was studied by sequencing the wzi gene and
determinants confirmed in silico. PCR-based replicon typing (PBRT) was performed to
identify plasmid incompatibility groups. Genetic relatedness of the isolates was determined by multilocus sequence typing (MLST), pulsed-field gel electrophoresis
(PFGE), and whole-genome based SNPs analysis. All of the isolates were nonsusceptible
to at least one of the three carbapenems tested, with 100% (34/34) of the
isolates being non-susceptible to ertapenem, 85.3% (29/34) to imipenem, and 70.6% (24/34) to meropenem. This phenotypic resistance was found to be due to either blaOXA-
48 (61.8%; 21/34) or blaNDM-1 (14.7%; 5/34) or blaNDM-7 (2.9%; 1/34), or the coupling of
ESBLs and outer membrane porin loss or modification (20.6%; 7/34). IncL and IncFIIK
were the most common replicons detected (91.2%; 31/34). Twenty and 21 different
capsular types (K-types) and sequence types (STs) were detected, respectively. Thus our
results reveal a very high level of diversity in the K. pneumoniae population circulating
in Lebanon. We also report the presence of carbapenem-resistant K. quasipneumoniae,
the circulation of multi-replicon plasmids harboring NDM type enzymes, and the
convergence of extensively drug resistant and hypervirulent features in Lebanon.
