Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry (MedVetKlebs)

Klebsiella pneumoniae (phylogroup Kp1), one of the most problematic pathogens
associated with antibiotic resistance worldwide, is phylogenetically closely related to
K. quasipneumoniae [subsp. quasipneumoniae (Kp2) and subsp. similipneumoniae
(Kp4)], K. variicola (Kp3) and two unnamed phylogroups (Kp5 and Kp6). Together,
Kp1 to Kp6 make-up the K. pneumoniae complex. Currently, the phylogroups can be
reliably identified only based on gene (or genome) sequencing. Misidentification using
standard laboratory methods is common and consequently, the clinical significance
of K. pneumoniae complex members is imprecisely defined. Here, we evaluated
and validated the potential of MALDI-TOF mass spectrometry (MS) to discriminate
K. pneumoniae complex members. We detected mass spectrometry biomarkers
associated with the phylogroups, with a sensitivity and specificity ranging between
80–100% and 97–100%, respectively. Strains within phylogroups Kp1, Kp2, Kp4, and
Kp5 each shared two specific peaks not observed in other phylogroups. Kp3 strains
shared a peak that was only observed otherwise in Kp5. Finally, Kp6 had a diagnostic
peak shared only with Kp1. Kp3 and Kp6 could therefore be identified by exclusion
criteria (lacking Kp5 and Kp1-specific peaks, respectively). Further, ranked Pearson
correlation clustering of spectra grouped strains according to their phylogroup. The
model was tested and successfully validated using different culture media. These results
demonstrate the potential of MALDI-TOF MS for precise identification of K. pneumoniae
complex members. Incorporation of spectra of all K. pneumoniae complex members
into reference MALDI-TOF spectra databases, in which they are currently lacking,
is desirable. MALDI-TOF MS may thereby enable a better understanding of the
epidemiology, ecology, and pathogenesis of members of the K. pneumoniae complex.