Klebsiella variicola: an emerging pathogen in humans

Abstract

The Klebsiella pneumoniae complex comprises seven K. pneumoniae-related species, including K. variicola. K. variicola is a versatile bacterium capable of colonizing different hosts such as plants, humans, insects and animals. Currently, K. variicola is gaining recognition as a cause of several human infections; nevertheless, its virulence profile is not fully characterized. The clinical significance of K. variicola infection is hidden by imprecise detection methods that underestimate its real prevalence; however, several methods have been developed to correctly identify this species. Recent studies of carbapenemase-producing and colistin-resistant strains demonstrate a potential reservoir of multidrug-resistant genes. This finding presents an imminent scenario for spreading antimicrobial resistant genes among close relatives and, more concerningly, in clinical and environmental settings. Since K. variicola was identified as a novel bacterial species, different research groups have contributed findings elucidating this pathogen; however, important details about its epidemiology, pathogenesis and ecology are still missing. This review highlights the most significant aspects of K. variicola, discussing its different phenotypes, mechanisms of resistance, and virulence traits, as well as the types of infections associated with this pathogen.

Keywords: Nitrogen fixation; bacterial infections; misclassification; molecular epidemiology; multidrug-resistant.

Figure 1.

Representation of the available methods that allow differentiating the K. pneumoniae complex. The black colour means that the indicated method distinguishes the species of the K. pneumoniae complex, and the grey colour implies the opposite. Microbiological methods refer to standard biochemical procedures. PCR refers to molecular methods based on the amplification of chromosomal β-lactamases or unique genes assembled in a multiplex PCR, or single PCR such as yggE. The phylogenetic analysis corresponds to the most commonly used gene, rpoB. KlebSeq is a sequencing tool for screening and epidemiological surveillance of the Klebsiella genus. Single nucleotide polymorphisms (SNPs) have been used for the differentiation of some species of the K. pneumoniae complex, but they are definitely feasible for all species of the complex. The average nucleotide identity (ANI) is a genomic tool used for species differentiation and is highly recommended for this purpose. With the recent update of the proteomic profile of the K. pneumoniae complex, it is possible to differentiate the species that constitute the K. pneumoniae complex by using MALDI-TOF. The Bruker reference library version 6.0.0.0 includes the reference spectra for proper identification of K. variicola from K. pneumoniae but not for the rest of the members of the K. pneumoniae complex. The asterisk symbol behind the species name means that the subspecies are included, for instance K. variicola subsp. variicola, K. variicola subsp. tropicalensis, K. quasipneumoniae subsp. quasipneumoniae and K. quasipneumoniae subsp. similipneumoniae.

Figure 2.

Map of reported multidrug-resistant (MDR) and hypervirulent K. variicola (hvKv) isolates from different isolation sources. The red circle indicates clinical isolates, the green circle refers to K. variicola plant isolates and the blue circle represents environmental isolates. The numerals between parentheses indicate the number of isolates reported for both MDR and hvKv.