Klebsiella variicola: an emerging pathogen in humans

Figures & data

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.

Table 1. Genetic and phenotypic traits of K. variicola and K. pneumoniae distinct phenotypes.

Bacterial species	Phenotype^a	Parameter
		Types of infection	Susceptible population	Primary acquired infection type	Virulence factors^b	Antibiotic resistance phenotype	String test^c	Capsule (KL)^d	Sequence type (ST)^e	AMR genes associated with ST^f	References
K. pneumoniae	cKpn	Bacteremia, UTI, pneumonia, meningitis	Immunosuppressed	HAI	Capsule, LPS, fimbriae type 3 and 1, ybt, kfu (all)	Multidrug-resistant	Negative	KL3 to KL134	ST258 ST512 ST11 ST340 ST437	KPC-2	75,97,98
	hmvKpn	Bacteremia and invasive syndromes	Immunosuppressed	HAI	Capsule, LPS, fimbriae type 3 and 1, ent (all), ybt	Susceptible and multidrug resistant	Positive	KL3 to KL134	ST1007 ST1022 and twenty-three different ST	ESBL-producers and quinolone resistance	16,19, 54, 55
	hvKpn	Pyogenic liver abscess; bacteremia; lung, neck, and kidney abscesses; pneumonia; cellulitis; necrotizing fasciitis; myositis, meningitis; endophthalmitis	Healthy and immunosuppressed	CAI	p iucA, piroB, peg-344, prmpA, and prmpA2	Mostly susceptible and less frequently multidrug-resistant	Positive	KL1, KL2 and KL54	ST23 ST86 ST375 ST380	KPC-2 CTX-M-3	23,75, 93, 94,98, 99
K. variicola	cKv	Bacteremia, UTI, pneumonia	Immunosuppressed	HAI and CAI	Capsule, LPS, fimbriae type 3 and 1, kva , kvi , fimV , ybt, ent (all), kfu (all)	Susceptible and multidrug resistant	Negative	KL3 to KL134	ST76 ND ST64 ST92 ST125 ST75	CTX-M-15/NDM-1 OXA-48 NDM-9 CTXM-15/KPC-2 CTXM-14/KPC-2 KPC-2	31, 32, 36, 62, 65, 69, 81
	hmvKv	Pneumonia	Immunosuppressed	HAI	Capsule, LPS, fimbriae type 3 and 1, fimV, ent (all), kfu (all)	Susceptible	Positive	KL114	ST2	Negative	34
	hvKv	Bacteremia	Immunosuppressed	HAI	R1. piucA, piroB, pybt, ent (all), prmpA, and pΔrmpA2	Susceptible to most antibiotic classes except for colistin	Negative	KL16	ND	D150G in PhoP	64
					R2. Capsule, LPS, fimbriae type 3 and 1, ent (all), kfu (all)	Multidrug-resistant	Negative	Novel KL	ST60	CTX-M-15 NDM-1	26

^acKpn, classical K. pneumoniae; hmvKpn, hypermucoviscous K. pneumoniae; hvKpn, hypervirulent K. pneumoniae; cKv, classical K. variicola; hmvKv, hypermucoviscous K. variicola; hvKv, hypervirulent K. variicola.

^bUnderline characters refers to new fimbrial type 1 systems; all, means identified the entire population of isolates analyzed. R1: refers to hypervirulent K. variicola colistin resistant and R2: refers to hypervirulent K. variicola responsible for causing an outbreak; _p, refers to plasmid localization of virulence factor

^c Positive string test define hypermucoviscous strains.

^d Capsule type determined by using K. pneumoniae capsule typing scheme.

^e ST was determined by using the MLST K. pneumoniae ( https://bigsdb.pasteur.fr/klebsiella/klebsiella.html ) [ 79] and MLST K. variicola ( http://mlstkv.insp.mx ) [ 80] schemes for K. pneumoniae and K. variicola isolates, respectively. In the case of classic K. variicola and K. pneumoniae the STs refers to clinically important MDR clones. ND; corresponding to K. variicola genomes without ST which was not possible to determine due to fragmentation of one from seven locus from MLST K. variicola scheme. Additionally other ST of MDR K. variicola with unpublished data could be consulted in Barrios-Camacho et al, 2019 [ 80].

^fAMR; antimicrobial resistance genes.

Dong N, Lin D, Zhang R, et al. Carriage of blaKPC-2 by a virulence plasmid in hypervirulent Klebsiella pneumoniae. J Antimicrob Chemother. 2018;73:3317–3321.

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Humberto B-C, Alejandro A-V, Marilu B-R, et al. Molecular epidemiology of Klebsiella variicola obtained from different sources. Sci Rep. 2019; under review.

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