Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Dec 18;9(6):e02481-18.
doi: 10.1128/mBio.02481-18.

Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella Variicola

Affiliations
Free PMC article

Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella Variicola

Robert F Potter et al. mBio. .
Free PMC article

Abstract

Klebsiella variicola is a member of the Klebsiella genus and often misidentified as Klebsiella pneumoniae or Klebsiella quasipneumoniae The importance of K. pneumoniae human infections has been known; however, a dearth of relative knowledge exists for K. variicola Despite its growing clinical importance, comprehensive analyses of K. variicola population structure and mechanistic investigations of virulence factors and antibiotic resistance genes have not yet been performed. To address this, we utilized in silico, in vitro, and in vivo methods to study a cohort of K. variicola isolates and genomes. We found that the K. variicola population structure has two distant lineages composed of two and 143 genomes, respectively. Ten of 145 K. variicola genomes harbored carbapenem resistance genes, and 6/145 contained complete virulence operons. While the β-lactam bla LEN and quinolone oqxAB antibiotic resistance genes were generally conserved within our institutional cohort, unexpectedly 11 isolates were nonresistant to the β-lactam ampicillin and only one isolate was nonsusceptible to the quinolone ciprofloxacin. K. variicola isolates have variation in ability to cause urinary tract infections in a newly developed murine model, but importantly a strain had statistically significant higher bladder CFU than the model uropathogenic K. pneumoniae strain TOP52. Type 1 pilus and genomic identification of altered fim operon structure were associated with differences in bladder CFU for the tested strains. Nine newly reported types of pilus genes were discovered in the K. variicola pan-genome, including the first identified P-pilus in Klebsiella spp.IMPORTANCE Infections caused by antibiotic-resistant bacterial pathogens are a growing public health threat. Understanding of pathogen relatedness and biology is imperative for tracking outbreaks and developing therapeutics. Here, we detail the phylogenetic structure of 145 K. variicola genomes from different continents. Our results have important clinical ramifications as high-risk antibiotic resistance genes are present in K. variicola genomes from a variety of geographic locations and as we demonstrate that K. variicola clinical isolates can establish higher bladder titers than K. pneumoniae Differential presence of these pilus genes inK. variicola isolates may indicate adaption for specific environmental niches. Therefore, due to the potential of multidrug resistance and pathogenic efficacy, identification of K. variicola and K. pneumoniae to a species level should be performed to optimally improve patient outcomes during infection. This work provides a foundation for our improved understanding of K. variicola biology and pathogenesis.

Keywords: Klebsiella; antibiotic resistance; emerging pathogens; microbial genomics; urinary tract infection.

Figures

FIG 1
FIG 1
Pairwise average nucleotide identity cluster map of WUSM and NCBI Klebsiella. Hierarchical clustering and heat map of pairwise ANIm values among all isolates. The source of isolates (WUSM or NCBI) and initial species delineation (K. variicola, K. pneumoniae, or K. quasipneumoniae) are shown as colored bars adjacent to the heat map. The three major blocks are labeled by their final species determination.
FIG 2
FIG 2
Population structure of K. variicola genomes. (a) Approximate-maximum-likelihood tree of the total 145 K. variicola genomes and annotation of FastGear lineage identification. (b) Recombination-free parSNP tree of the closely related lineage 2 genomes with quantitative clustering from ClusterPicker added as alternating teal and brown labels adjacent to cluster number (1 to 26). Bootstrap support values below 80% are depicted as node labels. (c) Monophyletic groups of these clusters were colored if they were similar in the dendrogram showing the evolutionary context of the cluster compared to K. pneumoniae (KP), K. quasipneumoniae (KQ), and K. aerogenes (KA). Relevant metadata for initial identification, geographic location, source of isolation, and body site are adjacent to the assembly names. Bootstrap support values below 80% are depicted as node labels.
FIG 3
FIG 3
Distribution of acquired antibiotic resistance and virulence genes in the K. variicola cohort. Presence/absence matrix of ARGs (a), virulence genes (b), and plasmid replicons (c) ordered for all K. variicola genomes against the dendrogram from Fig. 2c.
FIG 4
FIG 4
WUSM K. variicola strains have a low burden of ARGs and are generally susceptible to antibiotics. (a) Network diagram depicting each WUSM_KV isolate and ARG as nodes. ARGs are colored in accordance with predicted phenotypic resistance from ResFinder, and WUSM_KV genomes are colored by the burden of ARGs. (b) Scatter plots depicting Kirby-Bauer disk diffusion size (mm) from phenotypic susceptibility testing. Each plot represents an isolate, and the plots are colored according to CLSI interpretation. Those with atypical resistance are listed by name with putative ARGs.
FIG 5
FIG 5
Changes in fim operon are associated with outcomes in mouse UTI model. (a) CFU/bladder and CFU/kidney of K. pneumoniae TOP52 and WUSM_KV isolates 24 h after transurethral bladder inoculation of C3H/HeN mice. Short bars represent geometric means of each group, and dotted lines represent limits of detection. (b) fimS phase assay and quantification with respective bands indicating the “ON” and “OFF” position labeled. (c) Immunoblot for FimA and GroEL, with quantification shown below. (d) Easyfig illustration of genes in the fim operon and Jalview of the nucleotides and amino acids for the fimB/fimE intergenic region and fimD gene.
FIG 6
FIG 6
K. variicola carries both conserved and novel usher genes. (a) Approximate-maximum-likelihood tree of the usher amino acid sequences described by Nuccio and Baumler (25) and representatives of the 17 usher sequences identified in the WUSM_KV pan-genome. (b) Hierarchical clustering of the presence/absence matrix of each and annotation of relevant features related to each usher.

Similar articles

See all similar articles

Cited by 6 articles

See all "Cited by" articles

References

    1. Rosenblueth M, Martinez L, Silva J, Martinez-Romero E. 2004. Klebsiella variicola, a novel species with clinical and plant-associated isolates. Syst Appl Microbiol 27:27–35. doi:10.1078/0723-2020-00261. - DOI - PubMed
    1. Long SW, Linson SE, Ojeda Saavedra M, Cantu C, Davis JJ, Brettin T, Olsen RJ. 2017. Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere 2:e00290-17. doi:10.1128/mSphereDirect.00290-17. - DOI - PMC - PubMed
    1. Berry GJ, Loeffelholz MJ, Williams-Bouyer N. 2015. An investigation into laboratory misidentification of a bloodstream Klebsiella variicola infection. J Clin Microbiol 53:2793–2794. doi:10.1128/JCM.00841-15. - DOI - PMC - PubMed
    1. Maatallah M, Vading M, Kabir MH, Bakhrouf A, Kalin M, Naucler P, Brisse S, Giske CG. 2014. Klebsiella variicola is a frequent cause of bloodstream infection in the Stockholm area, and associated with higher mortality compared to K. pneumoniae. PLoS One 9:e113539. doi:10.1371/journal.pone.0113539. - DOI - PMC - PubMed
    1. Andrade BG, de Veiga Ramos N, Marin MF, Fonseca EL, Vicente AC. 2014. The genome of a clinical Klebsiella variicola strain reveals virulence-associated traits and a pl9-like plasmid. FEMS Microbiol Lett 360:13–16. doi:10.1111/1574-6968.12583. - DOI - PubMed

Publication types

MeSH terms

Feedback