Whole genome analysis of hypervirulent Klebsiella pneumoniae isolates from community and hospital acquired bloodstream infection

Abstract

Background: Hypervirulent K. pneumoniae (hvKp) causes severe community acquired infections, predominantly in Asia. Though initially isolated from liver abscesses, they are now prevalent among invasive infections such as bacteraemia. There have been no studies reported till date on the prevalence and characterisation of hvKp in India. The objective of this study is to characterise the hypervirulent strains isolated from bacteraemic patients for determination of various virulence genes and resistance genes and also to investigate the difference between healthcare associated and community acquired hvKp with respect to clinical profile, antibiogram, clinical outcome and molecular epidemiology.

Results: Seven isolates that were susceptible to all of the first and second line antimicrobials and phenotypically identified by positive string test were included in the study. They were then confirmed genotypically by presence of rmpA and rmpA2 by PCR. Among the study isolates, four were from patients with healthcare associated infections; none were fatal. All patients with community acquired infection possessed chronic liver disease with fatal outcome. Genes encoding for siderophores such as aerobactin, enterobactin, yersiniabactin, allantoin metabolism and iron uptake were identified by whole genome sequencing. Five isolates belonged to K1 capsular type including one K. quasipneumoniae. None belonged to K2 capsular type. Four isolates belonged to the international clone ST23 among which three were health-care associated and possessed increased virulence genes. Two novel sequence types were identified in the study; K. pneumoniae belonging to ST2319 and K. quasipneumoniae belonging to ST2320. Seventh isolate belonged to ST420.

Conclusion: This is the first report on whole genome analysis of hypervirulent K. pneumoniae from India. The novel sequence types described in this study indicate that these strains are evolving and hvKp is now spread across various clonal types. Studies to monitor the prevalence of hvKp is needed since there is a potential for the community acquired isolates to develop multidrug resistance in hospital environment and may pose a major challenge for clinical management.

Keywords: Bacteremia; Hypervirulent; K. pneumoniae; K. quasipneumoniae; Virulence factors; Whole genome sequencing.

Fig. 1

eBURST analysis of seven hypervirulent Klebsiella pneumoniae

Fig. 2

Phylogenetic tree of the hypervirulent K. pneumoniae. The phylogenetic tree for 10 genomes built out of a core of 2999 genes per genome and 29,990 in total. The core has 958,416 AA-residues/bp per genome, 9,584,160 in total. Each entry is represented by isolate name followed by sequence type and type of infection. HAI: Healthcare associated infection, CAI: Community acquired infection, ST: Sequence type

Fig. 3

a: Venn diagram of the four healthcare associated hypervirulent K. pneumoniae isolates. Isolate1: Kp3, isolate2: Kp2, isolate3: Kp1 and isolate4: Kp5. Kp3 and Kp5 have 181 and 813 genes respectively exclusive to the isolates and share a lot of genes with other two genomes. b: Venn diagram of community acquired K. pneumonia and K. quasipneumoniae isolates. Isolate1: Kp6, isolate2: Kp4 and isolate3: Kqp. Kp6 has 4220genes exclusive to the isolate and the community acquired isolates share lesser genes among themselves than the healthcare acquired isolates. K. quasipneumoniae is a smaller genome when compared to the K. pneumoniae isolates