Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution

Abstract

BackgroundIn recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity.MethodsTwo hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains.ResultsThe study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C2, IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp’s hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions.ConclusionTo the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

“…Nine STs in our study (ST14, ST23, ST39, ST76, ST86, ST218, ST219, ST268, and ST2674) were identified only for the isolates that caused severe bloodstream infections. Previously K. pneumoniae of ST23, ST86, ST76, and ST218 were described as a hypervirulent pathogen causing bacteremia, sepsis, and liver abscess in India, France, China, Taiwan, and Russia [ 21 , 22 , 23 , 24 , 25 ]. Three STs (ST14, ST39, and ST268) in our study were associated with fatal outcomes.…”

Virulence Factors in Hypervirulent Klebsiella pneumoniae

“…Increasing reports have described the emergence of multidrugresistant hypervirulent K. pneumoniae strains (Hao et al, 2020;Shankar et al, 2020). MDR-hvKP can arise by two different mechanisms.…”

Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence

“…The virulence plasmid described earlier such as the pLVPK and pK2044 lacked genes coding for antimicrobial resistance and typically belonged to IncHI1B ( Chen et al, 2004 ). However, recent reports suggest the acquisition of virulence plasmids by multidrug-resistant (MDR) Kp and hence insertion of antimicrobial resistance genes (ARGs) such as bla KPC-2 and catA1 into the virulence plasmid ( Dong et al, 2018 ; Chen et al, 2020 ; Shankar et al, 2020a ). In addition, reports of fusion/mosaic plasmids that carry two replicons such as IncHI1B–IncFIB and IncFIIK–IncFIBK are emerging, which code for antimicrobial resistance determinants as well as virulence genes ( Lam et al, 2019 ; Turton et al, 2019 ).…”

“…Although previous studies have reported the correlation of rmpA and rmpA2 as markers for hypervirulent and hypermucoviscous pathotypes, there is a dearth of comprehensive correlations between the constitutive virulence markers for hvKp, viz., rmpA , rmpA2 , and aerobactin , based on “genome-structure” perspectives. Our research group has extensively worked on genomics ( Jacob et al, 2019 ; Shankar et al, 2020a ; Vasudevan et al, 2020 ; Shankar et al, 2021 ) and in silico structural analysis ( Lavanya et al, 2013 ; Lavanya et al, 2014 ; Lavanya et al, 2015 ) to decipher the functional circuitry of various pathogenic proteins. The present study adopted a combination of whole-genome sequencing (WGS), genomic analysis, computational modeling, and structural dynamics studies, which have not been used previously to assess the concerned virulence markers as per our knowledge.…”