Mosaic antimicrobial resistance/virulence plasmid in hypervirulent ST2096Klebsiella pneumoniaein India: The rise of a new superbug?
Authors: Shankar Chaitra , Vasudevan Karthick , Jacob Jobin John , Baker Stephen , Isaac Barney J , Neeravi Ayyan Raj , Muthuirulandi Sethuvel Dhiviya Prabaa , George Biju , Veeraraghavan Balaji 
Published: December 2020

HypervirulentK. pneumoniae(HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed to characterise nine novel MDR hvKp isolates harbouring mosaic plasmids simultaneously carrying antimicrobial resistance (AMR) and virulence genes. Nine HvKp isolates obtained from hospitalised patients in southern India were characterized for antimicrobial susceptibility and hypervirulence phenotypes. All nine hvKp isolates were subjected to whole genome sequencing (WGS) using Ilumina HiSeq2500 and a subset of four were sequenced using Oxford Nanopore MinION. Among the nine isolates, seven were carbapenem-resistant, two of which carriedblaNDM-5on an IncFII plasmid and five carriedblaOXA-232on a ColKP3 plasmid. The virulence determinants were encoded in a mosaic plasmid (∼320 Kbp) that formed as a result of its insertion in a IncFIB-IncHI1B plasmid co-integrate. The mosaic plasmid carried AMR genes (aadA2, armA, blaOXA-1, msrE, mphE, sul1anddfrA14) in addition tormpA2, iutAandiucABCDvirulence genes. Interestingly the mosaic plasmid carried its own type IV-A3 CRISPR-cas system that is likely able to target the acquisition of IncF plasmid with the help of atraLspacer. The convergence of virulence and AMR is the biggest threat among invasiveK. pneumoniaeinfections. However, increasing reports of the presence of mosaic plasmid carrying both AMR and virulence genes suggests MDR-hvKp isolates are no longer confined to selected clones and the containment of such isolates is very challenging.

IMPORTANCE

Klebsiella pneumoniaeis an opportunistic pathogen that commonly associated with hospital-acquired infections in the urinary tract, respiratory tract, lung, wound sites. The organism has gained notoriety by acquiring additional genetic traits to become either hypervirulent (HV) phenotype or multidrug resistant (MDR) phenotype. Though the infections by both these phenotypes were very challenging to treat, the MDRK. pneumonia(MDR-Kp) were remained in the hospital settings while HVK. pneumonia(hvKp) strains were mostly originated from the community settings. In a recent turn of events, the evolution of MDR-Kp and hvKp has converged as both clones found to carry both MDR plasmids and virulence plasmid. These convergent strains are challenging to treat and is associated with higher mortality rate. As the recent hvKp isolates harbour mosaic plasmid encoding both AMR and virulence determinants there is a need to investigate the evolution of these pathogens. The significance of our research is in characterising the novel mosaic plasmid identified in MDR-hvKp isolates that belong sequence type (ST) 2096. Tracking the possible evolution pathway of MDR-hvKPs would greatly help in the proper surveillance and management of this superbugs.

Repositories

The whole genome sequences of the present study isolates have been deposited in GenBank, NCBI, with accession numbersCP053765-CP053770,CP053771–CP053780,CP058798-CP058806, JAARNO010000001.1 - JAARNO010000005.1, JAAQSG000000000, JAARNJ000000000, JAARMH000000000 and JAAQTC000000000