Whole genome sequencing of a hypermucoviscous, multidrug-resistant Klebsiella pneumoniae subsp. pneumoniae K219 isolated from human sputum

Multidrug-resistant (MDR) strains of Klebsiella pneumoniae pose a significant public health threat due to their ability to evade commonly used antibiotics, restricting therapeutic options and increasing mortality rates especially among immunocompromised individuals. This study aimed to sequence the genome of MDR K. pneumoniae subsp. pneumoniae K219 isolate procured from a tertiary care hospital, Chennai which was isolated from a human sputum sample. Sequencing was performed using third-generation Oxford Nanopore Technologies (MinION platform, FLO-MIN106 flow cell, R9.4.1 pore type) with the EXP-NBD114 barcoding kit and SQK-LSK109 sequencing kit. The genome was analysed using a suite of bioinformatics tools to identify virulence factors, resistance genes, mobile elements, and clustered regularly interspaced short palindromic repeats (CRISPR). The assembled genome of K. pneumoniae K219 comprises a single circular chromosome and four plasmids, with a total genome size of 5,038,803 base pairs. The plasmids measured 229,745; 134,193; 33,455; and 183,631 base pairs, respectively. One CRISPR array was identified. Genomic characterization of K. pneumoniae K219, including its four plasmids and a CRISPR array, offers valuable insights into the genetic architecture of this MDR strain. The data enhance our understanding of its resistance mechanisms, virulence determinants, and interaction with mobile genetic elements. These findings can guide targeted treatment strategies and infection control measures in clinical settings.