Draft genome sequence of a multidrug-resistant Klebsiella pneumoniae isolate from the urine of a hospitalized patient at CRH, Gangtok, Sikkim

Multidrug-resistant bacteria pose one of the greatest global challenges in modern healthcare. Numerous bacterial pathogens are responsible for difficult-to-manage infectious disease states leading to life-threatening conditions such as septicaemia. Among these, Klebsiella pneumoniae has emerged as one of the biggest threats, causing serious nosocomial infections. Treating patients of immunocompromised status, those admitted to ICUs, and the elderly with chronic clinical conditions like diabetes mellitus, as well as the paediatric population, is challenging if they are infected with this bacterial strain. K. pneumoniae is known for its high virulence capacity, enabling it to effectively invade host innate immunity. In addition, it has a higher preponderance to develop antibiotic resistance through multiple modes, including point mutations, formation of biofilms, cross resistance, and plasmid acquisition. These properties have rendered its categorisation under the ESKAPE group of bacteria, which are known for their capacity to escape the effects of antibacterial agents. In recognition of this threat, WHO has designated it as a priority drug-resistant organism. The alarming rise in MDR strains of K. pneumoniae infection has driven the interest of the researcher to investigate its peculiar genomic characteristic that confers resistance and virulence. Identifying these unique determinants is essential for developing novel therapeutic approaches targeting involved mechanisms before the organism becomes a serious global health threat. Another unique mechanism contributing to the ineffectiveness of antibiotics against this bacteria is its ability to produce carbapenemase (KPC-KP strain) and extended-spectrum beta-lactamases (ESBL-KP strain), which are resistant to the carbapenem group of antibiotics and extended-spectrum beta-lactamases, respectively, and both of which are associated with higher mortality rates. Therefore, the genome sequence analysis is crucial to detect the critical targets involved in delineating the poor efficacy of the existing antimicrobials. This study analyses the genomic architecture of a clinically isolated MDR K. pneumoniae strain obtained from the urine sample of a patient suffering from hypertension associated with cerebrovascular accident with urinary tract infection, admitted to the neurosurgical ICU of a tertiary care hospital in Gangtok, Sikkim, India. By thorough genome analysis, this study aims to identify the core components responsible for the development of multidrug resistance in this isolate. The whole-genome data analysis will contribute to guiding future research efforts to combat MDR challenges in this region and globally, facilitating the development of appropriate therapeutic intervention against this formidable pathogen.