Hypervirulent extensively-drug resistant (XDR) Klebsiella pneumoniae associated with complicated urinary tract infection in Northern India

Klebsiella pneumoniae associated with hospital acquired infections in South Asia are frequently extensively-drug resistant, making treatment and control problematic. It is important to understand the epidemiology and genetic structure of XDR K. pneumoniae and to determine their potential to be hypervirulent (hv) through the presence of siderophores. Here, we characterized the genomes of 20 colistin-resistant XDR K. pneumoniae isolated from 16 patients with complicated UTI over a six-month period in a healthcare facility in northern India. The 16 organisms comprised five STs: ST14 (10/20), ST147 (5/20), ST231 (3/20), ST2096 (1/20), and ST25 (1/20). Notably, several patients admitted to a single ward were infected with the same ST, potentially indicating a common infection source. Additionally, some patients had recurrent infections with multiple STs that were circulating concurrently in a particular ward, providing further evidence for hospital transmission. Beta lactamase genes (blaCTX-M-1, blaSHV, blaLEN, and blaAMP-H) were present in all isolates and the blaNDM, blaOXA1-90, and blaOXA48 carbapenemases were present in 17, 18, and 3 isolates, respectively. Disruption of mgrB with various IS elements was identified in six organisms and was the most common mechanism of colistin resistance. The most frequent K type was K2 (11/20), followed by K10, K51, and K64. Notably, we identified one XDR convergent hypervirulent K. pneumoniae (hvKp) associated with prolonged hospitalisation (iuc+ybt+ESBL+OXA-1, OXA-48), belonging to ST2096. Our data suggest that convergent XDR-hvKp is circulating in our healthcare facility. We speculate that such organisms may have outbreak potential, warranting more effective antimicrobial stewardship and better infection control strategies.