Genomic analysis reveals the re-emergence of a nosocomial outbreak caused by multidrug resistant Klebsiella pneumoniae

Multidrug resistant (MDR) K. pneumoniae is listed among the most urgent public health threats due to its virulence and insusceptibility to a wide range of antimicrobials. Infection with this pathogen frequently leads to fatal outcomes, especially in low-income hospital settings. Patan Hospital is a 450-bed government hospital located within the Kathmandu Valley, Nepal. The hospital has previously witnessed multiple outbreaks caused by MDR K. pneumoniae in the neonatal intensive care unit (NICU). Particularly, a carbapenemase producing sequence type (ST) 15 K. pneumoniae clone was responsible for an outbreak with mortality rate up to 75 % in 2012. Recently in 2015, this same NICU suffered again from an MDR K. pneumoniae outbreak. In this study, using whole genome sequencing (WGS) and state-of-the-art analytic approaches, we aimed to define the nature of this recent outbreak. We found that the 2015 outbreak in Patan Hospital was caused by the same MDR ST15 K. pneumoniae reported in 2012. Albeit genetically similar, these recent strains were susceptible to carbapenems due to deletion of the blaNDM-1 cassette. Using Bayesian phylogenetic inference, we determined the outbreak strain was introduced to Patan Hospital in late 2010 and subsequently caused major outbreaks in NICU in 2012 and again in 2015. This clone acquired four different plasmids encoding resistance to numerous therapeutic antimicrobials, and this may underlie its successful propagation and associated high mortality. Insights provided through this study are invaluable in tailoring infection control strategies as well as raising public awareness