Diversity of mobile genetic elements in carbapenem-resistant Enterobacterales isolated from the intensive care units of a tertiary care hospital in Northeast India
Shravani Mitra, Sharmi Naha, Joy Chakraborty, S. K. De, Harpreet Kaur, Tapan Majumdar, Sulagna Basu
Abstract
Introduction Mobile genetic elements (MGEs) play a crucial role in the spread of carbapenem resistance. A study was undertaken to characterize MGEs and evaluate their contribution to the spread of carbapenem resistance in Escherichia coli and Klebsiella pneumoniae collected from three intensive care units (ICUs) of a tertiary care hospital in Tripura. Methods Isolates were subjected to susceptibility testing, genotypic detection of carbapenemases and their transmissibility, whole-genome sequencing (WGS), and phylogenomic analysis. Results E. coli and K. pneumoniae were the dominant Enterobacterales, exhibiting resistance to the majority of antibiotics. WGS of carbapenemase-producing E. coli ( n = 15/48,31%) and K. pneumoniae ( n = 13/26,50%) revealed the presence of bla NDM-1,5,7 ( n = 21), bla KPC-2 ( n = 1), and bla OXA-181,232 ( n = 8). Isolates were diverse and belonged to different sequence types, including epidemic clones ( K. pneumoniae -ST16/101/147/231; E. coli -ST167/410/648). This study has noted the allelic shift of bla NDM-1 to bla NDM-5 similar to global reports. bla NDM-1,5,7 -bearing plasmids were conjugative but those carrying bla KPC-2 and bla OXA-181,232 were non-conjugative. bla NDM-1,5,7 were present in diverse replicons: IncF-types (predominant), IncHI1B, IncX3, and IncX4, etc., while bla OXA-181,232 were present in ColKP3, corroborating with global studies. bla NDM-1,5 was associated with intact/truncated IS Aba125 in Tn 125 , bla NDM-7 with IS 3000 , bla KPC-2 with IS Kpn6 , and IS Kpn7 in Tn 4401 b, and bla OXA-181,232 with ∆IS Ecp1 in Tn 2013 , depicting an ancestral genetic context noted globally. Study isolates were related to other Indian isolates, primarily from blood. Discussion The association with different MGEs noted in the study is similar to those in other parts of India and the globe, signifying that the genetic determinants are part of the global gene pool. These associations can facilitate the spread of carbapenem resistance, leading to outbreaks and treatment failures.