Mobile genetic elements of global Escherichia coli ST131 clades with carbapenemases

Escherichia coli ST131 is an important clone linked with carbapenemases. Limited data is available about the international distribution of ST131 clades and mobile genetic elements (MGEs) linked with carbapenemases.

Short and long read WGS were performed on ST131 with carbapenemases (n=53) obtained from 21 countries (2010-19). We fully assembled 51 of the carbapenenemase containing plasmids that were grouped into MOB-clusters using MOB-suite v3.1.9.

KPCs (n=37) were the most frequent carbapenemases followed by NDMs (n=8), OXA-48-like (n=7), VIMs (n=1) and IMPs (n=2). ST131 subclades were linked with different carbapenemases and clade C dominated the population structure. Plasmids with bla_KPCs (n=35) belonged to eight MOB-clusters that included IncU, IncF, ColRNAI, IncN1, IncR, pKPC-CAV1193, Col-pHAD28; bla_NDMs plasmids (n=7) belonged to four MOB-clusters that included IncF, IncX3, IncC, IncN2; bla_OXA-48-like plasmids (n=6) belonged to six MOB-clusters that included IncL. IncM1, Col(pHAD28), ColKP3, IncF, IncX3; bla_IMPs plasmids (n=2) belonged to IncN1 and IncC, while the bla_VIM-1 (n=1) plasmid belonged to IncC. Multiple transposable and antimicrobial resistance determinants were harboured on these plasmids.

The global spread of carbapenemase genes in ST131 clades were driven by multiple underlying mechanisms, including the local and international spread of highly similar plasmids as well as diverse plasmids, within the same geographical locations. This study provided references for future ST131 genomic studies on MGEs linked with carbapenemases.