Plasmid diversity in Klebsiella pneumoniae ST307 co-producing KPC plus NDM recovered during the COVID-19 pandemic

Abstract

The prevalence of carbapenemase-producing Klebsiella pneumoniae increased significantly during COVID-19 in Argentina, rising from 20 % in 2019 to 30 % in 2021. Additionally, there was a notable increase of K. pneumoniae ST307 co-producing KPC and NDM. We aimed to reveal the genetic structure of the plasmids harbored in six isolates of K. pneumoniae ST307 co-producing KPC and NDM and to expression levels of both carbapenemases in a cell. The isolates were collected between November 2020 and September 2021 and were selected according to: (i) diversity of allelic variant combinations: blaKPC-2 plus blaNDM-1 (n = 2), blaKPC-2 plus blaNDM-5 (n = 2), blaKPC-3 plus blaNDM-1 (n = 2); (ii) different hospitals and jurisdictions; and (iii) differences in pulsotype by Xba-I-PFGE. The isolates were studied by whole genome sequencing (Illumina NextSeq 550 and with GridION) and with a transcriptional analysis using quantitative real time-PCR. The isolates carried between two and four plasmids with sizes from 3.7 to 250 Kb. Twenty plasmids with nine replicons were identified including three distinct hybrid replicon combinations. blaKPC-2 was found in three plasmid backbones [IncM1, IncFIB(pQil)/IncFII(K), and IncFIB/H1B] while the rest were associated with a single plasmid type: blaNDM-1 (IncC), blaNDM-5 (IncFIB/H1B) and blaKPC-3 (IncR). The basal expression level of KPC-2 was statistically higher than that of NDM-1/5. Our results show that the dissemination of NDM and KPC in K. pneumoniae ST307 was driven through diverse plasmids, highlighting the capacity of this high-risk clone to acquire, maintain and spread multiple carbapenemases.