Clinical and Molecular Description of a High-Copy IncQ1 KPC-2 Plasmid Harbored by the International ST15 Klebsiella pneumoniae Clone

Abstract

This study provides the genomic characterization and clinical description of bloodstream infections (BSI) cases due to ST15 KPC-2 producer Klebsiella pneumoniae. Six KPC-K. pneumoniae isolates were recovered in 2015 in a tertiary Brazilian hospital and were analyzed by whole-genome sequencing (WGS) (Illumina MiSeq short reads). Of these, two isolates were further analyzed by Nanopore MinION sequencing, allowing complete chromosome and plasmid circularization (hybrid assembly), using Unicycler software. The clinical analysis showed that the 30-day overall mortality for these BSI cases was high (83%). The isolates exhibited meropenem resistance (MICs, 32 to 128 mg/liter), with 3/6 isolates resistant to polymyxin B. The conjugative properties of the blaKPC-2 plasmid and its copy number were assessed by standard conjugation experiments and sequence copy number analysis. We identified in all six isolates a small (8.3-kb), high-copy-number (20 copies/cell) non-self-conjugative IncQ plasmid harboring blaKPC-2 in a non-Tn4401 transposon. This plasmid backbone was previously reported to harbor blaKPC-2 only in Brazil, and it could be comobilized at a high frequency (10−4) into Escherichia coli J53 and into several high-risk K. pneumoniae clones (ST258, ST15, and ST101) by a common IncL/M helper plasmid, suggesting the potential of international spread. This study thus identified the international K. pneumoniae ST15 clone as a carrier of blaKPC-2 in a high-copy-number IncQ1 plasmid that is easily transmissible among other common Klebsiella strains. This finding is of concern since IncQ1 plasmids are efficient antimicrobial resistance determinant carriers across Gram-negative species. The spread of such carbapenemase-encoding IncQ1 plasmids should therefore be closely monitored. IMPORTANCE In many parts of the world, carbapenem resistance is a serious public health concern. In Brazil, carbapenem resistance in Enterobacterales is mostly driven by the dissemination of KPC-2-producing K. pneumoniae clones. Despite being endemic in this country, only a few reports providing both clinical and genomic data are available in Brazil, which limit the understanding of the real clinical impact caused by the dissemination of different clones carrying blaKPC-2 in Brazilian hospitals. Although several of these KPC-2-producer K. pneumoniae isolates belong to the clonal complex 258 and carry Tn4401 transposons located on large plasmids, a concomitant emergence and silent dissemination of small high-copy-number blaKPC-2 plasmids are of importance, as described in this study. Our data identify a small high-copy-number IncQ1 KPC plasmid, its clinical relevance, and the potential for conjugative transfer into several K. pneumoniae isolates, belonging to different international lineages, such as ST258, ST101, and ST15.

Characterization of Carbapenem-Resistant Klebsiella pneumoniae ST15 Clone Coproducing KPC-2, CTX-M-15 and SHV-28 Spread in an Intensive Care Unit of a Tertiary Hospital

“…All ST15 strains were susceptible to amikacin in our study, while the resistant rates to amikacin were 100% reported in Vietnam 11 and Shanghai, China. 16 The diversity of plasmid types acquired by ST15 clones in the different study locations, such as bla KPC-2 -bearing IncQ1 plasmid in Brazil, 17 bla KPC-2 -bearing IncFII plasmid in Bulgaria, 10 bla KPC-3 -bearing IncF plasmid in Portugal 12 and bla OXA-232 -bearing ColKP3 plasmid in China, 16 suggests this clone has a high capacity for horizontal acquisition of resistance.…”

“… 10–16 K. pneumoniae ST15 strains in different regions are variable in terms of antimicrobial resistance patterns and resistance genes, which is likely related to the differences in plasmid types carrying antimicrobial resistance genes. 17 …”

“…[10][11][12][13][14][15][16] K. pneumoniae ST15 strains in different regions are variable in terms of antimicrobial resistance patterns and resistance genes, which is likely related to the differences in plasmid types carrying antimicrobial resistance genes. 17 Here, we report a clustering of K. pneumoniae ST15 isolates in the cardiac surgery intensive care unit (CSICU), and investigate its molecular characteristics and drug resistance mechanisms, which can provide a basis for the control and prevention of nosocomial infections.…”

Convergence of MCR-8.2 and chromosome-mediated resistance to colistin and tigecycline in an NDM-5-producing ST656 Klebsiella pneumoniae from a lung transplant patient

“…IncQ1 type plasmids are efficient antimicrobial resistance determinants among Gram-negative bacteria (35). The truncated IncQ1 replicon in the plasmid pKP32558-2-mcr8 was also observed in the other two plasmids, pMCR8_020135 and pMCR8_095845, indicating that these three plasmids may share a common ancestor.…”

“…CC-BY-NC-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted July 23, 2021. ; https://doi.org/10.1101/2021.07.21.453302 doi: bioRxiv preprint IncQ1 type plasmids are efficient antimicrobial resistance determinants among Gram-negative bacteria (35). The truncated IncQ1 replicon in the plasmid pKP32558-2-mcr8 was also observed in the other two plasmids, pMCR8_020135 and pMCR8_095845, indicating that these three plasmids may share a common ancestor.…”