Convergence of MCR-8.2 and Chromosome-Mediated Resistance to Colistin and Tigecycline in an NDM-5-Producing ST656 Klebsiella pneumoniae Isolate From a Lung Transplant Patient in China

Abstract

We characterized the first NDM-5 and MCR-8.2 co-harboring ST656 Klebsiella pneumoniae clinical isolate, combining with chromosomal gene-mediated resistance to colistin and tigecycline. The K. pneumoniae KP32558 was isolated from the bronchoalveolar lavage fluid from a lung transplant patient. Complete genome sequences were obtained through Illumina HiSeq sequencing and nanopore sequencing. The acquired resistance genes and mutations in chromosome-encoded genes associated with colistin and tigecycline resistance were analyzed. Comparative genomic analysis was conducted between mcr-8.2-carrying plasmids. The K. pneumoniae KP32558 was identified as a pan-drug resistant bacteria, belonging to ST656, and harbored plasmid-encoded blaNDM-5 and mcr-8.2 genes. The blaNDM-5 gene was located on an IncX3 type plasmid. The mcr-8.2 gene was located on a conjugative plasmid pKP32558-2-mcr8, which had a common ancestor with another two mcr-8.2-carrying plasmids pMCR8_020135 and pMCR8_095845. The MIC of KP32558 for colistin was 256 mg/L. The mcr-8.2 gene and mutations in the two-component system, pmrA and crrB, and the regulator mgrB, had a synergistic effect on the high-level colistin resistance. The truncation in the acrR gene, related to tigecycline resistance, was also identified. K. pneumoniae has evolved a variety of complex resistance mechanisms to the last-resort antimicrobials, close surveillance is urgently needed to monitor the prevalence of this clone.

Genetic Diversity of Polymyxin-Resistance Mechanisms in Clinical Isolates of Carbapenem-Resistant Klebsiella pneumoniae: a Multicenter Study in China

“…The arnBCADTEF operon, lpxM and yciM , mediated LPS biosynthesis and modification ( 3 , 15 , 22 ). In the deleterious mutations in the above-mentioned genes, the mutations in arnB were prevalent, similar to the results of a previous study ( 14 ). However, in the present study, though predicted as deleterious mutations by PROVEAN, the genes lpxM (T229S), lpxM (N7I), and yciM (N212T) were 100% similar to the reference sequences in GenBank ( yciM [N212T]: NCBI reference sequence WP_002901781.1 ; lpxM [T229S] and lpxM [N7I]: NCBI reference sequence: WP_072353980.1 ) after alignment using the NCBI BLASTp online tool.…”

“…The mcr gene was detected only in strain CJFH07 ( mcr-8.2 ), in which the missense mutation in mgrB and crrB and disruption of acrR also played a major role in polymyxin resistance ( 14 ).…”

“…K. pneumonia ATCC 13883 was selected as the control strain. The primers used refer to previous studies ( 14 ). The relative expression (RE) of each strain was calculated as follows: …”

Co-transfer of IncFII/IncFIB and IncFII plasmids mediated by IS26 facilitates the transmission of mcr-8.1 and tmexCD1-toprJ1

“…2 b). The mcr-8 locus on pKP32558-2-mcr8 was characterized in previous research as comprising of ISKpn26-orf-mcr8.2-ISEcl1-copR-baeS-dgkA , with nearby IS903B [ 25 ]. Contrarily, the mcr8 region of plasmid pTGC-02-mcr8 appeared to lack ISKpn26 and ISEcl1 , while an ISAba32 transposon was identified downstream of mcr-8.1.…”

Emergence of high-level colistin resistance mediated by multiple determinants, including mcr-1.1, mcr-8.2 and crrB mutations, combined with tigecycline resistance in an ST656 Klebsiella pneumoniae

“…The plasmid curing assay confirmed the colistin resistance contribution of the chromosome-located crrB gene mutation because the cured isolate had an MIC that was 32 times higher than that of the transformant, which exhibited the same plasmid pattern but lacked the original crrB mutation. On the basis of the genetic context for mcr-8.2 -carrying plasmids, we suggest that IS 903B might play an important role in the mobility of the IS Ecl1 - mcr-8.2 - orf -IS Kpn26 region because two copies of IS 903B are also located on both sides of the mcr-8.2 -flanking regions on pD120-1 and pMCR8_020135 ( Zhao et al., 2022 ). Consequently, we inferred that it is possible that the high-level colistin resistance observed was caused by the accumulated effect of several factors on the chromosome and mcr -type plasmids together.…”