Co-Production of NDM-1, CTX-M-9 Family and mcr-1 in a Klebsiella pneumoniae ST4564 Strain in China

Abstract

Purpose To identify novel sequence types 4564 (ST4564) carbapenem-resistant Klebsiella pneumoniae (CRKP). Characterizing the feature of the clinic, resistance, and virulence of a co-producing NDM-1 and CTX-M-9 family and mcr-1 ST4564 strain. Methods A novel ST4564 CRKP was collected from June 2018 to July 2018. We investigated its antimicrobial susceptibility by the microdilution method. Using the modified carbapenem inactivation method (mCIM) to screen phenotype of carbapenemases. Resistance mechanisms, virulence-associated genes, multilocus sequence typing (MLST), and capsular serotypes were characterized by polymerase chain reaction (PCR) and DNA sequencing. Next-generation sequencing (NGS) was carried out to determine the genetic features of carbapenem resistance and virulence. Results ST4564, co-carrying NDM-1, CTX-M-9 and mcr-1, was resistant to carbapenems, cephamycin, third- or fourth-generation cephalosporins, β-lactam combination agents, quinolones and tigecycline but remained susceptible to amikacin (AMK) and colistin (COL). Through the NGS analysis with the G+C content of 56.65%, multiple resistance and virulence genomes were detected. The genes encoding the β-lactams, aminoglycosides, quinolones, macrolides, sulfonamide, polysaccharide capsule, type-I fimbriae cluster, siderophore genes, transporter and pumps, T6SS and pullulanase secretion protein. goeBURST analysis showed that ST4564 belonged to the CC1571 and it was not related to the prevalent high-risk clones. Conclusion We first identified the novel ST4564 CRKP. Our finding suggested that the urgent need for infection control of the new clone to prevent it from becoming a high-risk clone of CRKP.

Characterization of a mcr-1 and CRISPR-Cas System Co-harboring Plasmid in a Carbapenemase-Producing High-Risk ST11 Klebsiella pneumoniae Strain

“…Notably, other mcr-1 and type IV-A3 CRISPR-Cas system co-harboring plasmids have been isolated from different regions in Taiwan since 2018 ( Chen et al, 2021 ), suggesting this type of mcr-1 -carrying plasmid has already spread in Taiwan. Although the presence of mcr-1 and carbapenemases were not frequently detected in K. pneumoniae ( Di Pilato et al, 2016 ; Aires et al, 2017 ; Berglund et al, 2018 ; Dalmolin et al, 2018 ; Mendes et al, 2018 ; Srijan et al, 2018 ; Giordano et al, 2019 ; Wang et al, 2021 ), the further dissemination of highly stable pKP2509-MCR-like plasmids into clinical carbapenem-resistant K. pneumoniae could potentially change the current epidemiology, leading to the spread of colistin and carbapenem resistant successful clones.…”

“…This finding partially explains why mcr-1 is more frequently detected in E. coli and less abundant in K. pneumoniae ( Wang et al, 2017 ). The emergence of mcr-1 genes in CPKP is particularly concerning even though only sporadic clinical CPKP isolates with mcr-1 have been reported ( Di Pilato et al, 2016 ; Aires et al, 2017 ; Berglund et al, 2018 ; Dalmolin et al, 2018 ; Mendes et al, 2018 ; Srijan et al, 2018 ; Giordano et al, 2019 ; Wang et al, 2021 ). Studies regarding the impact of mcr-1 on the fitness of CPKP remain to be evaluated.…”

Three Novel Sequence Types Carbapenem-Resistant Klebsiella pneumoniae Strains ST5365, ST5587, ST5647 Isolated from Two Tertiary Teaching General Hospitals in Shanxi Province, in North China: Molecular Characteristics, Resistance and Virulence Factors

“…In the previous study, some researchers have demonstrated that ST profiles sharing 100% genetic identity in at least 6 of 7 MLST loci were grouped into a clonal complex (CC). 22 So that, we used the software goeBURST 1.2.1 version ( http://www.phyloviz.net/goeburst/ ) to identify the molecular epidemiological relationships of the CC.…”

“…Through this study, we could see that this novel ST was not related to the high- risk clones, hinting us to concentrate more on its resistance. 22 Thus, it can be seen that different STs show diversity in resistance and virulence. Under the circumstance, we began to monitor and analyze the novel ST of the isolates collected.…”

Genetic Characterization of an ST5571 Hypervirulent Klebsiella pneumoniae Strain Co-Producing NDM-1, MCR-1, and OXA-10 Causing Bacteremia

“…A low prevalence of mcr-1 in K. pneumoniae was observed, 10 although several mcr genes and their variants have been detected in K. pneumoniae . 11 , 12 In this work, we reported a bloodstream infection caused by a colistin-resistant CRKP strain. Whole-genome sequencing (WGS) and microbiological analysis revealed the emergence of colistin-resistant CRKP clinical strain co-producing NDM-1, MCR-1, and OXA-1.…”