Abstract
The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant K. pneumoniae were collected from nosocomial infections in southeast Brazil. After RAPD screening, the KPC-142 isolate, showing the most divergent DNA pattern, was selected for complete genome sequencing in an Illumina HiSeq 2500 instrument. Reads were assembled into scaffolds, gaps between scaffolds were resolved by in silico gap filling and extensive bioinformatics analyses were performed, using multiple comparative analysis tools and databases. Genome sequencing allowed to correct the classification of the KPC-142 isolate as K. quasipneumoniae subsp. similipneumoniae. To the best of our knowledge this is the first complete genome reported to date of a clinical isolate of this subspecies harboring both class A beta-lactamases KPC-2 and OKP-B-6 from South America. KPC-142 has one 5.2 Mbp chromosome (57.8% G+C) and two plasmids: 190 Kbp pKQPS142a (50.7% G+C) and 11 Kbp pKQPS142b (57.3% G+C). The 3 Kbp region in pKQPS142b containing the blaKPC−2 was found highly similar to that of pKp13d of K. pneumoniae Kp13 isolated in Southern Brazil in 2009, suggesting the horizontal transfer of this resistance gene between different species of Klebsiella. KPC-142 additionally harbors an integrative conjugative element ICEPm1 that could be involved in the mobilization of pKQPS142b and determinants of resistance to other classes of antimicrobials, including aminoglycoside and silver. We present the completely assembled genome sequence of a clinical isolate of K. quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 beta-lactamases producer and discuss the most relevant genomic features of this important resistant pathogen in comparison to several strains belonging to K. quasipneumoniae subsp. similipneumoniae (phylogroup II-B), K. quasipneumoniae subsp. quasipneumoniae (phylogroup II-A), K. pneumoniae (phylogroup I), and K. variicola (phylogroup III). Our study contributes to the description of the characteristics of a novel K. quasipneumoniae subsp. similipneumoniae strain circulating in South America that currently represent a serious potential risk for nosocomial settings.
Highlights
The prevalence of isolation of carbapenem-resistant Klebsiella pneumoniae strains in nosocomial infections is increasing, posing a serious therapeutic problem given the limited number of effective antimicrobial agents
We have sequenced to closure the genome of K. quasipneumoniae subsp. similipneumoniae Klebsiella pneumoniae carbapenemase (KPC)-142
This isolate was chosen for sequencing following a Randomly Amplified Polymorphic DNA (RAPD) analysis of a panel of multiple blaKPC−2-producing Klebsiella clinical isolates (Figure S1), in which KPC-142 presented a very divergent DNA pattern
Summary
The prevalence of isolation of carbapenem-resistant Klebsiella pneumoniae strains in nosocomial infections is increasing, posing a serious therapeutic problem given the limited number of effective antimicrobial agents. Similipneumoniae isolated from a patient with chronic liver disease in India that belongs to novel sequence type ST2320 and possesses the K1 capsular serotype has been reported (Shankar et al, 2017) These findings accentuate the concern for the potential spread of multidrug resistance and increased virulence capacity among various Klebsiella species. Core chromosomal beta-lactamases have been proposed as molecular markers to differentiate Klebsiella species, i.e., K. pneumoniae (SHV restricted), K. quasipneumoniae (OKP restricted), and K. variicola (LEN restricted) (Haeggman et al, 2004; Fonseca et al, 2017) This method has some complications, since there are some SHV betalactamase genes encoded on plasmids and K. variicola isolates carrying chromosomal OKP-B instead of LEN (Long et al, 2017). A better understanding of the genomics aspects of K. quasipneumoniae and K. variicola strains will help toward the development of improved diagnostics
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
