Comparative Genomic Analysis of a Clinical Isolate of subsp. , a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil.

The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of subsp. by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant 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 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 subsp. . 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 KQPS142a (50.7% G+C) and 11 Kbp KQPS142b (57.3% G+C). The 3 Kbp region in KQPS142b containing the was found highly similar to that of Kp13d of Kp13 isolated in Southern Brazil in 2009, suggesting the horizontal transfer of this resistance gene between different species of . KPC-142 additionally harbors an integrative conjugative element ICE that could be involved in the mobilization of KQPS142b 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 subsp. , 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 subsp. (phylogroup II-B), subsp. (phylogroup II-A), (phylogroup I), and (phylogroup III). Our study contributes to the description of the characteristics of a novel subsp. strain circulating in South America that currently represent a serious potential risk for nosocomial settings.