Genomic analysis of a KPC-2-producing Klebsiella pneumoniae ST15 from Argentina

DAMICO GONZALEZ GABRIELA; GAMBINO, ANAHÍ; GONZALES MACHUCA, ADRIÁN; ARDUINO, SONIA; ALVAREZ, VERÓNICA; GALAN, ANGELICA; POKLEPOVICH, TOMÁS; CENTRÓN, DANIELA; MASSO, MARIANA GUILLERMINA; KNECHT, CAMILA; CAMPOS, JOSEFINA; QUIROGA, MARÍA PAULA

Buenos aires

Congreso; Reunión Anual de Sociedades de Biociencias 2020; 2020

Sociedad Argentina de Investigación Clínica (SAIC), la Sociedad Argentina de Inmunología (SAI) y la Sociedad Argentina de Fisiología (SAFIS)

Genomic analysis of a KPC-2-producing Klebsiella pneumoniae ST15 from ArgentinaThe isolation of colistin and carbapenem resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, and is related to increased morbidity, mortality and health care costs. K. pneumoniae ST15 is a less common Sequence Type than ST258 and ST11 nevertheless is also reported around the globe as responsible for CaR-Kp outbreaks. The aim of this work was to carry out the whole-genome sequencing (WGS), genomic and phylogenetic analysis of a multidrug resistant (MDR) CCR-Kp from Argentina. The MDR CCR-Kp strain KpS26 was isolated from a bloodstream infection at a hospital setting from Ciudad Autónoma de Buenos Aires, in February 2020. WGS was carried out using Illumina MiSeq-I with Nextera XT libraries. De novo assembly was carried out using SPADES v.3.11. Contigs were re-ordered using the ST15 reference genome Klebsiella pneumoniae PMK1 (GenBank CP008929) and oriented with MAUVE Contig Mover. The coding regions were detected with the Rapid Annotations using Subsystems Technology (RAST) server. Multilocus sequence typing (MLST) was performed in silico using the MLST database and schema for K. pneumoniae at the Pasteur MLST website. A maximum-likelihood tree was created with MEGA7 based on core SNPs from whole-genome alignment obtained with SNP sites. The genomic, resistome, plasmids, IS and integrons content was analyzed with PathogenFinder, Resfinder, ISFinder, plasmid-SPAdes, PlasmidFinder and IntegronFinder. The KpS26 analysis revealed a genome of 5,815,319 bp (5342 CDS, 121 RNAs)of ST15. The Col(pHAD28), IncFIA(HI1), IncFIB(K), IncFII(K) and IncM1 plasmid replicons and 14 transferable associated antimicrobial resistance genes (ARGs), including blaKPC-2, comprising six drug classes were detected. A class 1 integron with dfrA14 as well as other gene cassettes were identified. The MDR CCR-Kp analyzed here shows that ST15 disseminates blaKPC-2 in Argentina alongside other antimicrobial resistance genes through Lateral Genetic Transfer.