Genomic analysis of a carbapenemase-producing Klebsiella pneumoniae ST13 harboring blaOXA-163 from Argentina

MARIANA MASSÓ; VERÓNICA ÁLVAREZ; GABRIELA DAMICO GONZALEZ ; ANAHÍ SAMANTA GAMBINO; FERNANDO MARTÍN ALONSO; CAROLINA LEGUINA; LAURA CARRERA PÁEZ; OLINCA AYALA; MARÍA PIEKAR; LORENA VIANNA; GABRIELA CAMICIA; NICOLÁS DONIS; TOMÁS POKLÉPOVICH; JOSEFINA CAMPOS; SONIA ARDUINO; DANIELA CENTRÓN ; MARÍA PAULA QUIROGA

CABA

Congreso; Reunión anual de sociedades de biosciencias SAI SAIC SAFIS 2020; 2020

SAI, SAIC y SAFIS

Carbapenem resistant Klebsiella pneumoniae (CR-Kp) causes outbreaks in hospital settings worldwide, and is related to increased morbidity, mortality and health care costs. Global epidemiology showed CR-Kp ST13 are not predominant but nevertheless are reported around the globe. The aim of this work was to perform the whole-genome sequencing (WGS) of a multidrug resistant (MDR) CR-Kp from Argentina to carry out a genomic and phylogenetic analysis. The strain KpS27 was isolated from a bloodstream infection at a hospital setting from Ciudad Autónoma de Buenos Aires, in January 2020. KpS27 strain was an MDR CR-Kp, susceptible only to amikacin, tigecycline and colistin. WGS was carried out using Illumina MiSeq-I with Nextera XT libraries. De novo assembly was carried out using SPADES v.3.11, fastqc, trimmomatic and cutadapt. Contigs were re-ordered and oriented with the MAUVE Contig Mover. The coding regions were detected with the Rapid Annotations using Subsystems Technology (RAST) server. Multilocus sequence typing (MLST) was analyzed in silico using the MLST database and schema for K. pneumoniae at the Pasteur MLST website. A maximum-likelihood tree was created using MEGA7 based on core SNPs from whole-genome alignment obtained with SNP sites. The genomic, resistome, plasmids, IS and integrons content was analyzed i.e. with PathogenFinder, Resfinder, ISFinder, plasmid-SPAdes, PlasmidFinder and IntegronFinder. The phylogenetic analysis showed that KpS27 belonged to ST13. The Col(pHAD28), IncC and IncFIB(pQil) plasmid replicons and 15 transferable associated antimicrobial resistance genes (ARG) comprising eight drug classes were detected. Among the ARG we highlight the presence of blaOXA-163 a blaOXA-48-like gene, which codes for a carbapenemase. A class 1 integron as well as the gene cassettes aac(6´)-Ib-cr and dfrA14 were identified. This MDR CR-Kp strain carries a variety of mobile elements and shows that ST13 with blaOXA-163 are nowadays disseminating in Argentina.