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

MASSO, MARIANA; ALVAREZ VERONICA; DAMICO GONZALES GABRIELA; GAMBINO ANAHI SAMANTA; ALONSO FERNANDO; LEGUINA CAROLINA; CARRERA PAEZ LAURA; AYALA OLINCA; PIEKAR MARIA; VIANNA LORENA; CAMICIA GABRIELA; DONIS NICOLAS; POKLEPOVICH TOMAS; CAMPOS JOSEFINA; ARDUINO SONIA; CENTRON DANIELA; QUIROGA MARIA PAULA

CABA

Congreso; Reunion anual de sociedades de biociencias SAI SAIC SAFIS 2020; 2020

SAI, SAIC y SAFIS

Carbapenem resistant Klebsiella pneumoniae (CR-Kp) causes outbreaks inhospital settings worldwide, and is related to increased morbidity, mortality andhealth care costs. CR-Kp ST13 are not predominant but nevertheless arereported around the globe. The aim of this work was to perform the wholegenome sequencing (WGS) of a multidrug resistant (MDR) CR-Kp from Argentinato carry out a genomic and phylogenetic analysis. The strain KpS27 was isolatedfrom a bloodstream infection at a hospital setting from Ciudad Autónoma deBuenos Aires, in January 2020. KpS27 strain was an MDR CR-Kp, susceptibleonly to amikacin, tigecycline and colistin. WGS was carried out using IlluminaMiSeq-I with Nextera XT libraries. Reads were quality trimmed and analyzed withfastqc, trimmomatic and cutadapt. Assembly were done with SPADES v.3.11.Contigs were re-ordered and oriented with MAUVE Contig Mover. The codingregions were detected with the Rapid Annotations using Subsystems Technology(RAST) server. Multilocus sequence typing (MLST) was analyzed in silico usingthe MLST database and schema for K. pneumoniae at the Pasteur MLSTwebsite. A maximum-likelihood tree was created using MEGA7 based on coreSNPs from whole-genome alignment obtained with SNP-sites. The genomic,resistome, plasmids, IS and integrons content was analyzed i.e. withPathogenFinder, Resfinder, ISFinder, plasmid-SPAdes, PlasmidFinder andIntegronFinder. The phylogenetic analysis showed that KpS27 belonged to ST13.The Col(pHAD28), IncC and IncFIB(pQil) plasmid replicons and 15 transferableassociated antimicrobial resistance genes (ARG) comprising eight drug classeswere detected. Among the ARG we highlight the presence of blaOXA-163 a blaOXA48-like gene, which codes for a carbapenemase. A class 1 integron as well as thegene cassettes aac(6´)-Ib-cr and dfrA14 were identified. This MDR CR-Kp straincarries a variety of mobile elements and shows that ST13 with blaOXA-163 arenowadays disseminating in Argentina.