First report of Klebsiella quasipneumoniae harboring blaKPC-2 in Saudi Arabia

Background Nosocomial infections caused by multi-drug resistantEnterobacteriaceaeare a global public health threat that ought to be promptly identified, reported, and addressed accurately. Many carbapenem-resistantEnterobacteriaceae-associated genes have been identified in Saudi Arabia but not the endemicKlebsiella pneumoniaecarbapenemases (KPCs), which are encoded byblaKPC-typegenes. KPCs are known for their exceptional spreading potential. Methods We collectedn = 286 multi-drug resistant (MDR)Klebsiella spp.isolates as part of screening for resistant patterns from a tertiary hospital in Saudi Arabia between 2014 and 2018. Antimicrobial susceptibility testing was carried out using both VITEK II and the broth microdilution of all collected isolates. Detection of resistance-conferring genes was carried out using Illumina whole-genome shotgun sequencing and PacBio SMRT sequencing protocols. Results A Carbapenem-resistantEnterobacteriaceae(CRE)Klebsiella quasipneumoniaesubsp.similipneumoniaestrain was identified as a novel ST-3510 carrying ablaKPC-2carbapenemase encoding gene. The isolate, designated as NGKPC-421, was obtained from shotgun Whole Genome Sequencing (WGS) surveillance of 286 MDRKlebsiella spp. clinical isolates. The NGKPC-421 isolate was collected from a septic patient in late 2017 and was initially misidentified asK. pneumoniae. The sequencing and assembly of the NGKPC-421 genome resulted in the identification of a putative ~ 39.4 kb IncX6 plasmid harboring ablaKPC-2gene, flanked by transposable elements (ISKpn6-blaKPC-2–ISKpn27). Conclusion This is the first identification of a KPC-2-producing CRE in the Gulf region. The impact on this finding is of major concern to the public health in Saudi Arabia, considering that it is the religious epicenter with a continuous mass influx of pilgrims from across the world. Our study strongly highlights the importance of implementing rapid sequencing-based technologies in clinical microbiology for precise taxonomic classification and monitoring of antimicrobial resistance patterns.