Background Nosocomial infections caused by multi-drug resistant Enterobacteriaceae are a global public health threat that ought to be promptly identified, reported, and addressed accurately. Many carbapenem-resistant Enterobacteriaceae-associated genes have been identified in Saudi Arabia but not the endemic Klebsiella pneumoniae carbapenemases (KPCs), which are encoded by bla KPC-type genes. KPCs are known for their exceptional spreading potential. Methods We collected n = 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-resistant Enterobacteriaceae (CRE) Klebsiella quasipneumoniae subsp. similipneumoniae strain was identified as a novel ST-3510 carrying a bla KPC-2 carbapenemase encoding gene. The isolate, designated as NGKPC-421, was obtained from shotgun Whole Genome Sequencing (WGS) surveillance of 286 MDR Klebsiella spp. clinical isolates. The NGKPC-421 isolate was collected from a septic patient in late 2017 and was initially misidentified as K. pneumoniae. The sequencing and assembly of the NGKPC-421 genome resulted in the identification of a putative ~ 39.4 kb IncX6 plasmid harboring a bla KPC-2 gene, flanked by transposable elements (ISKpn6-bla KPC-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.

中文翻译：

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在沙特阿拉伯窝藏bla KPC-2的克雷伯氏菌的首次报道。

背景技术由多重耐药性肠杆菌科细菌引起的医院内感染是全球性的公共卫生威胁，应及时发现，报告和准确解决。在沙特阿拉伯已经发现了许多与碳青霉烯类耐药的肠杆菌科相关基因，但还没有发现由bla KPC型基因编码的地方性肺炎克雷伯菌肺炎克雷伯菌（KPCs）。KPC以其出色的传播潜力而闻名。方法我们收集了n = 286的多药抗性（MDR）克雷伯菌属（Klebsiella spp）。在2014年至2018年之间，从沙特阿拉伯一家三级医院筛查了耐药菌，作为耐药性筛查的一部分。使用了VITEK II和所有收集到的分离菌的肉汤微稀释液，进行了药敏试验。使用Illumina全基因组shot弹枪测序和PacBio SMRT测序方案对赋予抗性的基因进行检测。结果耐碳青霉烯的肠杆菌科（CRE）克雷伯氏菌肺炎克雷伯菌亚种。鉴定出一种新的ST-3510携带了bla KPC-2碳青霉烯酶编码基因。该分离株命名为NGKPC-421，是从对286 MDR克雷伯菌属（Klebsiella spp）的shot弹枪全基因组测序（WGS）监视中获得的。临床分离株。NGKPC-421分离株于2017年底从一名败血症患者中收集，最初被误认为肺炎克雷伯菌。NGKPC-421基因组的测序和组装导致鉴定出一个推定的〜39.4 kb IncX6质粒，该质粒带有bla KPC-2基因，两侧是转座因子（ISKpn6-bla KPC-2-ISKpn27）。结论这是在海湾地区首次鉴定出生产KPC-2的CRE。这一发现的影响是沙特阿拉伯公共卫生的主要关注点，因为它是宗教的中心，世界各地的朝圣者不断涌入。我们的研究强烈强调了在临床微生物学中实施基于快速测序的技术对于精确分类学分类和监测抗菌素耐药性模式的重要性。