Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring blaNDM and blaOXA-48 recovered from Saudi Arabia.

BACKGROUND: This study presents a comprehensive genomic analysis of NDM and OXA-48-producing Klebsiella pneumoniae in the Western region of Saudi Arabia, traversed by tens of millions of Muslims from various countries annually. This significant influx of visitors invariably leads to the spread and diversity of MDR bacteria. METHODS: Genome sequencing was performed using MiSeq system of 29 CPKP isolates that were NDM and OXA-48-positive isolated from nosocomial infections and demonstrated resistance to most antibiotics, including carbapenems. RESULTS: WGS analysis showed that 12 (41.3%) isolates co-harbored blaOXA-48,blaCTX-M-15 and blaNDM genes. Notably, 16 (55.1%) isolates were identified as high-risk clone ST14, with 50% of these isolates co-harbored blaOXA-48, blaNDM and blaCTX-M-15 genes. All ST14 isolates were identified as capsular genotype KL2 and O1/O2v1 antigen with yersiniabactin locus ypt 14 carried by ICEKp5. The two isolates were identified as ST2096/KL64 hypervirulent K. pneumoniae (hvKp) clone harboring several virulence factors, including the regulator of the mucoid phenotype rmpA2 and aerobactin (iuc-1). Interestingly, two of the hvKp ST383/KL30 isolates were resistant to all tested antimicrobials except colistin and tigecycline, and simultaneously carried numerous ESBLs and carbapenemase genes. These isolates also harbor several virulence factors such as rmpA1, rmpA2, carried on KpVP-1, and aerobactin (iuc-1). CONCLUSION: this study provides insights into the spread and prevalence of high-risk clones of CPKP in the Western region of Saudi Arabia. The ST14 high-risk clone appears to be the predominant CPKP clone in this region, posing a significant threat to public health. This study also reports the presence of two globally disseminated hypervirulent K. pneumoniae (hvKp) clones, namely ST2096 and ST383. Therefore, it is essential to improve surveillance and implement strict infection control measures in this region, which receives a substantial number of visitors to effectively monitor and reduce the spread of high-risk clones of antimicrobial-resistant bacteria, including CPKP.

Prevalence and molecular determinants of carbapenemase-producing Klebsiella pneumoniae isolated from Jazan, Saudi Arabia.

INTRODUCTION: The World Health Organization (WHO) designated Carbapenem-resistant Enterobacterales (CRE), formerly Enterobacteriaceae, among the global priority list of antibiotic-resistant bacteria. The rate of CRE in Arabian countries, including Saudi Arabia has increased. Here, we report the prevalence of carbapenemase-producing Klebsiella pneumoniae (CPKP) in the Jazan region, a southern coastal province of Saudi Arabia. METHODOLOGY: Eighty-six non-repetitive clinical isolates of K. pneumoniae that showed resistance to at least one of the carbapenem drugs were collected from three tertiary hospitals in the Jazan region from March 2020 to April 2021. The identification and antimicrobial susceptibility testing (AST) of isolates were performed using various automated systems. Molecular detection of carbapenemase genes was conducted using a multiplex PCR. RESULTS: Out of the 86 tested CRKP isolates, 64 (74.4%) were carbapenemase-producing isolates. The blaOXA-48 gene was the most predominant carbapenemase gene, detected in 65.1% (n = 56) of isolates. The blaNDM gene was detected in only 9.3% (n = 8) of isolates; three were found to be co-harbored with blaVIM. Interestingly, one isolate of CRKP was found to have carbapenemase genes (blaNDM, blaVIM and blaKPC), which was associated with COVID-19 patient. CONCLUSIONS: The incidence of carbapenemase-producing K. pneumoniae in Jazan hospitals seemed to be high, confirming the continued prevalence of carbapenem resistance in Saudi Hospitals. We report K. pneumoniae strain with triple carbapenemase genes in southern Saudi Arabia. The emergence of such an isolate could threaten patients and healthcare workers and requires great attention to rapid interventions to avoid further dissemination, particularly during the COVID-19 pandemic.