Genomic insights and antimicrobial resistance profiles of CRKP and non-CRKP isolates in a Beijing geriatric medical center: emphasizing the blaKPC-2 carrying high-risk clones and their spread

Xin Ge; Yu Zhou; Hang Jin; Kangkang Liu; Kunpeng Zhu; Yulong Yu; Jingzhuang Xue; Qi Wang; Xinying Du; Hui Wang; Ying Xiang; Wenjun Li; Sai Tian; Zhongqiang Yan; Shaofu Qiu

doi:10.3389/fmicb.2024.1359340

Genomic insights and antimicrobial resistance profiles of CRKP and non-CRKP isolates in a Beijing geriatric medical center: emphasizing the bla_KPC-2 carrying high-risk clones and their spread

Front Microbiol. 2024 Feb 13:15:1359340. doi: 10.3389/fmicb.2024.1359340. eCollection 2024.

Authors

Xin Ge^#^{1

2}, Yu Zhou^#³, Hang Jin^{2

4}, Kangkang Liu⁵, Kunpeng Zhu⁶, Yulong Yu^{2

4}, Jingzhuang Xue⁷, Qi Wang², Xinying Du², Hui Wang², Ying Xiang², Wenjun Li², Sai Tian², Zhongqiang Yan⁸, Shaofu Qiu^{1

2}

Affiliations

¹ Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.
² The Chinese PLA Center for Disease Control and Prevention, Beijing, China.
³ Department of Laboratory Medicine, The Second Medical Center of PLA General Hospital, Beijing, China.
⁴ School of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
⁵ Academy of Military Medical Sciences, Beijing, China.
⁶ Kaifeng Center for Disease Control and Prevention, Kaifeng, Henan, China.
⁷ Beijing University of Chemical Technology, Beijing, China.
⁸ Department of Disease Prevention and Control, The Second Medical Center of PLA General Hospital, Beijing, China.

^# Contributed equally.

Abstract

Background: The escalating resistance of Klebsiella pneumoniae, a prevalent pathogen in healthcare settings, especially its carbapenem-resistant K. pneumoniae (CRKP), to a wide array of antibiotics, notably β-lactams, constitutes a formidable challenge for healthcare and global public health management.

Methods: This research compared the resistance phenotypes and genomic profiles of CRKP and Non-CRKP isolates in a Beijing hospital, focusing on high-risk bla_KPC-2 gene-bearing CRKP clones and the structure of mobile genetic elements facilitating their spread across hospital departments. Forty K. pneumoniae isolates were collected from various departments of the hospital and subjected to antimicrobial susceptibility testing and whole-genome sequencing to analyze their resistance phenotypes and genomic features.

Results: The study revealed that among the 31 CRKP isolates, ST11 is the most common sequence type, with K47 and OL101 being the dominant capsule types, primarily observed in the respiratory department. In terms of antimicrobial susceptibility: 87.5% of the isolates exhibited multidrug resistance (MDR), with a high resistance rate of 30% against tigecycline. All CRKP isolates demonstrated resistance to multiple drug classes (≥5 CLSI classes). Non-CRKP isolates also showed high resistance rates to minocycline and doxycycline (77.8%). the ST11-KL47-OL101 type emerged as the predominant clone among the CRKP isolates carrying the bla_KPC-2 gene. This dominance appears to be mediated by the pKpnR03_2 plasmid, which harbors not only bla_KPC-2 and rmtb but also gene clusters pertinent to iron transport and arsenic resistance. These isolates, clustering in the C3 clade of the phylogenetic tree, exhibited minor genetic variations and close evolutionary relationships, suggesting a plasmid-driven spread across various hospital departments.

Conclusion: In summary, our study highlights the extensive spread of antibiotic-resistant K. pneumoniae across various departments in our hospital, with a particular emphasis on the dominant clonal proliferation of the ST11-KL47-OL101 CRKP strain. This finding underscores the significant role of plasmid-mediated gene transfer in the evolution and dissemination of resistant strains within hospital environments. The study emphasizes the necessity for ongoing surveillance of antibiotic resistance and genomic analysis in hospital settings to effectively monitor and manage these challenges.

Keywords: CRKP; ST11-KL47-OL101; blaKPC-2; drug resistance; non-CRKP; plasmid horizontal transfer.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Nature Science Foundation of China (Nos. 82173580 and 32141003).