Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam

Quynh Nguyen, Yen Thi Phuong Nguyen, Tuyen Thanh Ha, Dung Thi Ngoc Tran, Phat Vinh Voong, Vinh Chau, Phuong Luong Nha Nguyen, Ngan Thi Quynh Le, Lan Phu Huong Nguyen, To Thi Nguyen Nguyen, Tan Van Trinh, Juan J. Carrique-Mas, Stephen Baker, Guy Thwaites, Maia A. Rabaa, Marc Choisy, Hao The Chung and Duy Thanh Pham ()
Additional contact information
Quynh Nguyen: Oxford University Clinical Research Unit
Yen Thi Phuong Nguyen: Oxford University Clinical Research Unit
Tuyen Thanh Ha: Oxford University Clinical Research Unit
Dung Thi Ngoc Tran: Oxford University Clinical Research Unit
Phat Vinh Voong: Oxford University Clinical Research Unit
Vinh Chau: Oxford University Clinical Research Unit
Phuong Luong Nha Nguyen: Hospital for Tropical Diseases
Ngan Thi Quynh Le: Hospital for Tropical Diseases
Lan Phu Huong Nguyen: Hospital for Tropical Diseases
To Thi Nguyen Nguyen: Oxford University Clinical Research Unit
Tan Van Trinh: Oxford University Clinical Research Unit
Juan J. Carrique-Mas: Oxford University Clinical Research Unit
Stephen Baker: University of Cambridge
Guy Thwaites: Oxford University Clinical Research Unit
Maia A. Rabaa: Oxford University Clinical Research Unit
Marc Choisy: Oxford University Clinical Research Unit
Hao The Chung: Oxford University Clinical Research Unit
Duy Thanh Pham: Oxford University Clinical Research Unit

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.

Date: 2024
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DOI: 10.1038/s41467-024-48206-3

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