Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings
Abstract Background Ongoing studies have revealed the global prevalence of severe infections caused by the hypervirulent strains of Klebsiella pneumoniae (K. pneumoniae). Meanwhile, the World Health Organization and the Centers for Disease Control declared carbapenem-resistant K. pneumoniae as an ur...
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2024-10-01
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| Online Access: | https://doi.org/10.1186/s12879-024-10056-1 |
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| author | Nehal Adel Abdelsalam Shahira A. ElBanna Shaimaa F. Mouftah José F. Cobo-Díaz Ahmed H. Shata Sherine M. Shawky Reham Atteya Mohamed Elhadidy |
| author_facet | Nehal Adel Abdelsalam Shahira A. ElBanna Shaimaa F. Mouftah José F. Cobo-Díaz Ahmed H. Shata Sherine M. Shawky Reham Atteya Mohamed Elhadidy |
| author_sort | Nehal Adel Abdelsalam |
| collection | DOAJ |
| description | Abstract Background Ongoing studies have revealed the global prevalence of severe infections caused by the hypervirulent strains of Klebsiella pneumoniae (K. pneumoniae). Meanwhile, the World Health Organization and the Centers for Disease Control declared carbapenem-resistant K. pneumoniae as an urgent public health threat, requiring swift and effective action to mitigate its spread. Low- and middle-income countries are severely impacted by such devastating infectious diseases owing to the ill implementation of antimicrobial practices and infection control policies. Having both hypervirulence and carbapenemase gene determinants, the emergence of convergent hypervirulent carbapenem-resistant K. pneumoniae is now being reported worldwide. Methods In this study, we sequenced 19 carbapenemase-producing K. pneumoniae strains recovered from various clinical specimens. Additionally, we evaluated the phenotypic antimicrobial susceptibility to multiple antimicrobial classes using the VITEK2 automated system. Utilizing the sequencing data, we characterized the sequence types, serotypes, pangenome, resistance profiles, virulence profiles, and mobile genetic elements of the examined isolates. We highlighted the emergence of high-risk clones carrying hypervirulence genetic determinants among the screened isolates. Results Our findings revealed that all carbapenem-resistant isolates exhibited either extensive- or pan-drug resistance and harbored multiple variants of resistance genes spanning nearly all the antimicrobial classes. The most prevalent carbapenemase genes detected within the isolates were bla NDM−5 and bla OXA−48 . We identified high-risk clones, such as ST383-K30, ST147-K64, ST11-K15, and ST14-K2, which may have evolved into putative convergent strains by acquiring the full set of hypervirulence-associated genetic determinants (iucABCD, rmpA and/ or rmpA2, putative transporter peg-344). Additionally, this study identified ST709-K9 as a high-risk clone for the first time and uncovered that capsule types K15 and K9 carried hypervirulence genetic determinants. The most frequent Inc types found in these isolates were Col440I, IncHI1B, and Inc FII(K). Conclusion This study highlights the emergence of high-risk, extensively carbapenem-resistant K. pneumoniae strains co-carrying hypervirulence determinants in Egyptian clinical settings. This poses an imminent threat not only to Egypt but also to the global community, underscoring the urgent need for enhanced surveillance and control strategies to combat this pathogen. |
| format | Article |
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| institution | DOAJ |
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| language | English |
| publishDate | 2024-10-01 |
| publisher | BMC |
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| spelling | doaj-art-e6ece4ecdf1d45c29d417efcc326eccb2025-08-20T02:50:03ZengBMCBMC Infectious Diseases1471-23342024-10-0124111310.1186/s12879-024-10056-1Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settingsNehal Adel Abdelsalam0Shahira A. ElBanna1Shaimaa F. Mouftah2José F. Cobo-Díaz3Ahmed H. Shata4Sherine M. Shawky5Reham Atteya6Mohamed Elhadidy7Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and TechnologyDepartment of Microbiology and Immunology, Faculty of Pharmacy, Cairo UniversityCenter for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and TechnologyDepartment of Food Hygiene and Technology, Institute of Food Science and Technology, Universidad de LeónCenter for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and TechnologyDepartment of Microbiology, Medical Research Institute, Alexandria UniversityCenter for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and TechnologyCenter for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and TechnologyAbstract Background Ongoing studies have revealed the global prevalence of severe infections caused by the hypervirulent strains of Klebsiella pneumoniae (K. pneumoniae). Meanwhile, the World Health Organization and the Centers for Disease Control declared carbapenem-resistant K. pneumoniae as an urgent public health threat, requiring swift and effective action to mitigate its spread. Low- and middle-income countries are severely impacted by such devastating infectious diseases owing to the ill implementation of antimicrobial practices and infection control policies. Having both hypervirulence and carbapenemase gene determinants, the emergence of convergent hypervirulent carbapenem-resistant K. pneumoniae is now being reported worldwide. Methods In this study, we sequenced 19 carbapenemase-producing K. pneumoniae strains recovered from various clinical specimens. Additionally, we evaluated the phenotypic antimicrobial susceptibility to multiple antimicrobial classes using the VITEK2 automated system. Utilizing the sequencing data, we characterized the sequence types, serotypes, pangenome, resistance profiles, virulence profiles, and mobile genetic elements of the examined isolates. We highlighted the emergence of high-risk clones carrying hypervirulence genetic determinants among the screened isolates. Results Our findings revealed that all carbapenem-resistant isolates exhibited either extensive- or pan-drug resistance and harbored multiple variants of resistance genes spanning nearly all the antimicrobial classes. The most prevalent carbapenemase genes detected within the isolates were bla NDM−5 and bla OXA−48 . We identified high-risk clones, such as ST383-K30, ST147-K64, ST11-K15, and ST14-K2, which may have evolved into putative convergent strains by acquiring the full set of hypervirulence-associated genetic determinants (iucABCD, rmpA and/ or rmpA2, putative transporter peg-344). Additionally, this study identified ST709-K9 as a high-risk clone for the first time and uncovered that capsule types K15 and K9 carried hypervirulence genetic determinants. The most frequent Inc types found in these isolates were Col440I, IncHI1B, and Inc FII(K). Conclusion This study highlights the emergence of high-risk, extensively carbapenem-resistant K. pneumoniae strains co-carrying hypervirulence determinants in Egyptian clinical settings. This poses an imminent threat not only to Egypt but also to the global community, underscoring the urgent need for enhanced surveillance and control strategies to combat this pathogen.https://doi.org/10.1186/s12879-024-10056-1Klebsiella pneumoniaeConvergenceESBLCarbapenemHypervirulence genetic determinantsExtensive-drug resistance |
| spellingShingle | Nehal Adel Abdelsalam Shahira A. ElBanna Shaimaa F. Mouftah José F. Cobo-Díaz Ahmed H. Shata Sherine M. Shawky Reham Atteya Mohamed Elhadidy Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings BMC Infectious Diseases Klebsiella pneumoniae Convergence ESBL Carbapenem Hypervirulence genetic determinants Extensive-drug resistance |
| title | Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings |
| title_full | Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings |
| title_fullStr | Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings |
| title_full_unstemmed | Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings |
| title_short | Genomic dynamics of high-risk carbapenem-resistant Klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings |
| title_sort | genomic dynamics of high risk carbapenem resistant klebsiella pneumoniae clones carrying hypervirulence determinants in egyptian clinical settings |
| topic | Klebsiella pneumoniae Convergence ESBL Carbapenem Hypervirulence genetic determinants Extensive-drug resistance |
| url | https://doi.org/10.1186/s12879-024-10056-1 |
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