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Jiang J, Wang L, Hu Y, Chen X, Li P, Zhang J, Zhang Y, Su J, Xu X, Xiao Y, Liu Z, Yu Y, Gao H, Doi Y, van Duin D, Fowler VG, Chen L, Wang M. Global emergence of Carbapenem-resistant Hypervirulent Klebsiella pneumoniae driven by an IncFII K34 KPC-2 plasmid. EBioMedicine 2025; 113:105627. [PMID: 40024096 PMCID: PMC11919442 DOI: 10.1016/j.ebiom.2025.105627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 02/14/2025] [Accepted: 02/16/2025] [Indexed: 03/04/2025] Open
Abstract
BACKGROUND Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) has been increasingly reported worldwide, posing a severe challenge to public health; however, the mechanisms driving its emergence and global dissemination remain unclear. METHODS We analysed CR-hvKp strains derived from canonical hvKp backgrounds, and acquired a carbapenemase-encoding gene. These strains were identified from 485 CRKp isolates in the CRACKLE-2 China cohort, 259 CRKp isolates from a multi-centre study, and 67,631 K. pneumoniae genomes available in GenBank. Clinical isolates harbouring the IncFIIK34 KPC-2 plasmid were selected for genome sequencing, RNA-Seq, conjugation assays, in vivo, ex vivo, and in vitro phenotypic characterisation. FINDINGS Analysis of clinical CR-hvKp isolates and the 414 genomes from 24 countries available in GenBank identified an IncFIIK34 KPC-2 plasmid as the prevalent KPC plasmid (detected in 25%, 45/178 of KPC-producing CR-hvKp). Compared with the epidemic IncFIIK2 KPC-2 plasmid, the IncFIIK34 KPC-2 plasmid exhibited a 100- to 1000-fold increase in conjugation frequency (10-4-10-5 vs. 10-7) and an in vitro growth advantage under meropenem challenge-likely due to the overexpression of conjugation-related genes and an increased blaKPC copy number and expression. CR-hvKp isolates and hvKp transconjugants carrying this plasmid often exhibited reduced mucoviscosity, while retaining hypervirulence in both murine models and human neutrophil assays. INTERPRETATION The IncFIIK34 plasmid may be a key factor driving the global dissemination of CR-hvKp, underscoring the urgent need for enhanced molecular surveillance of this emerging pathogen. FUNDING National Natural Science Foundation of China and National Institutes of Health.
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Affiliation(s)
- Jianping Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China; Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Yiyi Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Jianfeng Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Yixin Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Jiachun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, China
| | - Zhengyin Liu
- Infectious Disease Section, Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hainv Gao
- Department of Infectious Diseases, Key Laboratory of Artificial Organs and Computational Medicine of Zhejiang Province, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA; Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, and Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China.
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Li X, Chen S, Lu Y, Shen W, Wang W, Gao J, Gao J, Shao P, Zhou Z. Molecular epidemiology and genetic dynamics of carbapenem-resistant hypervirulent Klebsiella pneumoniae in China. Front Cell Infect Microbiol 2025; 15:1529929. [PMID: 40028179 PMCID: PMC11868059 DOI: 10.3389/fcimb.2025.1529929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 01/31/2025] [Indexed: 03/05/2025] Open
Abstract
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CRhvKP) poses a significant global health threat due to its enhanced virulence and resistance. This study analyzed 5,036 publicly available K. pneumoniae genomes from China (2005-2023), identifying 1,538 CRhvKP genomes, accounting for 44.6% of carbapenem-resistant isolates and 69.5% of hypervirulent isolates. Predominant carbapenemases included bla KPC (92.1%), with an increasing prevalence of bla NDM and bla OXA-48-like genes. Most isolates (93.6%) carried both aerobactin and yersiniabactin genes. The genetic background showed high diversity, characterized by 36 sequence types (STs) and 22 capsule types, with high-risk endemic STs such as ST11, ST15, and ST23 being predominant. ST23 demonstrated enhanced virulence, whereas ST11 carried more resistance genes but showed minimal presence of iroBCDN genes. A core genome MLST analysis revealed that 89.0% of CRhvKP isolates clustered into 131 clonal groups, indicating widespread dissemination, particularly in eastern China. CR and hv plasmids, primarily IncF, IncH, and IncR types, showed distinct community structures, with CR plasmids demonstrating higher mobility and diversity. Crucially, we identified 40 CR-hv convergent plasmids across five STs, likely resulting from plasmid fusions, which have become increasingly prevalent in eastern China over the last decade. Furthermore, chromosomal integration of hv genes and bla KPC-2 was detected, underscoring the stable inheritance of these traits. Class 1 Integrons were present in 84.5% of CRhvKP strains, most notably in ST11 and least in ST23. These integrons harbored genes that confer resistance to various antibiotics, including bla IMP and bla VIM, with their content varying across different STs. This study highlights the genetic complexity, rapid dissemination, and increasing prevalence of CRhvKP in China, emphasizing the urgent need for enhanced genomic surveillance and targeted interventions to mitigate the threat posed by these multidrug-resistant and hypervirulent strains.
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Affiliation(s)
- Xiangchen Li
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Sisi Chen
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Yewei Lu
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Weifeng Shen
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Department of Clinical Laboratory, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Weixin Wang
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Junli Gao
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Junshun Gao
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, Hangzhou, Zhejiang, China
| | - Pingyang Shao
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
- Department of Clinical Laboratory, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Zhuxian Zhou
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
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3
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García-Cobos S, Oteo-Iglesias J, Pérez-Vázquez M. Hypervirulent Klebsiella pneumoniae: Epidemiology outside Asian countries, antibiotic resistance association, methods of detection and clinical management. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2025; 43:102-109. [PMID: 39914938 DOI: 10.1016/j.eimce.2024.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 12/23/2024] [Indexed: 05/07/2025]
Abstract
Two main Klebsiella pneumoniae pathotypes are of public health concern, classical K. pneumoniae (cKP), with high antibiotic resistance acquisition capacity, and hypervirulent K. pneumoniae (hvKP). The emergence of hypervirulent and antibiotic-resistant K. pneumoniae, especially carbapenem resistance, is worrisome and require effective methods for detection and treatment. Different evolutionary paths contribute to the emergence of hypervirulence and antibiotic resistance, commonly via the acquisition of resistance plasmids by hvKP (CR-hvKP) or the acquisition of virulence plasmids by CRKp (hv-CRKp). ST11-KL64 together with blaKPC-2, is the most extended hv-CRKP lineage acquiring virulence plasmids with associated biomarkers, rmpA, rmpa2, iroBCDEN, iucABCDiutA, and peg344. In addition to ST11, other hv-CRKP clones have been reported in Europe such as ST101, ST147 and ST512, highlighting the association of ST147 with OXA-48 and NDM carbapenemases. Although still very rare in Spain, hvKP cases are increasing in recent years, mainly due to ST23-K1, ST380-K2 and ST86-K2. Management of hvKP infections requires active antibiotic therapy based primarily on antibiotic susceptibility patters and site of infection.
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Affiliation(s)
- Silvia García-Cobos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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4
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Gomez-Simmonds A, Annavajhala MK, Seeram D, Hokunson TW, Park H, Uhlemann AC. Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla KPC. Genome Res 2024; 34:1895-1907. [PMID: 39366703 PMCID: PMC11610580 DOI: 10.1101/gr.279355.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024]
Abstract
Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of bla KPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 bla KPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized bla KPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding bla KPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of bla KPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading bla KPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of bla KPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.
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Affiliation(s)
- Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Dwayne Seeram
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Todd W Hokunson
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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5
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Gálvez-Silva M, Arros P, Berríos-Pastén C, Villamil A, Rodas PI, Araya I, Iglesias R, Araya P, Hormazábal JC, Bohle C, Chen Y, Gan YH, Chávez FP, Lagos R, Marcoleta AE. Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile. Biol Res 2024; 57:7. [PMID: 38475927 DOI: 10.1186/s40659-024-00485-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The convergence of hypervirulence and carbapenem resistance in the bacterial pathogen Klebsiella pneumoniae represents a critical global health concern. Hypervirulent K. pneumoniae (hvKp) strains, frequently from sequence type 23 (ST23) and having a K1 capsule, have been associated with severe community-acquired invasive infections. Although hvKp were initially restricted to Southeast Asia and primarily antibiotic-sensitive, carbapenem-resistant hvKp infections are reported worldwide. Here, within the carbapenemase production Enterobacterales surveillance system headed by the Chilean Public Health Institute, we describe the isolation in Chile of a high-risk ST23 dual-carbapenemase-producing hvKp strain, which carbapenemase genes are encoded in a single conjugative plasmid. RESULTS Phenotypic and molecular tests of this strain revealed an extensive resistance to at least 15 antibiotic classes and the production of KPC-2 and VIM-1 carbapenemases. Unexpectedly, this isolate lacked hypermucoviscosity, challenging this commonly used hvKp identification criteria. Complete genome sequencing and analysis confirmed the K1 capsular type, the KpVP-1 virulence plasmid, and the GIE492 and ICEKp10 genomic islands carrying virulence factors strongly associated with hvKp. Although this isolate belonged to the globally disseminated hvKp clonal group CG23-I, it is unique, as it formed a clade apart from a previously reported Chilean ST23 hvKp isolate and acquired an IncN KPC-2 plasmid highly disseminated in South America (absent in other hvKp genomes), but now including a class-I integron carrying blaVIM-1 and other resistance genes. Notably, this isolate was able to conjugate the double carbapenemase plasmid to an E. coli recipient, conferring resistance to 1st -5th generation cephalosporins (including combinations with beta-lactamase inhibitors), penicillins, monobactams, and carbapenems. CONCLUSIONS We reported the isolation in Chile of high-risk carbapenem-resistant hvKp carrying a highly transmissible conjugative plasmid encoding KPC-2 and VIM-1 carbapenemases, conferring resistance to most beta-lactams. Furthermore, the lack of hypermucoviscosity argues against this trait as a reliable hvKp marker. These findings highlight the rapid evolution towards multi-drug resistance of hvKp in Chile and globally, as well as the importance of conjugative plasmids and other mobile genetic elements in this convergence. In this regard, genomic approaches provide valuable support to monitor and obtain essential information on these priority pathogens and mobile elements.
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Affiliation(s)
- Matías Gálvez-Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Aura Villamil
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Paula I Rodas
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Ingrid Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Rodrigo Iglesias
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Pamela Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | | | | | - Yahua Chen
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Yunn-Hwen Gan
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile.
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6
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Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
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7
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López-Cubillos JF, Díaz A, Cárdenas VC, Camacho-Moreno G, Cantor E, Arcila EM, Hurtado IC, Correa AM, Tierradentro TM, Ramirez O, Portilla CA, Aponte-Barrios N, López P, Torres D, Bustos-Paz M, Bravo AM, Escobar JJ, Calle JP, Dávalos DM, López-Medina E. Carbapenem resistance in Enterobacterales bloodstream infections among children with cancer or post-haematopoietic stem cell transplant: a retrospective cohort study. J Antimicrob Chemother 2023; 78:2462-2470. [PMID: 37583091 PMCID: PMC10545507 DOI: 10.1093/jac/dkad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Risk factors for carbapenem resistance in Enterobacterales bloodstream infections among children with cancer or post-HSCT have not been thoroughly explored. METHODS All children with cancer or post-HSCT who developed Enterobacterales bloodstream infections in two cancer referral centres in major Colombian cities between 2012 and 2021 were retrospectively examined. When the infection episode occurred, carbapenem resistance mechanisms were evaluated according to the available methods. Data were divided in a training set (80%) and a test set (20%). Three internally validated carbapenem-resistant Enterobacterales (CRE) prediction models were created: a multivariate logistic regression model, and two data mining techniques. Model performances were evaluated by calculating the average of the AUC, sensitivity, specificity and predictive values. RESULTS A total of 285 Enterobacterales bloodstream infection episodes (229 carbapenem susceptible and 56 carbapenem resistant) occurred [median (IQR) age, 9 (3.5-14) years; 57% male]. The risk of CRE was 2.1 times higher when the infection was caused by Klebsiella spp. and 5.8 times higher when a carbapenem had been used for ≥3 days in the previous month. A model including these two predictive variables had a discriminatory performance of 77% in predicting carbapenem resistance. The model had a specificity of 97% and a negative predictive value of 81%, with low sensitivity and positive predictive value. CONCLUSIONS Even in settings with high CRE prevalence, these two variables can help early identification of patients in whom CRE-active agents are unnecessary and highlight the importance of strengthening antibiotic stewardship strategies directed at preventing carbapenem overuse.
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Affiliation(s)
| | - Alejandro Díaz
- Hospital General de Medellín & Hospital Pablo Tobón Uribe, Medellín, Colombia
| | - Vicky C Cárdenas
- Department of Pediatrics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - German Camacho-Moreno
- HOMI, Fundación Hospital Pediátrico la Misericordia, Bogotá, Colombia
- Department of Pediatrics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Erika Cantor
- Centro de Estudios en Infectología Pediátrica, CEIP, Cali, Colombia
- Department of Clinical Epidemiology and Biostatistics, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Eliana M Arcila
- Department of Pediatrics, Corporación Universitaria Remington, Medellín, Colombia
| | - Isabel C Hurtado
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
- State Department of Health, Valle del Cauca, Colombia
| | - Adriana M Correa
- Clínica Imbanaco Grupo Quironsalud, Cali, Colombia
- Faculty of Basic Sciences, Universidad Santiago de Cali, Cali, Colombia
| | | | - Oscar Ramirez
- Clínica Imbanaco Grupo Quironsalud, Cali, Colombia
- Registro Poblacional de Cáncer de Cali, Cali, Colombia
| | - Carlos A Portilla
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
- Clínica Imbanaco Grupo Quironsalud, Cali, Colombia
| | | | - Pio López
- Centro de Estudios en Infectología Pediátrica, CEIP, Cali, Colombia
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
| | - Daniela Torres
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
| | | | - Ana M Bravo
- Department of Pediatrics, Universidad del Cauca, Popayán, Colombia
- Hospital Universitario San José, Popayán, Colombia
- Clínica Nueva, Cali, Colombia
| | | | - Juan P Calle
- Centro de Estudios en Infectología Pediátrica, CEIP, Cali, Colombia
- Departament of Pediatrics, Universidad del Quindío, Armenia, Colombia
| | - Diana M Dávalos
- Centro de Estudios en Infectología Pediátrica, CEIP, Cali, Colombia
| | - Eduardo López-Medina
- Centro de Estudios en Infectología Pediátrica, CEIP, Cali, Colombia
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
- Clínica Imbanaco Grupo Quironsalud, Cali, Colombia
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8
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Chen Y, Yong M, Li M, Si Z, Koh CH, Lau P, Chang YW, Teo J, Chan-Park MB, Gan YH. A hydrophilic polyimidazolium antibiotic targeting the membranes of Gram-negative bacteria. J Antimicrob Chemother 2023; 78:2581-2590. [PMID: 37671807 PMCID: PMC10545527 DOI: 10.1093/jac/dkad274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
OBJECTIVES The rise of MDR Gram-negative bacteria (GNB), especially those resistant to last-resort drugs such as carbapenems and colistin, is a global health risk and calls for increased efforts to discover new antimicrobial compounds. We previously reported that polyimidazolium (PIM) compounds exhibited significant antimicrobial activity and minimal mammalian cytotoxicity. However, their mechanism of action is relatively unknown. We examined the efficacy and mechanism of action of a hydrophilic PIM (PIM5) against colistin- and meropenem-resistant clinical isolates. METHODS MIC and time-kill testing was performed for drug-resistant Escherichia coli and Klebsiella pneumoniae clinical isolates. N-phenyl-1-naphthylamine and propidium iodide dyes were employed to determine membrane permeabilization. Spontaneous resistant mutants and single deletion mutants were generated to understand potential resistance mechanisms to the drug. RESULTS PIM5 had the same effectiveness against colistin- and meropenem-resistant strains as susceptible strains of GNB. PIM5 exhibited a rapid bactericidal effect independent of bacterial growth phase and was especially effective in water. The polymer disrupts both the outer and cytoplasmic membranes. PIM5 binds and intercalates into bacterial genomic DNA upon entry of cells. GNB do not develop high resistance to PIM5. However, the susceptibility and uptake of the polymer is moderately affected by mutations in the two-component histidine kinase sensor BaeS. PIM5 has negligible cytotoxicity on human cells at bacterial-killing concentrations, comparable to the commercial antibiotics polymyxin B and colistin. CONCLUSIONS PIM5 is a potent broad-spectrum antibiotic targeting GNB resistant to last-resort antibiotics.
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Affiliation(s)
- Yahua Chen
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Melvin Yong
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Ming Li
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Zhangyong Si
- School of Chemistry, Chemical and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Chong Hui Koh
- School of Chemistry, Chemical and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Pearlyn Lau
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Yi Wei Chang
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeanette Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Mary B Chan-Park
- School of Chemistry, Chemical and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yunn-Hwen Gan
- Infectious Diseases Translational Research Programme, Department of Biochemistry, National University of Singapore, Singapore, Singapore
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9
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Zhu J, Ju Y, Zhou X, Chen T, Zhuge X, Dai J. Epidemiological characteristics of SHV, cmlv, and FosA6-producing carbapenem-resistant Klebsiella pneumoniae based on whole genome sequences in Jiangsu, China. Front Microbiol 2023; 14:1219733. [PMID: 37538843 PMCID: PMC10394843 DOI: 10.3389/fmicb.2023.1219733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), particularly those with high virulence, cause invasive disease in clinical settings. An epidemiological investigation was conducted on the evolution, virulence, and antimicrobial resistance of CRKP isolates in two tertiary teaching hospitals in Jiangsu, China from November 2020 to December 2021. There were 31 different CRKP strains discovered. We performed whole genome sequencing (WGS) on 13 SHV, cmlv, and FosA6-producing CRKP to reveal molecular characteristics. Five ST15/ST11 isolates had CRISPR-Cas systems. By conjugation tests, KPC-2 can be transmitted horizontally to E. coil. A conjugative pHN7A8-related multi-resistance plasmid (KPC-2, blaCTX-M-65, blaTEM-1, fosA3, catII, and rmtB) was first discovered in CRKP clinical isolates. Using bacteriological testing, a serum killing assay, and an infection model with Galleria mellonella, three ST11-K64 KPC-2 generating carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) were identified. These strains harbored a virulent plasmid and an IncFII-family pKPC/pHN7A8 conjugative plasmid, which led to hypervirulence and resistance. One of these CR-hvKPs, which co-harbored KPC-2, NDM-6, SHV-182, SHV-64, and blaCTX-M-122 genes, was first discovered. Importantly, this CR-hvKP strain also produced biofilm and had non-inferior fitness. The widespread use of ceftazidime/avibactam might provide this CR-hvKP with a selective advantage; hence, immediate action is required to stop its dissemination. Another important finding is the novel ST6136 in K. pneumoniae. Finally, the sterilization efficiency rates of Fe2C nanoparticles in CRKP were more than 98%. Furthermore, our novel antibacterial Fe2C nanoparticles may also provide a therapeutic strategy for infections.
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Affiliation(s)
- Jiaying Zhu
- College of Pharmacy, China Pharmaceutical University, Nanjing, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yanmin Ju
- College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xinyu Zhou
- College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Taoyu Chen
- Department of Orthopedics, The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xiangkai Zhuge
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Jianjun Dai
- College of Pharmacy, China Pharmaceutical University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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10
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Spadar A, Perdigão J, Campino S, Clark TG. Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. Genome Med 2023; 15:3. [PMID: 36658655 PMCID: PMC9850321 DOI: 10.1186/s13073-023-01153-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae (Kp) Gram-negative bacteria cause nosocomial infections and rapidly acquire antimicrobial resistance (AMR), which makes it a global threat to human health. It also has a comparatively rare hypervirulent phenotype that can lead to severe disease in otherwise healthy individuals. Unlike classic Kp, canonical hypervirulent strains usually have limited AMR. However, after initial case reports in 2015, carbapenem-resistant hypervirulent Kp has increased in prevalence, including in China, but there is limited understanding of its burden in other geographical regions. METHODS Here, we examined the largest collection of publicly available sequenced Kp isolates (n=13,178), containing 1603 different sequence types (e.g. ST11 15.0%, ST258 9.5%), and 2174 (16.5%) hypervirulent strains. We analysed the plasmid replicons and carbapenemase and siderophore encoding genes to understand the movement of hypervirulence and AMR genes located on plasmids, and their convergence in carbapenem-resistant hypervirulent Kp. RESULTS We identified and analysed 3034 unique plasmid replicons to inform the epidemiology and transmission dynamics of carbapenem-resistant hypervirulent Kp (n=1028, 7.8%). We found several outbreaks globally, including one involving ST11 strains in China and another of ST231 in Asia centred on India, Thailand, and Pakistan. There was evidence of global flow of Kp, including across multiple continents. In most cases, clusters of Kp isolates are the result of hypervirulence genes entering classic strains, instead of carbapenem resistance genes entering canonical hypervirulent ones. CONCLUSIONS Our analysis demonstrates the importance of plasmid analysis in the monitoring of carbapenem-resistant and hypervirulent strains of Kp. With the growing adoption of omics-based technologies for clinical and surveillance applications, including in geographical regions with gaps in data and knowledge (e.g. sub-Saharan Africa), the identification of the spread of AMR will inform infection control globally.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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