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Abbas R, Chakkour M, Zein El Dine H, Obaseki EF, Obeid ST, Jezzini A, Ghssein G, Ezzeddine Z. General Overview of Klebsiella pneumonia: Epidemiology and the Role of Siderophores in Its Pathogenicity. Biology (Basel) 2024; 13:78. [PMID: 38392297 PMCID: PMC10886558 DOI: 10.3390/biology13020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024]
Abstract
The opportunistic pathogen Klebsiella pneumoniae (K. pneumoniae) can colonize mucosal surfaces and spread from mucosae to other tissues, causing fatal infections. Medical equipment and the healthcare setting can become colonized by Klebsiella species, which are widely distributed in nature and can be found in water, soil, and animals. Moreover, a substantial number of community-acquired illnesses are also caused by this organism worldwide. These infections are characterized by a high rate of morbidity and mortality as well as the capacity to spread metastatically. Hypervirulent Klebsiella strains are thought to be connected to these infections. Four components are critical to this bacterium's pathogenicity-the capsule, lipopolysaccharide, fimbriae, and siderophores. Siderophores are secondary metabolites that allow iron to sequester from the surrounding medium and transport it to the intracellular compartment of the bacteria. A number of variables may lead to K. pneumoniae colonization in a specific area. Risk factors for infection include local healthcare practices, antibiotic use and misuse, infection control procedures, nutrition, gender, and age.
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Affiliation(s)
- Rim Abbas
- Faculty of Health Sciences, Beirut Arab University, Beirut P.O. Box 11-5020, Lebanon
| | - Mohamed Chakkour
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Hiba Zein El Dine
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | | | - Soumaya T Obeid
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Aya Jezzini
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Ghassan Ghssein
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Zeinab Ezzeddine
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
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Ilyas M, Purkait D, Atmakuri K. Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. Brief Funct Genomics 2024; 23:55-68. [PMID: 36528816 DOI: 10.1093/bfgp/elac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.
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Affiliation(s)
- Mohd Ilyas
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Dyuti Purkait
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
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Baqer AA, Fang K, Mohd-Assaad N, Adnan SNA, Md Nor NS. In Vitro Activity, Stability and Molecular Characterization of Eight Potent Bacteriophages Infecting Carbapenem-Resistant Klebsiella pneumoniae. Viruses 2022; 15:117. [PMID: 36680156 PMCID: PMC9860934 DOI: 10.3390/v15010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment, including bacteriophage therapy. Bacteriophages are considered very safe and effective in treating bacterial infections. In this study, we characterize eight lytic bacteriophages that were previously isolated by our team against carbapenem-resistant Klebsiella pneumoniae. METHODS The one-step-growth curves, stability and lytic ability of eight bacteriophages were characterized. Restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD) typing analysis and protein profiling were used to characterize the microbes at the molecular level. Phylogenetic trees of four important proteins were constructed for the two selected bacteriophages. RESULTS AND CONCLUSIONS All eight bacteriophages showed high efficiency for reducing bacterial concentration with high stability under different physical and chemical conditions. We found four major protein bands out of at least ten 15-190 KDa bands that were clearly separated by SDS-PAGE, which were assumed to be the major head and tail proteins. The genomes were found to be dsDNA, with sizes of approximately 36-87 Kb. All bacteriophages reduced the optical density of the planktonic K. pneumoniae abruptly, indicating great potential to reduce K. pneumoniae infection. In this study, we have found that tail fiber protein can further distinguished closely related bacteriophages. The characterised bacteriophages showed promising potential as candidates against carbapenem-resistant Klebsiella pneumoniae via bacteriophage therapy.
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Affiliation(s)
- Abeer Ameen Baqer
- Medical Laboratory Techniques Department, Dijlah University College, Baghdad 10021, Iraq;
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
| | - Kokxin Fang
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
| | - Norfarhan Mohd-Assaad
- Department of Applied Physics, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
- Institute for Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia
| | - Siti Noor Adnalizawati Adnan
- Faculty of Dentistry, Universiti Sains Islam Malaysia, Level 15, Tower B, Persiaran MPAJ, Jalan Pandan Utama, Kuala Lumpur 55100, SGR, Malaysia;
| | - Norefrina Shafinaz Md Nor
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
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Huang M, He P, He P, Wu Y, Munir S, He Y. Novel Virulence Factors Deciphering Klebsiella pneumoniae KpC4 Infect Maize as a Crossing-Kingdom Pathogen: An Emerging Environmental Threat. Int J Mol Sci 2022; 23:ijms232416005. [PMID: 36555647 PMCID: PMC9785288 DOI: 10.3390/ijms232416005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Klebsiella pneumoniae is not only a human and animal opportunistic pathogen, but a food-borne pathogen. Cross-kingdom infection has been focused on since K. pneumoniae was identified as the pathogen of maize, banana, and pomegranate. Although the pathogenicity of K. pneumoniae strains (from ditch water, maize, and human) on plant and mice has been confirmed, there are no reports to explain the molecular mechanisms of the pathogen. This study uncovered the K. pneumoniae KpC4 isolated from maize top rot for the determination of various virulence genes and resistance genes. At least thirteen plant disease-causing genes are found to be involved in the disruption of plant defense. Among them, rcsB is responsible for causing disease in both plants and animals. The novel sequence types provide solid evidence that the pathogen invades plant and has robust ecological adaptability. It is imperative to perform further studies on the verification of these KpC4 genes’ functions to understand the molecular mechanisms involved in plant−pathogen interactions.
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Affiliation(s)
- Min Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- College of Agronomy and Life Sciences and Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province, Kunming University, Kunming 650214, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (S.M.); (Y.H.)
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Serral F, Pardo AM, Sosa E, Palomino MM, Nicolás MF, Turjanski AG, Ramos PIP, Fernández Do Porto D. Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. Front Cell Infect Microbiol 2022; 12:773405. [PMID: 35174104 PMCID: PMC8841789 DOI: 10.3389/fcimb.2022.773405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-KP) represents an emerging threat to public health. CR-KP infections result in elevated morbidity and mortality. This fact, coupled with their global dissemination and increasingly limited number of therapeutic options, highlights the urgency of novel antimicrobials. Innovative strategies linking genome-wide interrogation with multi-layered metabolic data integration can accelerate the early steps of drug development, particularly target selection. Using the BioCyc ontology, we generated and manually refined a metabolic network for a CR-KP, K. pneumoniae Kp13. Converted into a reaction graph, we conducted topological-based analyses in this network to prioritize pathways exhibiting druggable features and fragile metabolic points likely exploitable to develop novel antimicrobials. Our results point to the aptness of previously recognized pathways, such as lipopolysaccharide and peptidoglycan synthesis, and casts light on the possibility of targeting less explored cellular functions. These functions include the production of lipoate, trehalose, glycine betaine, and flavin, as well as the salvaging of methionine. Energy metabolism pathways emerged as attractive targets in the context of carbapenem exposure, targeted either alone or in conjunction with current therapeutic options. These results prompt further experimental investigation aimed at controlling this highly relevant pathogen.
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Affiliation(s)
- Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Agustin M. Pardo
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Ezequiel Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Mercedes Palomino
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Buenos Aires, Argentina
| | - Marisa F. Nicolás
- Laboratório de Bioinformática (LABINFO), Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Adrian G. Turjanski
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Buenos Aires, Argentina
| | - Pablo Ivan P. Ramos
- Centro de Integração de Dados e Conhecimentos para a Saúde (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz - Bahia), Salvador, Brazil
- *Correspondence: Darío Fernández Do Porto, ; Pablo Ivan P. Ramos,
| | - Darío Fernández Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Cdad. Universitaria, Buenos Aires, Argentina
- *Correspondence: Darío Fernández Do Porto, ; Pablo Ivan P. Ramos,
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Cesur MF, Siraj B, Uddin R, Durmuş S, Çakır T. Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale. Front Cell Infect Microbiol 2020; 9:447. [PMID: 31993376 PMCID: PMC6970976 DOI: 10.3389/fcimb.2019.00447] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 12/12/2019] [Indexed: 01/28/2023] Open
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen leading to life-threatening nosocomial infections. Emergence of highly resistant strains poses a major challenge in the management of the infections by healthcare-associated K. pneumoniae isolates. Thus, despite intensive efforts, the current treatment strategies remain insufficient to eradicate such infections. Failure of the conventional infection-prevention and treatment efforts explicitly indicates the requirement of new therapeutic approaches. This prompted us to systematically analyze the K. pneumoniae metabolism to investigate drug targets. Genome-scale metabolic networks (GMNs) facilitating the systematic analysis of the metabolism are promising platforms. Thus, we used a GMN of K. pneumoniae MGH 78578 to determine putative targets through gene- and metabolite-centric approaches. To develop more realistic infection models, we performed the bacterial growth simulations within different host-mimicking media, using an improved biomass formation reaction. We selected more suitable targets based on several property-based prioritization procedures. KdsA was identified as the high-ranked putative target satisfying most of the target prioritization criteria specified under the gene-centric approach. Through a structure-based virtual screening protocol, we identified potential KdsA inhibitors. In addition, the metabolite-centric approach extended the drug target list based on synthetic lethality. This revealed the importance of combined metabolic analyses for a better understanding of the metabolism. To our knowledge, this is the first comprehensive effort on the investigation of the K. pneumoniae metabolism for drug target prediction through the constraint-based analysis of its GMN in conjunction with several bioinformatic approaches. This study can guide the researchers for the future drug designs by providing initial findings regarding crucial components of the Klebsiella metabolism.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Bushra Siraj
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Turkey
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Volozhantsev NV, Shpirt AM, Kislichkina AA, Shashkov AS, Verevkin VV, Fursova NK, Knirel YA. Structure and gene cluster of the capsular polysaccharide of multidrug resistant carbapenemase OXA-48-producing Klebsiella pneumoniae strain KPB536 of the genetic line ST147. Res Microbiol 2019; 171:74-79. [PMID: 31606486 DOI: 10.1016/j.resmic.2019.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 01/09/2023]
Abstract
The Gram-negative opportunistic pathogen Klebsiella pneumoniae is a significant cause of community-acquired and healthcare-associated infections for which multidrug resistance is a concern worldwide. A major virulence determinant of K. pneumoniae is a polysaccharide capsule (CPS) which forms a barrier around the bacterial cell wall, providing protection from environmental pressures and immune responses of eukaryotic organisms. More than 70 chemical capsule structures of serologically typeable K. pneumoniae strains are known. However, there are little data on the CPS structure and cps gene cluster organization of clinical multidrug resistant K. pneumoniae strains. Our investigation of multidrug resistant carbapenemase OXA-48-producing K. pneumoniae strain KPB536 identified a capsular type that was structurally similar to K. pneumoniae K10 but different from any K. pneumoniae CPS reported so far. The content and organization of the cps gene cluster in K. pneumoniae KPB536 also was determined. The catalytic functions of glycosyltransferases coded by the cps_KPB536 gene cluster were assigned by comparison with those responsible for the synthesis of glycoside linkages in the CPSs of K. pneumoniae types K10 and K61.
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Affiliation(s)
- Nikolay V Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Anna M Shpirt
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Angelina A Kislichkina
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Vladimir V Verevkin
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Nadezhda K Fursova
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
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Zhao W, Tian Q, Luo Y, Wang Y, Yang ZX, Yao XP, Cheng JG, Zhou X, Wang WY. ISOLATION, IDENTIFICATION, AND GENOME ANALYSIS OF LUNG PATHOGENIC KLEBSIELLA PNEUMONIAE (LPKP) IN FOREST MUSK DEER. J Zoo Wildl Med 2017; 48:1039-48. [PMID: 29297821 DOI: 10.1638/2016-0241.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic infections. In this study, lung pathogenic K. pneumoniae (LPKP) was isolated and identified from suppurative pneumoniae in forest musk deer by conventional methods and by 16S ribosomal RNA sequence analysis. Median lethal dose and histopathologic analysis were used to demonstrate pathogenicity of the organism in mice. Furthermore, a draft genome of LPKP was sequenced, and its virulence genes were detected. One hundred and twenty-two virulence genes encoded determinant of capsule polysaccharide (CPS), lipopolysaccharide, fimbriae, outer membrane proteins, iron acquisition, and urease. In particular, 20 CPS-related genes were highly conserved in LPKP, K. pneumoniae U, K. pneumoniae NTUH-KP35, and K. pneumoniae KP-1. All of the strains were identified as capsular type K54. This is the first report of capsular type K54 K. pneumoniae causing suppurative pneumonia in an animal. The results of this study provided the basis for understanding the pathogenicity of LPKP and laid a foundation for the development of vaccines for the capsular type K54 K. pneumoniae disease.
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Ramos PIP, Fernández Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM, Klein CC, Sagot MF, de Vasconcelos ATR, Gales AC, Marti M, Turjanski AG, Nicolás MF. An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. Sci Rep 2018; 8:10755. [PMID: 30018343 PMCID: PMC6050338 DOI: 10.1038/s41598-018-28916-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae (Kp) is a globally disseminated opportunistic pathogen that can cause life-threatening infections. It has been found as the culprit of many infection outbreaks in hospital environments, being particularly aggressive towards newborns and adults under intensive care. Many Kp strains produce extended-spectrum β-lactamases, enzymes that promote resistance against antibiotics used to fight these infections. The presence of other resistance determinants leading to multidrug-resistance also limit therapeutic options, and the use of 'last-resort' drugs, such as polymyxins, is not uncommon. The global emergence and spread of resistant strains underline the need for novel antimicrobials against Kp and related bacterial pathogens. To tackle this great challenge, we generated multiple layers of 'omics' data related to Kp and prioritized proteins that could serve as attractive targets for antimicrobial development. Genomics, transcriptomics, structuromic and metabolic information were integrated in order to prioritize candidate targets, and this data compendium is freely available as a web server. Twenty-nine proteins with desirable characteristics from a drug development perspective were shortlisted, which participate in important processes such as lipid synthesis, cofactor production, and core metabolism. Collectively, our results point towards novel targets for the control of Kp and related bacterial pathogens.
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Affiliation(s)
- Pablo Ivan Pereira Ramos
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Darío Fernández Do Porto
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Germán Burguener
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Agustín M Pardo
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Cecilia C Klein
- Inria Grenoble Rhône-Alpes, Grenoble, France
- Université Claude Bernard Lyon 1, Lyon, France
- Centre for Genomic Regulation (CRG), Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marie-France Sagot
- Inria Grenoble Rhône-Alpes, Grenoble, France
- Université Claude Bernard Lyon 1, Lyon, France
| | | | - Ana Cristina Gales
- Laboratório Alerta. Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo Marti
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Adrián G Turjanski
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina.
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil.
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Abstract
The increasing prevalence of KPC-producing Klebsiella pneumoniae strains in clinical settings has been largely attributed to dissemination of organisms of specific multilocus sequence types, such as ST258 and ST11. Compared with the ST258 clone, which is prevalent in North America and Europe, ST11 is common in China but information regarding its genetic features remains scarce. In this study, we performed detailed genetic characterization of ST11 K. pneumoniae strains by analyzing whole-genome sequences of 58 clinical strains collected from diverse geographic locations in China. The ST11 genomes were found to be highly heterogeneous and clustered into at least three major lineages based on the patterns of single-nucleotide polymorphisms. Exhibiting five different capsular types, these ST11 strains were found to harbor multiple resistance and virulence determinants such as the blaKPC-2 gene, which encodes carbapenemase, and the yersiniabactin-associated virulence genes irp, ybt and fyu. Moreover, genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype (rmpA) were detectable in six genomes, whereas genes encoding salmochelin were found in three genomes. In conclusion, our data indicated that carriage of a wide range of resistance and virulence genes constitutes the underlying basis of the high level of prevalence of ST11 in clinical settings. Such findings provide insight into the development of novel strategies for prevention, diagnosis and treatment of K. pneumoniae infections.
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Affiliation(s)
- Ning Dong
- 1Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China.,2State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Kowloon, Hong Kong SAR
| | - Rong Zhang
- 3Second Affiliated Hospital of Zhejiang University, hospital of Zhejiang University, Hangzhou, PR China
| | - Lizhang Liu
- 1Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China
| | - Ruichao Li
- 1Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China.,2State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Kowloon, Hong Kong SAR
| | - Dachuan Lin
- 1Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China.,2State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Kowloon, Hong Kong SAR
| | - Edward Wai-Chi Chan
- 2State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Kowloon, Hong Kong SAR
| | - Sheng Chen
- 2State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Kowloon, Hong Kong SAR.,1Shenzhen Key lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China
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de Paula-Petroli SB, Campana EH, Bocchi M, Bordinhão T, Picão RC, Yamada-Ogatta SF, Carrara-Marroni FE. Early detection of a hypervirulent KPC-2-producing Pseudomonas aeruginosa ST235 in Brazil. J Glob Antimicrob Resist 2018; 12:153-154. [PMID: 29391216 DOI: 10.1016/j.jgar.2018.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Suelen Balero de Paula-Petroli
- Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina (UEL), Londrina, PR, Brazil
| | - Eloiza Helena Campana
- Laboratório de Investigação de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Mayara Bocchi
- Laboratório de Microbiologia Clínica, Hospital Universitário de Londrina, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina (UEL), Londrina, PR, Brazil
| | - Thiago Bordinhão
- Laboratório de Microbiologia Clínica, Hospital Universitário de Londrina, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina (UEL), Londrina, PR, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina (UEL), Londrina, PR, Brazil
| | - Floristher Elaine Carrara-Marroni
- Laboratório de Microbiologia Clínica, Hospital Universitário de Londrina, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina (UEL), Avenida Robert Koch 60, Vila Operária, 86038-360, Londrina, PR, Brazil.
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Andrade LN, Novais Â, Stegani LMM, Ferreira JC, Rodrigues C, Darini ALC, Peixe L. Virulence genes, capsular and plasmid types of multidrug-resistant CTX-M(-2, -8, -15) and KPC-2-producing Klebsiella pneumoniae isolates from four major hospitals in Brazil. Diagn Microbiol Infect Dis 2018; 91:164-168. [PMID: 29459053 DOI: 10.1016/j.diagmicrobio.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/06/2017] [Accepted: 01/08/2018] [Indexed: 01/20/2023]
Abstract
We performed a single-month snapshot study of the population diversity of multidrug resistant (MDR) Klebsiella pneumoniae isolates producing carbapenemases and/or extended-spectrum β-lactamases from four major hospitals in Brazil. Isolates produced diverse ESBL (CTX-M-2, -8, -15, SHV-2), KPC-2 or both (CTX-M-2 and KPC-2), linked to specific genetic backgrounds and plasmids from a few families (IncR, IncFIIk, IncL/M) that were shared among clonal lineages within and between hospitals. A high clonal diversity was identified, among isolates from the same ST (ST11, ST15, ST101 or ST340). Diverse capsular types (n=13 K-types) were identified, most of which linked to specific ST (ST11 and K27 or K64, ST101 and K17, ST340 and KL151, ST15 and K24 or ST17 and KL112). Isolates shared a common set of virulence genes (ureA, fimH, uge, wabG, mrkD, entB) and occasionally ybtS (42%) and kfuBC (18%). Our data suggest intra- and inter-hospital spread of common genetic structures and international MDR K. pneumoniae clones.
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Affiliation(s)
- Leonardo Neves Andrade
- Universidade de São Paulo (USP) - Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Ribeirão Preto, SP, Brazil
| | - Ângela Novais
- UCIBIO@REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Lenita Maria Marcato Stegani
- Universidade de São Paulo (USP) - Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Ribeirão Preto, SP, Brazil
| | - Joseane Cristina Ferreira
- Universidade de São Paulo (USP) - Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Ribeirão Preto, SP, Brazil
| | - Carla Rodrigues
- UCIBIO@REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana Lucia Costa Darini
- Universidade de São Paulo (USP) - Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Ribeirão Preto, SP, Brazil
| | - Luisa Peixe
- UCIBIO@REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.
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Ramos PI, Custódio MG, Quispe Saji GD, Cardoso T, da Silva GL, Braun G, Martins WM, Girardello R, de Vasconcelos AT, Fernández E, Gales AC, Nicolás MF. The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets. BMC Genomics 2016; 17:737. [PMID: 27801293 DOI: 10.1186/s12864-016-3070-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background The emergence of multidrug-resistant Klebsiella pneumoniae is a major public health concern. Many K. pneumoniae infections can only be treated when resorting to last-line drugs such as polymyxin B (PB). However, resistance to this antibiotic is also observed, although insufficient information is described on its mode of action as well as the mechanisms used by resistant bacteria to evade its effects. We aimed to study PB resistance and the influence of abiotic stresses in a clinical K. pneumoniae strain using whole transcriptome profiling. Results We sequenced 12 cDNA libraries of K. pneumoniae Kp13 bacteria, from two biological replicates of the original strain Kp13 (Kp13) and five derivative strains: induced high-level PB resistance in acidic pH (Kp13pH), magnesium deprivation (Kp13Mg), high concentrations of calcium (Kp13Ca) and iron (Kp13Fe), and a control condition with PB (Kp13PolB). Our results show the involvement of multiple regulatory loci that differentially respond to each condition as well as a shared gene expression response elicited by PB treatment, and indicate the participation of two-regulatory components such as ArcA-ArcB, which could be involved in re-routing the K. pneumoniae metabolism following PB treatment. Modules of co-expressed genes could be determined, which correlated to growth in acid stress and PB exposure. We hypothesize that polymyxin B induces metabolic shifts in K. pneumoniae that could relate to surviving against the action of this antibiotic. Conclusions We obtained whole transcriptome data for K. pneumoniae under different environmental conditions and PB treatment. Our results supports the notion that the K. pneumoniae response to PB exposure goes beyond damaged membrane reconstruction and involves recruitment of multiple gene modules and intracellular targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3070-y) contains supplementary material, which is available to authorized users.
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Abstract
Typical Klebsiella pneumoniae is an opportunistic pathogen, which mostly affects those with weakened immune systems and tends to cause nosocomial infections. A subset of hypervirulent K. pneumoniae serotypes with elevated production of capsule polysaccharide can affect previously healthy persons and cause life-threatening community-acquired infections, such as pyogenic liver abscess, meningitis, necrotizing fasciitis, endophthalmitis and severe pneumonia. K. pneumoniae utilizes a variety of virulence factors, especially capsule polysaccharide, lipopolysaccharide, fimbriae, outer membrane proteins and determinants for iron acquisition and nitrogen source utilization, for survival and immune evasion during infection. This article aims to present the state-of-the-art understanding of the molecular pathogenesis of K. pneumoniae.
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Affiliation(s)
- Bei Li
- Department of Dermatology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
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15
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Wyres KL, Gorrie C, Edwards DJ, Wertheim HFL, Hsu LY, Van Kinh N, Zadoks R, Baker S, Holt KE. Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258. Genome Biol Evol 2015; 7:1267-79. [PMID: 25861820 PMCID: PMC4453057 DOI: 10.1093/gbe/evv062] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae clonal group (CG) 258, comprising sequence types (STs) 258, 11, and closely related variants, is associated with dissemination of the K. pneumoniae carbapenemase (KPC). Hospital outbreaks of KPC CG258 infections have been observed globally and are very difficult to treat. As a consequence, there is renewed interest in alternative infection control measures such as vaccines and phage or depolymerase treatments targeting the K. pneumoniae polysaccharide capsule. To date, 78 immunologically distinct capsule variants have been described in K. pneumoniae. Previous investigations of ST258 and a small number of closely related strains suggested that capsular variation was limited within this clone; only two distinct ST258 capsule polysaccharide synthesis (cps) loci have been identified, both acquired through large-scale recombination events (>50 kb). In contrast to previous studies, we report a comparative genomic analysis of the broader K. pneumoniae CG258 (n = 39). We identified 11 different cps loci within CG258, indicating that capsular switching is actually common within the complex. We observed several insertion sequences (IS) within the cps loci, and show further intraclone diversification of two cps loci through IS activity. Our data also indicate that several large-scale recombination events have shaped the genomes of CG258, and that definition of the complex should be broadened to include ST395 (also reported to harbor KPC). As only the second report of extensive intraclonal cps variation among Gram-negative bacterial species, our findings alter our understanding of the evolution of these organisms and have key implications for the design of control measures targeting K. pneumoniae capsules.
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Affiliation(s)
- Kelly L Wyres
- IBM Research-Australia, Carlton, Victoria, Australia Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Claire Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Heiman F L Wertheim
- Wellcome Trust Major Overseas Programme, Clinical Research Unit, Oxford University Hanoi, Vietnam Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Li Yang Hsu
- National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Nguyen Van Kinh
- Wellcome Trust Major Overseas Programme, Clinical Research Unit, Oxford University Hanoi, Vietnam Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Ruth Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom Moredun Research Institute, Pentlands Science Park, Penicuik, Midlothian, United Kingdom
| | - Stephen Baker
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, United Kingdom The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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Wright MS, Perez F, Brinkac L, Jacobs MR, Kaye K, Cober E, van Duin D, Marshall SH, Hujer AM, Rudin SD, Hujer KM, Bonomo RA, Adams MD. Population structure of KPC-producing Klebsiella pneumoniae isolates from midwestern U.S. hospitals. Antimicrob Agents Chemother 2014; 58:4961-5. [PMID: 24913165 DOI: 10.1128/AAC.00125-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Genome sequencing of carbapenem-resistant Klebsiella pneumoniae isolates from regional U.S. hospitals was used to characterize strain diversity and the bla(KPC) genetic context. A phylogeny based on core single-nucleotide variants (SNVs) supports a division of sequence type 258 (ST258) into two distinct groups. The primary differences between the groups are in the capsular polysaccharide locus (cps) and their plasmid contents. A strict association between clade and KPC variant was found. The bla(KPC) gene was found on variants of two plasmid backbones. This study indicates that highly similar K. pneumoniae subpopulations coexist within the same hospitals over time.
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Andrade LN, Vitali L, Gaspar GG, Bellissimo-Rodrigues F, Martinez R, Darini AL. Expansion and evolution of a virulent, extensively drug-resistant (polymyxin B-resistant), QnrS1-, CTX-M-2-, and KPC-2-producing Klebsiella pneumoniae ST11 international high-risk clone. J Clin Microbiol 2014; 52:2530-5. [PMID: 24808234 DOI: 10.1128/JCM.00088-14] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this study, we report the early expansion, evolution, and characterization of a multiresistant Klebsiella pneumoniae clone that was isolated with increasing frequency from inpatients in a tertiary-care university hospital in Brazil. Seven carbapenem- and quinolone-resistant and polymyxin B-susceptible or -resistant K. pneumoniae isolates isolated between December 2012 and February 2013 were investigated. Beta-lactamase- and plasmid-mediated quinolone resistance (PMQR)-encoding genes and the genetic environment were investigated using PCR, sequencing, and restriction fragment length polymorphism (RFLP). Clonal relatedness was established using XbaI-pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and phylogenetic group characterization. Plasmid analyses included PCR-based replicon typing (PBRT) and hybridization of the S1-PFGE product, plasmid MLST, and conjugation experiments. Virulence potential was assessed by PCR by searching for 10 virulence factor-encoding genes (ureA, fimH, kfuBC, uge, wabG, magA, mrkD, allS, rmpA, and cf29a) and by phenotypic tests to analyze the hypermucoviscous phenotype. The genetic context of a multidrug-resistant and extensively drug-resistant K. pneumoniae ST11-KpI clone harboring IncFIIk-Tn4401a-blaKPC-2, qnrS1, and blaCTX-M-2 was found. Moreover, three isolates displayed high resistance to polymyxin B (MICs = 32, 32, and 128 mg/liter) as well as mucous and hypermucoviscous phenotypes. These bacteria also harbored ureA, fimH, uge, wabG, and mrkD, which code for virulence factors associated with binding, biofilm formation, and the ability to colonize and escape from phagocytosis. Our study describes the association of important coresistance and virulence factors in the K. pneumoniae ST11 international high-risk clone, which makes this pathogen successful at infections and points to the quick expansion and evolution of this multiresistant and virulent clone, leading to a pandrug-resistant phenotype and persistent bacteria in a Brazilian hospital.
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Chen L, Chavda KD, Findlay J, Peirano G, Hopkins K, Pitout JD, Bonomo RA, Woodford N, DeLeo FR, Kreiswirth BN. Multiplex PCR for identification of two capsular types in epidemic KPC-producing Klebsiella pneumoniae sequence type 258 strains. Antimicrob Agents Chemother 2014; 58:4196-9. [PMID: 24733470 DOI: 10.1128/AAC.02673-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a multiplex PCR assay capable of identifying two capsular polysaccharide synthesis sequence types (sequence type 258 [ST258] cps-1 and cps-2) in epidemic Klebsiella pneumoniae ST258 strains. The assay performed with excellent sensitivity (100%) and specificity (100%) for identifying cps types in 60 ST258 K. pneumoniae sequenced isolates. The screening of 419 ST258 clonal isolates revealed a significant association between cps type and K. pneumoniae carbapenemase (KPC) variant: cps-1 is largely associated with KPC-2, while cps-2 is primarily associated with KPC-3.
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Ramos PIP, Picão RC, Almeida LGPD, Lima NCB, Girardello R, Vivan ACP, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos ATRD, Gales AC, Nicolás MF. Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms. BMC Genomics 2014; 15:54. [PMID: 24450656 PMCID: PMC3904158 DOI: 10.1186/1471-2164-15-54] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/26/2013] [Indexed: 11/24/2022] Open
Abstract
Background Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. In this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342. Results We have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. The rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains. Conclusions Our results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. The general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/loss of genomic segments appears to be driving the evolution of these strains.
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Kubler-Kielb J, Vinogradov E, Ng WI, Maczynska B, Junka A, Bartoszewicz M, Zelazny A, Bennett J, Schneerson R. The capsular polysaccharide and lipopolysaccharide structures of two carbapenem resistant Klebsiella pneumoniae outbreak isolates. Carbohydr Res 2012; 369:6-9. [PMID: 23360863 DOI: 10.1016/j.carres.2012.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
Carbapenem resistant Klebsiella pneumoniae (CRKP) are isolated with increasing frequency, especially from immunocompromized patients. The capsular polysaccharide (CPS) types of CPKP were not determined. Investigation of two CRKP isolates from a 2011 outbreak at the Clinical Center, the National Institutes of Health, identified a new capsular type shared by the two isolates, similar to K. pneumonia K19 and K34 but structurally different than any published K. pneumoniae CPS repeating unit: The LPS of the two isolates was found to have no O-specific polysaccharide and the chemical structure of the core oligosaccharides agreed with the published data. If this structure type will be prevalent among CPKP isolates, our findings could facilitate rapid diagnosis and help to develop new therapeutic solutions to this antibiotic resistant pathogen.
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Affiliation(s)
- Joanna Kubler-Kielb
- Program on Developmental and Molecular Immunity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, United States.
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Hirvonen JJ, Lepistö I, Mero S, Kaukoranta SS. First isolation of Dietzia cinnamea from a dog bite wound in an adult patient. J Clin Microbiol 2012; 50:4163-5. [PMID: 23035183 DOI: 10.1128/JCM.01939-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first case of deep-wound colonization by Dietzia cinnamea in a patient who had been bitten by a dog.
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