1
|
Koller BH, Jania LA, Li H, Barker WT, Melander RJ, Melander C. Adjuvants restore colistin sensitivity in mouse models of highly colistin-resistant isolates, limiting bacterial proliferation and dissemination. Antimicrob Agents Chemother 2024:e0067124. [PMID: 39194205 DOI: 10.1128/aac.00671-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
Antimicrobial resistance (AMR) has led to a marked reduction in the effectiveness of many antibiotics, representing a substantial and escalating concern for global health. Particularly alarming is resistance in Gram-negative bacteria due to the scarcity of therapeutic options for treating infections caused by these pathogens. This challenge is further compounded by the rising incidence of resistance to colistin, an antibiotic traditionally considered a last resort for the treatment of multi-drug resistant (MDR) Gram-negative bacterial infections. In this study, we demonstrate that adjuvants restore colistin sensitivity in vivo. We previously reported that the salicylanilide kinase inhibitor IMD-0354, which was originally developed to inhibit the human kinase IKKβ in the NFκB pathway, is a potent colistin adjuvant. Subsequent analog synthesis using an amide isostere approach led to the creation of a series of novel benzimidazole compounds with enhanced colistin adjuvant activity. Herein, we demonstrate that both IMD-0354 and a lead benzimidazole effectively restore colistin susceptibility in mouse models of highly colistin-resistant Klebsiella pneumoniae and Acinetobacter baumannii-induced peritonitis. These novel adjuvants show low toxicity in vivo, significantly reduce bacterial load, and prevent dissemination that could otherwise result in systemic infection.
Collapse
Affiliation(s)
- Beverly H Koller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leigh A Jania
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haoting Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - William T Barker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Roberta J Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Christian Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
2
|
Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [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: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
Collapse
Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ifeoluwa J Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M Marcovici
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| |
Collapse
|
3
|
Beig M, Aghamohammad S, Majidzadeh N, Asforooshani MK, Rezaie N, Abed S, Khiavi EHG, Sholeh M. Antibiotic resistance rates in hypervirulent Klebsiella pneumoniae strains: A systematic review and meta-analysis. J Glob Antimicrob Resist 2024; 38:376-388. [PMID: 39069234 DOI: 10.1016/j.jgar.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/26/2024] [Accepted: 06/16/2024] [Indexed: 07/30/2024] Open
Abstract
OBJECTIVES In response to the growing global concerns regarding antibiotic resistance, we conducted a meta-analysis to assess the prevalence of antibiotic resistance in hypervirulent Klebsiella pneumoniae (hvKp) strains. METHODS We conducted a meta-analysis of antibiotic resistance in the hvKp strains. Eligible studies published in English until April 10, 2023, were identified through a systematic search of various databases. After removing duplicates, two authors independently assessed and analysed the relevant publications, and a third author resolved any discrepancies. Data extraction included publication details and key information on antibiotic resistance. Data synthesis employed a random-effects model to account for heterogeneity, and various statistical analyses were conducted using R and the metafor package. RESULTS This meta-analysis of 77 studies from 17 countries revealed the prevalence of antibiotic resistance in hvKp strains. A high resistance rates have been observed against various classes of antibiotics. Ampicillin-sulbactam faced 45.3% resistance, respectively, rendering them largely ineffective. The first-generation cephalosporin cefazolin exhibited a resistance rate of 38.1%, whereas second-generation cefuroxime displayed 26.7% resistance. Third-generation cephalosporins, cefotaxime (65.8%) and ceftazidime (57.1%), and fourth-generation cephalosporins, cefepime (51.3%), showed substantial resistance. The last resort carbapenems, imipenem (45.7%), meropenem (51.0%) and ertapenem (40.6%), were not spared. CONCLUSION This study emphasizes the growing issue of antibiotic resistance in hvKp strains, with notable resistance to both older and newer antibiotics, increasing resistance over time, regional disparities and methodological variations. Effective responses should involve international cooperation, standardized testing and tailored regional interventions.
Collapse
Affiliation(s)
- Masoumeh Beig
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Student Research Committee, Pasteur Institute of Iran, Tehran, Iran
| | | | - Nahal Majidzadeh
- Departments of Biological and Biomedical Sciences, Cancer Biomedical Center, Tehran, Iran
| | - Mahshid Khazani Asforooshani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Niloofar Rezaie
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | | | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
4
|
Han X, Yao J, He J, Liu H, Jiang Y, Zhao D, Shi Q, Zhou J, Hu H, Lan P, Zhou H, Li X. Clinical and laboratory insights into the threat of hypervirulent Klebsiella pneumoniae. Int J Antimicrob Agents 2024; 64:107275. [PMID: 39002700 DOI: 10.1016/j.ijantimicag.2024.107275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/15/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKP) typically causes severe invasive infections affecting multiple sites in healthy individuals. In the past, hvKP was characterized by a hypermucoviscosity phenotype, susceptibility to antimicrobial agents, and its tendency to cause invasive infections in healthy individuals within the community. However, there has been an alarming increase in reports of multidrug-resistant hvKP, particularly carbapenem-resistant strains, causing nosocomial infections in critically ill or immunocompromised patients. This presents a significant challenge for clinical treatment. Early identification of hvKP is crucial for timely infection control. Notably, identifying hvKP has become confusing due to its prevalence in nosocomial settings and the limited predictive specificity of the hypermucoviscosity phenotype. Novel virulence predictors for hvKP have been discovered through animal models or machine learning algorithms, while standardization of identification criteria is still necessary. Timely source control and antibiotic therapy have been widely employed for the treatment of hvKP infections. Additionally, phage therapy is a promising alternative approach due to escalating antibiotic resistance. In summary, this narrative review highlights the latest research progress in the development, virulence factors, identification, epidemiology of hvKP, and treatment options available for hvKP infection.
Collapse
Affiliation(s)
- Xinhong Han
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jiayao Yao
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haiyang Liu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiucheng Shi
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huangdu Hu
- Department of Infectious Diseases, Centre for General Practice Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Peng Lan
- Department of Infectious Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China.
| |
Collapse
|
5
|
Kelly SD, Williams DM, Zhu S, Kim T, Jana M, Nothof J, Thota VN, Lowary TL, Whitfield C. Klebsiella pneumoniae O-polysaccharide biosynthesis highlights the diverse organization of catalytic modules in ABC transporter-dependent glycan assembly. J Biol Chem 2024; 300:107420. [PMID: 38815868 PMCID: PMC11231755 DOI: 10.1016/j.jbc.2024.107420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/19/2024] [Indexed: 06/01/2024] Open
Abstract
Klebsiella pneumoniae provides influential prototypes for lipopolysaccharide O antigen (OPS) biosynthesis in Gram-negative bacteria. Sequences of OPS-biosynthesis gene clusters in serotypes O4 and O7 suggest fundamental differences in the organization of required enzyme modules compared to other serotypes. Furthermore, some required activities were not assigned by homology shared with characterized enzymes. The goal of this study was therefore to resolve the serotype O4 and O7 pathways to expand our broader understanding of glycan polymerization and chain termination processes. The O4 and O7 antigens were produced from cloned genetic loci in recombinant Escherichia coli. Systematic in vivo and in vitro approaches were then applied to assign each enzyme in each of the pathways, defining the necessary components for polymerization and chain termination. OPS assembly is accomplished by multiprotein complexes formed by interactions between polymerase components variably distributed in single and multimodule proteins. In each complex, a terminator function is present in a protein containing a characteristic coiled-coil molecular ruler, which determines glycan chain length. In serotype O4, we discovered a CMP-α-3-deoxy-ᴅ-manno-octulosonic acid-dependent chain-terminating glycosyltransferase that is the founding member of a new glycosyltransferase family (GT137) and potentially identifies a new glycosyltransferase fold. The O7 OPS is terminated by a methylphosphate moiety, like the K. pneumoniae O3 antigen, but the methyltransferase-kinase enzyme pairs responsible for termination in these serotypes differ in sequence and predicted structures. Together, the characterization of O4 and O7 has established unique enzyme activities and provided new insight into glycan-assembly strategies that are widely distributed in bacteria.
Collapse
Affiliation(s)
- Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shawna Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taeok Kim
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Manas Jana
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Nothof
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| |
Collapse
|
6
|
Müller JU, Schwabe M, Swiatek LS, Heiden SE, Schlüter R, Sittner M, Bohnert JA, Becker K, Idelevich EA, Guenther S, Eger E, Schaufler K. Temperatures above 37°C increase virulence of a convergent Klebsiella pneumoniae sequence type 307 strain. Front Cell Infect Microbiol 2024; 14:1411286. [PMID: 38947124 PMCID: PMC11211929 DOI: 10.3389/fcimb.2024.1411286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/23/2024] [Indexed: 07/02/2024] Open
Abstract
Background Convergence of Klebsiella pneumoniae (KP) pathotypes has been increasingly reported in recent years. These pathogens combine features of both multidrug-resistant and hypervirulent KP. However, clinically used indicators for hypervirulent KP identification, such as hypermucoviscosity, appear to be differentially expressed in convergent KP, potential outbreak clones are difficult to identify. We aimed to fill such knowledge gaps by investigating the temperature dependence of hypermucoviscosity and virulence in a convergent KP strain isolated during a clonal outbreak and belonging to the high-risk sequence type (ST)307. Methods Hypermucoviscosity, biofilm formation, and mortality rates in Galleria mellonella larvae were examined at different temperatures (room temperature, 28°C, 37°C, 40°C and 42°C) and with various phenotypic experiments including electron microscopy. The underlying mechanisms of the phenotypic changes were explored via qPCR analysis to evaluate plasmid copy numbers, and transcriptomics. Results Our results show a temperature-dependent switch above 37°C towards a hypermucoviscous phenotype, consistent with increased biofilm formation and in vivo mortality, possibly reflecting a bacterial response to fever-like conditions. Furthermore, we observed an increase in plasmid copy number for a hybrid plasmid harboring carbapenemase and rmpA genes. However, transcriptomic analysis revealed no changes in rmpA expression at higher temperatures, suggesting alternative regulatory pathways. Conclusion This study not only elucidates the impact of elevated temperatures on hypermucoviscosity and virulence in convergent KP but also sheds light on previously unrecognized aspects of its adaptive behavior, underscoring its resilience to changing environments.
Collapse
Affiliation(s)
- Justus U. Müller
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Michael Schwabe
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Lena-Sophie Swiatek
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Stefan E. Heiden
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Max Sittner
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Evgeny A. Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Sebastian Guenther
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Elias Eger
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
| | - Katharina Schaufler
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research (HZI), Greifswald, Germany
- University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
7
|
Ruhland E, Siemers M, Gerst R, Späth F, Vogt LN, Figge MT, Papenfort K, Fröhlich KS. The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division. Proc Natl Acad Sci U S A 2024; 121:e2317322121. [PMID: 38377209 PMCID: PMC10907235 DOI: 10.1073/pnas.2317322121] [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: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.
Collapse
Affiliation(s)
- Eric Ruhland
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Malte Siemers
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Ruman Gerst
- Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Felix Späth
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Laura Nicole Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Kathrin Sophie Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| |
Collapse
|
8
|
Russo TA, Alvarado CL, Davies CJ, Drayer ZJ, Carlino-MacDonald U, Hutson A, Luo TL, Martin MJ, Corey BW, Moser KA, Rasheed JK, Halpin AL, McGann PT, Lebreton F. Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance. mBio 2024; 15:e0286723. [PMID: 38231533 PMCID: PMC10865842 DOI: 10.1128/mbio.02867-23] [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: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Distinguishing hypervirulent (hvKp) from classical Klebsiella pneumoniae (cKp) strains is important for clinical care, surveillance, and research. Some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g., siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Furthermore, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49 K. pneumoniae strains that possessed some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N = 16) or cKp (N = 33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid's Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression, the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49), respectively. These findings can be used to inform the identification of hvKp.IMPORTANCEHypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistant K. pneumoniae isolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all five of the biomarkers iucA, iroB, peg-344, rmpA, and rmpA2 was most accurate (94%); the presence of ≥4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which, in turn, would assist in optimizing patient care.
Collapse
Affiliation(s)
- Thomas A. Russo
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Cassandra L. Alvarado
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Connor J. Davies
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Zachary J. Drayer
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Ulrike Carlino-MacDonald
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ting L. Luo
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Melissa J. Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Brendan W. Corey
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kara A. Moser
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J. Kamile Rasheed
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison L. Halpin
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Patrick T. McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| |
Collapse
|
9
|
Selvaraj Anand S, Wu CT, Bremer J, Bhatti M, Treangen TJ, Kalia A, Shelburne SA, Shropshire WC. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microb Genom 2024; 10:001201. [PMID: 38407244 PMCID: PMC10926705 DOI: 10.1099/mgen.0.001201] [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: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 02/27/2024] Open
Abstract
Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.
Collapse
Affiliation(s)
- Selvalakshmi Selvaraj Anand
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Chin-Ting Wu
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Micah Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| |
Collapse
|
10
|
Cheung BH, Alisoltani A, Kochan TJ, Lebrun-Corbin M, Nozick SH, Axline CMR, Bachta KER, Ozer EA, Hauser AR. Genome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by Klebsiella pneumoniae. mBio 2023; 14:e0212823. [PMID: 37877703 PMCID: PMC10746194 DOI: 10.1128/mbio.02128-23] [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: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Klebsiella pneumoniae is a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistant K. pneumoniae has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization in patients with K. pneumoniae has been linked to subsequent infection, making it a key process to control in the prevention of multidrug-resistant infections. However, the bacterial factors which contribute to K. pneumoniae colonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain dependent. This study identifies the enteric colonization factors of three classical strains using transposon mutant screens to define a core colonization program for K. pneumoniae as well as detecting strain-to-strain differences in colonization strategies.
Collapse
Affiliation(s)
- Bettina H. Cheung
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Travis J. Kochan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sophia H. Nozick
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christopher M. R. Axline
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E. R. Bachta
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| |
Collapse
|
11
|
Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [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: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
Collapse
Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
12
|
Russo TA, Alvarado CL, Davies CJ, Drayer ZJ, Carlino-MacDonald U, Hutson A, Luo TL, Martin MJ, Corey BW, Moser KA, Rasheed JK, Halpin AL, McGann PT, Lebreton F. Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547231. [PMID: 37961280 PMCID: PMC10634668 DOI: 10.1101/2023.06.30.547231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Distinguishing hypervirulent (hvKp) from classical Klebsiella pneumoniae (cKp) strains is important for clinical care, surveillance, and research. Some combination of iucA, iroB, peg-344, rmpA, and rmpA2 are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g. siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Further, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49 K. pneumoniae strains that possessed some combination of iucA, iroB, peg-344, rmpA, and rmpA2 and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N=16) or cKp (N=33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid's Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥ 4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49) respectively. These findings can be used to inform the identification of hvKp. Importance Hypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistant K. pneumoniae isolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all 5 of the biomarkers iucA, iroB, peg-344, rmpA, and rmpA2 was most accurate (94%); the presence of ≥ 4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which in turn would assist in optimizing patient care.
Collapse
|
13
|
Paniagua-Contreras GL, Bautista-Cerón A, Morales-Espinosa R, Delgado G, Vaca-Paniagua F, Díaz-Velásquez CE, de la Cruz-Montoya AH, García-Cortés LR, Sánchez-Yáñez MP, Monroy-Pérez E. Extensive Expression of the Virulome Related to Antibiotic Genotyping in Nosocomial Strains of Klebsiella pneumoniae. Int J Mol Sci 2023; 24:14754. [PMID: 37834205 PMCID: PMC10573248 DOI: 10.3390/ijms241914754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The emergence of hyper-virulent and multidrug-resistant (MDR) strains of Klebsiella pneumoniae isolated from patients with hospital- and community-acquired infections is a serious health problem that increases mortality. The molecular analysis of virulome expression related to antimicrobial-resistant genotype and infection type in K. pneumoniae strains isolated from patients with hospital- and community-acquired infections has been poorly studied. In this study, we analyzed the overall expression of the virulence genotype associated with the antimicrobial resistance genotype and pulse field gel electrophoresis (PFGE) type (PFtype) in K. pneumoniae. We studied 25 strains of K. pneumoniae isolated from patients who developed bacteremia and pneumonia during their hospital stay and 125 strains from outpatients who acquired community-acquired infections. Susceptibility to 12 antimicrobials was determined by Kirby-Bauer. The identification of K. pneumoniae and antibiotic-resistance genes was performed using polymerase chain reaction (PCR). To promote the expression of the virulence genes of K. pneumoniae, an in vitro infection model was used in human epithelial cell lines A549 and A431. Bacterial RNA was extracted with the QIAcube robotic workstation, and reverse transcription to cDNA was performed with the Reverse Transcription QuantiTect kit (Qiagen). The determination of the expression of the virulence genes was performed by real-time PCR. In addition, 57.3% (n = 86) of the strains isolated from patients with hospital- and community-acquired infections were multidrug-resistant (MDR), mainly to beta-lactam antibiotics (CB, AM, CFX, and CF), aminoglycosides (GE), quinolones (CPF and NOF), nitrofurantoin (NF), and sulfamethoxazole/trimethoprim (SXT). The most frequently expressed genes among strains isolated from hospital- and community-acquired infections were adhesion-type, ycfm (80%), mrkD (51.3%), and fimH (30.7%); iron uptake, irp2 (84%), fyuA (68.7%), entB (64.7%), and irp1 (56.7%); and protectins, rpmA (26%), which were related to antibiotic-resistance genes, blaTEM (96%), blaSHV (64%), blaCITM (52.6%), blaCTXM-1 (44.7%), tetA (74%), sul1 (57.3%), aac(3)-IV (40.7%), and aadA1 (36%). The results showed the existence of different patterns of expression of virulome related to the genotype of resistance to antimicrobials and to the PFtypes in the strains of K. pneumoniae that cause hospital- and community-acquired infections. These findings are important and may contribute to improving medical treatment strategies against infections caused by K. pneumoniae.
Collapse
Affiliation(s)
- Gloria Luz Paniagua-Contreras
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (A.B.-C.); (M.P.S.-Y.)
| | - Areli Bautista-Cerón
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (A.B.-C.); (M.P.S.-Y.)
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico; (R.M.-E.); (G.D.)
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico; (R.M.-E.); (G.D.)
| | - Felipe Vaca-Paniagua
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (F.V.-P.); (C.E.D.-V.); (A.H.d.l.C.-M.)
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14160, Mexico
| | - Clara Estela Díaz-Velásquez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (F.V.-P.); (C.E.D.-V.); (A.H.d.l.C.-M.)
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | - Aldo Hugo de la Cruz-Montoya
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (F.V.-P.); (C.E.D.-V.); (A.H.d.l.C.-M.)
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | | | - María Patricia Sánchez-Yáñez
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (A.B.-C.); (M.P.S.-Y.)
| | - Eric Monroy-Pérez
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico; (A.B.-C.); (M.P.S.-Y.)
| |
Collapse
|
14
|
Ramkisson T, Rip D. Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context. AIMS Microbiol 2023; 9:668-691. [PMID: 38173973 PMCID: PMC10758576 DOI: 10.3934/microbiol.2023034] [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: 07/20/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024] Open
Abstract
Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.
Collapse
Affiliation(s)
- Taish Ramkisson
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Diane Rip
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
| |
Collapse
|
15
|
Elgriw N, Métayer V, Drapeau A, François P, Azaiez S, Mastouri M, Rhim H, Elzagheid A, Soufiyah N, Madec JY, Chaouch C, Mansour W, Haenni M. Clonal, Plasmidic and Genetic Diversity of Multi-Drug-Resistant Enterobacterales from Hospitalized Patients in Tripoli, Libya. Antibiotics (Basel) 2023; 12:1430. [PMID: 37760726 PMCID: PMC10525897 DOI: 10.3390/antibiotics12091430] [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: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESC) and carbapenems in Enterobacterales is a major issue in public health. Carbapenem resistance in particular is associated with increased morbidity and mortality. Moreover, such resistance is often co-harbored with resistance to non-beta-lactam antibiotics, and pathogens quickly become multi-drug-resistant (MDR). Only a few studies have been published on AMR in Libyan hospitals, but all reported worrisome results. Here, we studied 54 MDR isolates that were collected from 49 patients at the Tripoli University Hospital between 2019 and 2021. They were characterized using phenotypic methods, PCR and PFGE, and a sub-set of isolates were short- and long-read whole-genome sequenced. The results showed the frequent occurrence of Klebsiella pneumoniae (49/54), among which several high-risk clones were responsible for the spread of resistance, namely, ST11, ST17, ST101 and ST147. ESC and carbapenem resistance was due to a wide variety of enzymes (CTX-M, OXA-48, NDM, KPC), with their corresponding genes carried by different plasmids, including IncF-IncHI2 and IncF-IncR hybrids. This study highlights that implementation of infection prevention, control and surveillance measures are needed in Libya to fight against AMR.
Collapse
Affiliation(s)
- Nada Elgriw
- Department of Microbiology, Libyan Biotechnology Reseaerch Center, Tripoli P.O. Box 30313, Libya;
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Véronique Métayer
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Pauline François
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Sana Azaiez
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, LR12ES02, Sousse 4002, Tunisia; (S.A.); (W.M.)
| | - Maha Mastouri
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Hajer Rhim
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Reseaerch Center, Tripoli P.O. Box 30313, Libya;
| | - Najeeb Soufiyah
- Medical Microbiology and Immunology Department, Faculty of Pharmacy, University of Tripoli, Tripoli P.O. Box 13275, Libya;
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| | - Cherifa Chaouch
- Faculty of pharmacy Monastir, Doctoral commission in Pharmaceutical Sciences, University of Monastir, Monastir 5000, Tunisia; (M.M.); (H.R.); (C.C.)
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
| | - Wejdene Mansour
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, LR12ES02, Sousse 4002, Tunisia; (S.A.); (W.M.)
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES—Université de Lyon, 69007 Lyon, France; (V.M.); (A.D.); (P.F.); (J.-Y.M.)
| |
Collapse
|
16
|
Cheung BH, Alisoltani A, Kochan TJ, Lebrun-Corbin M, Nozick SH, Axline CMR, Bachta KER, Ozer EA, Hauser AR. Genome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by Klebsiella pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555643. [PMID: 37693543 PMCID: PMC10491162 DOI: 10.1101/2023.08.30.555643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Gastrointestinal (GI) colonization by Klebsiella pneumoniae is a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. Thus, we aimed to study strain-specific requirements for K. pneumoniae GI colonization by applying transposon insertion sequencing to three classical clinical strains: a carbapenem-resistant strain, an extended-spectrum beta-lactamase producing strain, and a non-epidemic antibiotic-susceptible strain. The transposon insertion libraries were screened in a murine model of GI colonization. At three days post-inoculation, 27 genes were required by all three strains for colonization. Isogenic deletion mutants for three genes/operons (acrA, carAB, tatABCD) confirmed colonization defects in each of the three strains. Additionally, deletion of acrA reduced bile tolerance in vitro, while complementation restored both bile tolerance in vitro and colonization ability in vivo. Transposon insertion sequencing suggested that some genes were more important for colonization of one strain than the others. For example, deletion of the sucrose porin-encoding gene scrY resulted in a colonization defect in the carbapenemase-producing strain but not in the extended-spectrum beta-lactamase producer or the antibiotic-susceptible strain. These findings demonstrate that classical K. pneumoniae strains use both shared and strain-specific strategies to colonize the mouse GI tract. IMPORTANCE Klebsiella pneumoniae is a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistant K. pneumoniae (CR-Kp) has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization of patients with K. pneumoniae has been linked to subsequent infection, making it a key process to control in prevention of multidrug-resistant infections. However, the bacterial factors which contribute to K. pneumoniae colonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain-dependent. This study identifies the enteric colonization factors of 3 classical strains using transposon mutant screens to define a core colonization program for K. pneumoniae as well as detecting strain-to-strain differences in colonization strategies.
Collapse
Affiliation(s)
- Bettina H Cheung
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Travis J Kochan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Christopher MR Axline
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Kelly ER Bachta
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
17
|
Kelly SD, Ovchinnikova OG, Müller F, Steffen M, Braun M, Sweeney RP, Kowarik M, Follador R, Lowary TL, Serventi F, Whitfield C. Identification of a second glycoform of the clinically prevalent O1 antigen from Klebsiella pneumoniae. Proc Natl Acad Sci U S A 2023; 120:e2301302120. [PMID: 37428935 PMCID: PMC10629545 DOI: 10.1073/pnas.2301302120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/15/2023] [Indexed: 07/12/2023] Open
Abstract
Carbapenemase and extended β-lactamase-producing Klebsiella pneumoniae isolates represent a major health threat, stimulating increasing interest in immunotherapeutic approaches for combating Klebsiella infections. Lipopolysaccharide O antigen polysaccharides offer viable targets for immunotherapeutic development, and several studies have described protection with O-specific antibodies in animal models of infection. O1 antigen is produced by almost half of clinical Klebsiella isolates. The O1 polysaccharide backbone structure is known, but monoclonal antibodies raised against the O1 antigen showed varying reactivity against different isolates that could not be explained by the known structure. Reinvestigation of the structure by NMR spectroscopy revealed the presence of the reported polysaccharide backbone (glycoform O1a), as well as a previously unknown O1b glycoform composed of the O1a backbone modified with a terminal pyruvate group. The activity of the responsible pyruvyltransferase (WbbZ) was confirmed by western immunoblotting and in vitro chemoenzymatic synthesis of the O1b terminus. Bioinformatic data indicate that almost all O1 isolates possess genes required to produce both glycoforms. We describe the presence of O1ab-biosynthesis genes in other bacterial species and report a functional O1 locus on a bacteriophage genome. Homologs of wbbZ are widespread in genetic loci for the assembly of unrelated glycostructures in bacteria and yeast. In K. pneumoniae, simultaneous production of both O1 glycoforms is enabled by the lack of specificity of the ABC transporter that exports the nascent glycan, and the data reported here provide mechanistic understanding of the capacity for evolution of antigenic diversity within an important class of biomolecules produced by many bacteria.
Collapse
Affiliation(s)
- Steven D. Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | - Olga G. Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| | | | | | - Martin Braun
- LimmaTech Biologics AG, Schlieren8952, Switzerland
| | - Ryan P. Sweeney
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
| | | | | | - Todd L. Lowary
- Department of Chemistry, University of Alberta, Edmonton, ABT6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Taipei, Nangang11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei10617, Taiwan
| | | | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ONN1G 2W1, Canada
| |
Collapse
|
18
|
Prince A, Wong Fok Lung T. Immunometabolic control by Klebsiella pneumoniae. IMMUNOMETABOLISM (COBHAM, SURREY) 2023; 5:e00028. [PMID: 37492184 PMCID: PMC10364963 DOI: 10.1097/in9.0000000000000028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Klebsiella pneumoniae is a common Gram-negative pathogen associated with community-acquired and healthcare-associated infections. Its ability to acquire genetic elements resulted in its rapid development of resistance to virtually all antimicrobial agents. Once infection is established, K. pneumoniae is able to evade the host immune response and perhaps more importantly, undergo metabolic rewiring to optimize its ability to maintain infection. K. pneumoniae lipopolysaccharide and capsular polysaccharide are central factors in the induction and evasion of immune clearance. Less well understood is the importance of immunometabolism, the intersection between cellular metabolism and immune function, in the host response to K. pneumoniae infection. Bacterial metabolism itself is perceived as a metabolic stress to the host, altering the microenvironment at the site of infection. In this review, we will discuss the metabolic responses induced by K. pneumoniae, particularly in response to stimulation with the metabolically active bacteria versus pathogen-associated molecular patterns alone, and their implications in shaping the nature of the immune response and the infection outcome. A better understanding of the immunometabolic response to K. pneumoniae may help identify new targets for therapeutic intervention in the treatment of multidrug-resistant bacterial infections.
Collapse
Affiliation(s)
- Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, USA
| | | |
Collapse
|
19
|
Gatica S, Fuentes B, Rivera-Asín E, Ramírez-Céspedes P, Sepúlveda-Alfaro J, Catalán EA, Bueno SM, Kalergis AM, Simon F, Riedel CA, Melo-Gonzalez F. Novel evidence on sepsis-inducing pathogens: from laboratory to bedside. Front Microbiol 2023; 14:1198200. [PMID: 37426029 PMCID: PMC10327444 DOI: 10.3389/fmicb.2023.1198200] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Sepsis is a life-threatening condition and a significant cause of preventable morbidity and mortality globally. Among the leading causative agents of sepsis are bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Streptococcus pyogenes, along with fungal pathogens of the Candida species. Here, we focus on evidence from human studies but also include in vitro and in vivo cellular and molecular evidence, exploring how bacterial and fungal pathogens are associated with bloodstream infection and sepsis. This review presents a narrative update on pathogen epidemiology, virulence factors, host factors of susceptibility, mechanisms of immunomodulation, current therapies, antibiotic resistance, and opportunities for diagnosis, prognosis, and therapeutics, through the perspective of bloodstream infection and sepsis. A list of curated novel host and pathogen factors, diagnostic and prognostic markers, and potential therapeutical targets to tackle sepsis from the research laboratory is presented. Further, we discuss the complex nature of sepsis depending on the sepsis-inducing pathogen and host susceptibility, the more common strains associated with severe pathology and how these aspects may impact in the management of the clinical presentation of sepsis.
Collapse
Affiliation(s)
- Sebastian Gatica
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Brandon Fuentes
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Elizabeth Rivera-Asín
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Paula Ramírez-Céspedes
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Javiera Sepúlveda-Alfaro
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo A. Catalán
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M. Bueno
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Simon
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Claudia A. Riedel
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Felipe Melo-Gonzalez
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| |
Collapse
|
20
|
Shelenkov A, Mikhaylova Y, Voskanyan S, Egorova A, Akimkin V. Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates. Microorganisms 2023; 11:1314. [PMID: 37317293 DOI: 10.3390/microorganisms11051314] [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: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.
Collapse
Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Shushanik Voskanyan
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Anna Egorova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| |
Collapse
|
21
|
Faccone D, Gomez SA, de Mendieta JM, Sanz MB, Echegorry M, Albornoz E, Lucero C, Ceriana P, Menocal A, Martino F, De Belder D, Corso A, Pasterán F. Emergence of Hyper-Epidemic Clones of Enterobacterales Clinical Isolates Co-Producing KPC and Metallo-Beta-Lactamases during the COVID-19 Pandemic. Pathogens 2023; 12:pathogens12030479. [PMID: 36986401 PMCID: PMC10052147 DOI: 10.3390/pathogens12030479] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND The global spread of carbapenemase-producing Enterobacterales has become an epidemiological risk for healthcare systems by limiting available antimicrobial treatments. The COVID-19 pandemic worsened this scenario, prompting the emergence of extremely resistant microorganisms. METHODS Between March 2020 and September 2021, the NRL confirmed 82 clinical Enterobacterales isolates harboring a combination of blaKPC and MBL genes. Molecular typing was analyzed by PFGE and MLST. Modified double-disk synergy (MDDS) tests were used for phenotypic studies. RESULTS Isolates were submitted from 28 hospitals located in seven provinces and Buenos Aires City, including 77 K. pneumoniae, 2 K. oxytoca, 2 C. freundii, and 1 E. coli. Almost half of K. pneumoniae isolates (n = 38; 49.4%), detected in 15 hospitals, belong to the CC307 clone. CC11 was the second clone, including 29 (37.7%) isolates (22, ST11 and 7, ST258) from five cities and 12 hospitals. Three isolates belonging to CC45 were also detected. The carbapenemase combinations observed were as follows: 55% blaKPC-2 plus blaNDM-5; 32.5% blaKPC-2 plus blaNDM-1; 5% blaKPC-3 plus blaNDM-1; 5% blaKPC-2 plus blaIMP-8; and 2.5% strain with blaKPC-2 plus blaNDM-5 plus blaOXA-163. Aztreonam/avibactam and aztreonam/relebactam were the most active combinations (100% and 91% susceptible, respectively), followed by fosfomycin (89%) and tigecycline (84%). CONCLUSIONS The MDDS tests using ceftazidime-avibactam/EDTA and aztreonam/boronic acid disks improved phenotypic classification as dual producers. The successful high-risk clones of K. pneumoniae, such as hyper-epidemic CC307 and CC11 clones, drove the dissemination of double carbapenemase-producing isolates during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Diego Faccone
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, Buenos Aires City 2290 (C1425FQB), Argentina
| | - Sonia A Gomez
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, Buenos Aires City 2290 (C1425FQB), Argentina
| | - Juan Manuel de Mendieta
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - María Belén Sanz
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Mariano Echegorry
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Ezequiel Albornoz
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Celeste Lucero
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Paola Ceriana
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Alejandra Menocal
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Florencia Martino
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, Buenos Aires City 2290 (C1425FQB), Argentina
| | - Denise De Belder
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| | - Fernando Pasterán
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS "Dr. Carlos G. Malbrán", Ave. Velez Sarsfield, 563, Buenos Aires City 1281, Argentina
| |
Collapse
|
22
|
Kot B, Piechota M, Szweda P, Mitrus J, Wicha J, Grużewska A, Witeska M. Virulence analysis and antibiotic resistance of Klebsiella pneumoniae isolates from hospitalised patients in Poland. Sci Rep 2023; 13:4448. [PMID: 36932105 PMCID: PMC10023695 DOI: 10.1038/s41598-023-31086-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Klebsiella pneumoniae (KP) is a nosocomial pathogen causing difficult-to-treat infections. The presence of virulence genes and antibiotic resistance of 109 KP isolates from hospitalized patients were investigated. Among them, 68.8% were multi-drug resistant (MDR) and 59.6% produced extended-spectrum beta-lactamases (ESBLs). Metallo-β-lactamases (MBLs) were produced by 22% of isolates (mainly from anus), including 16.5% of isolates producing New Delhi metallo-β-lactamase (NDM-1). The genes encoding adhesins (fimH-91.7%, mrkD-96.3%), enterobactin (entB-100%) and yersiniabactin (irp-1-88%) were frequently identified. The genes encoding salmochelin (iroD-9.2%, iroN-7.3%) and colibactin (clbA, clbB-0.9%) were identified rarely. Iron acquisition system-related kfu gene and wcaG gene involved in capsule production were identified in 6.4% and 11% of isolates, respectively. The rmpA gene associated with hypermucoviscosity was present in 6.4% of isolates. In 19.2% of isolates magA gene was detected, specific for K1 capsule serotype, while 22.9% of isolates showed K2 capsule serotype. The rmpA, iroD or iroN genes being diagnostic biomarkers for hypervirulent KP (hvKP) were detected in 16.5% of isolates. We found that 55.5% of hvKP were MDR and produced ESBLs, thus hospital KP isolates pose a serious threat to the healthcare system.
Collapse
Affiliation(s)
- Barbara Kot
- Institute of Biological Sciences, Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 14 Bolesława Prusa Str., 08-110, Siedlce, Poland.
| | - Małgorzata Piechota
- Institute of Biological Sciences, Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 14 Bolesława Prusa Str., 08-110, Siedlce, Poland
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, 11/12 G. Narutowicza Str., 80-233, Gdańsk, Poland
| | - Joanna Mitrus
- Institute of Biological Sciences, Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 14 Bolesława Prusa Str., 08-110, Siedlce, Poland
| | - Jolanta Wicha
- Medical Microbiological Laboratory, Our Lady of Perpetual Help Hospital, 1/3 Gdyńska Str., 05-200, Wołomin, Poland
| | - Agata Grużewska
- Institute of Agriculture and Horticulture, Faculty of Agrobioengineering and Animal Husbandry, Siedlce University of Natural Sciences and Humanities, 12 Bolesława Prusa Str., 08-110, Siedlce, Poland
| | - Małgorzata Witeska
- Department of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| |
Collapse
|
23
|
Shaidullina ER, Schwabe M, Rohde T, Shapovalova VV, Dyachkova MS, Matsvay AD, Savochkina YA, Shelenkov AA, Mikhaylova YV, Sydow K, Lebreton F, Idelevich EA, Heiden SE, Becker K, Kozlov RS, Shipulin GA, Akimkin VG, Lalk M, Guenther S, Zautner AE, Bohnert JA, Mardanova AM, Bouganim R, Marchaim D, Hoff KJ, Schaufler K, Edelstein MV. Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395. Genome Med 2023; 15:9. [PMID: 36782220 PMCID: PMC9926764 DOI: 10.1186/s13073-023-01159-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. METHODS We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. RESULTS Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. CONCLUSIONS To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
Collapse
Affiliation(s)
- Elvira R. Shaidullina
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - Michael Schwabe
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Rohde
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Valeria V. Shapovalova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Marina S. Dyachkova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Alina D. Matsvay
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Yuliya A. Savochkina
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Katharina Sydow
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - François Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA
| | - Evgeny A. Idelevich
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany ,grid.16149.3b0000 0004 0551 4246Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan E. Heiden
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Roman S. Kozlov
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - German A. Shipulin
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | - Michael Lalk
- grid.5603.0Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastian Guenther
- grid.5603.0Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas E. Zautner
- grid.5807.a0000 0001 1018 4307Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jürgen A. Bohnert
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ayslu M. Mardanova
- grid.77268.3c0000 0004 0543 9688Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ruth Bouganim
- grid.413990.60000 0004 1772 817XDepartment of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Dror Marchaim
- grid.12136.370000 0004 1937 0546Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katharina J. Hoff
- grid.5603.0Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany. .,Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Mikhail V. Edelstein
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| |
Collapse
|
24
|
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: 19] [Impact Index Per Article: 19.0] [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.
Collapse
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.
| |
Collapse
|
25
|
Kamau E, Ranson EL, Tsan AT, Bergmann-Leitner ES, Garner OB, Yang S. Clinical and genomic characterization of hypervirulent Klebsiella pneumoniae (hvKp) infections via passive surveillance in Southern California, 2020–2022. Front Microbiol 2022; 13:1001169. [PMID: 36312975 PMCID: PMC9614223 DOI: 10.3389/fmicb.2022.1001169] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is more invasive and virulent than classical K. pneumoniae, and requires specialized treatment. To raise clinical awareness, this study determined the prevalence, clinical characteristics, and genomic epidemiology of hvKp infections in Southern California (SoCal) by conducting a passive surveillance in a single large academic medical center. We report here that hvKp infections were more common than expected, accounting for 2.6% of invasive K. pneumoniae infections, and presented with a wide disease spectrum, occasionally mimicking tumors, even co-infecting a COVID-19 patient. Most infections were community acquired with no recent international travel, suggesting hvKp strains are circulating in the community. Genomic analysis revealed genetic diversity, with the K1-ST23 lineage predominating but not clonal, and multiple sequence types of K2 including a SoCal unique K2-ST66 sublineage that had been unrecognized. Our findings highlight the urgency of heightened awareness of hvKp infection in the US, the need for rapid diagnosis of hvKp, and the necessity of implementing robust surveillance programs for hvKp at the institutional or local level.
Collapse
Affiliation(s)
- Edwin Kamau
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Elizabeth L. Ranson
- Division of Infectious Diseases, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Allison T. Tsan
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Elke S. Bergmann-Leitner
- Biologics Research and Development, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Omai B. Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
- *Correspondence: Shangxin Yang
| |
Collapse
|