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Vornhagen J, Rao K, Bachman MA. Gut community structure as a risk factor for infection in Klebsiella pneumoniae-colonized patients. mSystems 2024; 9:e0078624. [PMID: 38975759 PMCID: PMC11334466 DOI: 10.1128/msystems.00786-24] [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: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
The primary risk factor for infection with members of the Klebsiella pneumoniae species complex is prior gut colonization, and infection is often caused by the colonizing strain. Despite the importance of the gut as a reservoir for infectious K. pneumoniae, little is known about the association between the gut microbiome and infection. To explore this relationship, we undertook a case-control study comparing the gut community structure of K. pneumoniae-colonized intensive care and hematology/oncology patients. Cases were K. pneumoniae-colonized patients infected by their colonizing strain (N = 83). Controls were K. pneumoniae-colonized patients who remained asymptomatic (N = 149). First, we characterized the gut community structure of K. pneumoniae-colonized patients agnostic to case status. Next, we determined that gut community data is useful for classifying cases and controls using machine learning models and that the gut community structure differed between cases and controls. K. pneumoniae relative abundance, a known risk factor for infection, had the greatest feature importance, but other gut microbes were also informative. Finally, we show that integration of gut community structure with bacterial genotype data enhanced the ability of machine learning models to discriminate cases and controls. Interestingly, inclusion of patient clinical variables failed to improve the ability of machine learning models to discriminate cases and controls. This study demonstrates that including gut community data with K. pneumoniae-derived biomarkers improves our ability to classify infection in K. pneumoniae-colonized patients.IMPORTANCEColonization is generally the first step in pathogenesis for bacteria with pathogenic potential. This step provides a unique window for intervention since a given potential pathogen has yet to cause damage to its host. Moreover, intervention during the colonization stage may help alleviate the burden of therapy failure as antimicrobial resistance rises. Yet, to understand the therapeutic potential of interventions that target colonization, we must first understand the biology of colonization and if biomarkers at the colonization stage can be used to stratify infection risk. The bacterial genus Klebsiella includes many species with varying degrees of pathogenic potential. Members of the K. pneumoniae species complex have the highest pathogenic potential. Patients colonized in their gut by these bacteria are at higher risk of subsequent infection with their colonizing strain. However, we do not understand if other members of the gut microbiota can be used as a biomarker to predict infection risk. In this study, we show that the gut microbiota differs between colonized patients who develop an infection versus those who do not. Additionally, we show that integrating gut microbiota data with bacterial factors improves the ability to classify infections. Surprisingly, patient clinical factors were not useful for classifying infections alone or when added to microbiota-based models. This indicates that the bacterial genotype and the microbial community in which it exists may determine the progression to infection. As we continue to explore colonization as an intervention point to prevent infections in individuals colonized by potential pathogens, we must develop effective means for predicting and stratifying infection risk.
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Affiliation(s)
- Jay Vornhagen
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Krishna Rao
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Sun W, Rong C, Chen L, Li J, An Z, Yue J, Wei H, Han K, Hua M, Zeng H, Chen C. Microaerobic-mediated suppression of Klebsiella pneumoniae mucoviscosity is restored by rmpD overexpression. J Appl Microbiol 2024; 135:lxae192. [PMID: 39090973 DOI: 10.1093/jambio/lxae192] [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: 03/17/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/04/2024]
Abstract
AIMS Hypervirulent Klebsiella pneumoniae (hvKp) causes invasive community-acquired infections in healthy individuals, and hypermucoviscosity (HMV) is the main phenotype associated with hvKp. This study investigates the impact of microaerobic environment availability on the mucoviscosity of K. pneumoniae. METHODS AND RESULTS By culturing 25 clinical strains under microaerobic and aerobic environments, we observed a notable reduction in mucoviscosity in microaerobic environments. RNA sequencing and qRT-PCR revealed downregulated expressions of capsule synthesis genes (galf, orf2, wzi, wza, wzb, wzc, wcaj, manC, manB, and ugd) and regulatory genes (rmpA, rmpD, and rmpC) under microaerobic conditions. Transmission electron microscopy and Indian ink staining analysis were performed, revealing that the capsular thickness of K. pneumoniae decreased by half in microaerobic conditions compared to aerobic conditions. Deletion of rmpD and rmpC caused the loss of the HMV phenotype in both aerobic and microaerobic conditions. However, compared to wild-type strain in microaerobic condition, only rmpD overexpression strain, and not rmpC overexpression strain, displayed a significant increase in capsule thickness in microaerobic conditions. CONCLUSIONS Microaerobic conditions can suppress the mucoviscosity of K. pneumoniae, but this suppression can be overcome by altering the expression of rmpD, indicating a specific function for rmpD in the oxygen environmental adaptation of K. pneumoniae.
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Affiliation(s)
- Wangnan Sun
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Chengbo Rong
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Liang Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Jiarui Li
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Zhijing An
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Jinglin Yue
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Hengkun Wei
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Kai Han
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Mingxi Hua
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Hui Zeng
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Chen Chen
- Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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Todd K, Gunter K, Bowen JM, Holmes CL, Tilston-Lunel NL, Vornhagen J. Type-2 diabetes mellitus enhances Klebsiella pneumoniae pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596766. [PMID: 38853822 PMCID: PMC11160788 DOI: 10.1101/2024.05.31.596766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen and an important cause of pneumonia, bacteremia, and urinary tract infection. K. pneumoniae infections are historically associated with diabetes mellitus. There is a fundamental gap in our understanding of how diabetes mellitus, specifically type 2 diabetes, influences K. pneumoniae pathogenesis. K. pneumoniae pathogenesis is a multifactorial process that often begins with gut colonization, followed by an escape from the gut to peripheral sites, leading to host damage and infection. We hypothesized that type 2 diabetes enhances K. pneumoniae pathogenesis. To test this, we used well-established mouse models of K. pneumoniae colonization and lung infection in conjunction with a mouse model of spontaneous type 2 diabetes mellitus (T2DM). We show that T2DM enhances susceptibility to both K. pneumoniae colonization and infection. The enhancement of gut colonization is dependent on T2DM-induced modulation of the gut microbiota community structure. In contrast, lung infection is exacerbated by the increased availability of amino acids in the lung, which is associated with higher levels of vascular endothelial growth factor. These data lay the foundation for mechanistic interrogation of the relationship between K. pneumoniae pathogenesis and type 2 diabetes mellitus, and explicitly establish T2DM as a risk factor for K. pneumoniae disease.
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Affiliation(s)
- Katlyn Todd
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indiana University, Indianapolis, USA
| | - Krista Gunter
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indiana University, Indianapolis, USA
| | - James M. Bowen
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indiana University, Indianapolis, USA
| | - Caitlyn L. Holmes
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Natasha L. Tilston-Lunel
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indiana University, Indianapolis, USA
| | - Jay Vornhagen
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indiana University, Indianapolis, USA
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Fostervold A, Raffelsberger N, Hetland MAK, Bakksjø R, Bernhoff E, Samuelsen Ø, Sundsfjord A, Afset JE, Berntsen CF, Bævre-Jensen R, Ebbesen MH, Gammelsrud KW, Guleng AD, Handal N, Jakovljev A, Johal SK, Marvik Å, Natvik A, Sandnes RA, Tofteland S, Bjørnholt JV, Löhr IH. Risk of death in Klebsiella pneumoniae bloodstream infections is associated with specific phylogenetic lineages. J Infect 2024; 88:106155. [PMID: 38574775 DOI: 10.1016/j.jinf.2024.106155] [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: 01/31/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Klebsiella pneumoniae species complex (KpSC) bloodstream infections (BSIs) are associated with considerable morbidity and mortality, particularly in elderly and multimorbid patients. Multidrug-resistant (MDR) strains have been associated with poorer outcome. However, the clinical impact of KpSC phylogenetic lineages on BSI outcome is unclear. METHODS In an 18-month nationwide Norwegian prospective study of KpSC BSI episodes in adults, we used whole-genome sequencing to describe the molecular epidemiology of KpSC, and multivariable Cox regression analysis including clinical data to determine adjusted hazard ratios (aHR) for death associated with specific genomic lineages. FINDINGS We included 1078 BSI episodes and 1082 bacterial isolates from 1055 patients. The overall 30-day case-fatality rate (CFR) was 12.5%. Median patient age was 73.4, 61.7% of patients were male. Median Charlson comorbidity score was 3. Klebsiella pneumoniae sensu stricto (Kp) (79.3%, n = 858/1082) and K. variicola (15.7%, n = 170/1082) were the dominating phylogroups. Global MDR-associated Kp clonal groups (CGs) were prevalent (25.0%, n = 270/1082) but 78.9% (n = 213/270) were not MDR, and 53.7% (n = 145/270) were community acquired. The major findings were increased risk for death within 30 days in monomicrobial BSIs caused by K. variicola (CFR 16.9%, n = 21; aHR 1.86, CI 1.10-3.17, p = 0.02), and global MDR-associated Kp CGs (CFR 17.0%, n = 36; aHR 1.52, CI 0.98-2.38, p = 0.06) compared to Kp CGs not associated with MDR (CFR 10.1%, n = 46). CONCLUSION Bacterial traits, beyond antimicrobial resistance, have a major impact on the clinical outcome of KpSC BSIs. The global spread of MDR-associated Kp CGs is driven by other mechanisms than antibiotic selection alone. Further insights into virulence determinants, and their association with phylogenetic lineages are needed to better understand the epidemiology of KpSC infection and clinical outcome.
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Affiliation(s)
- Aasmund Fostervold
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.
| | - Niclas Raffelsberger
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Marit A K Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway; Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Ragna Bakksjø
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jan E Afset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Microbiology, St. Olav's Hospital, Trondheim University hospital, Trondheim, Norway
| | - Christopher F Berntsen
- Department of Internal Medicine, Lovisenberg Diaconal Hospital, Oslo, Norway; Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Roar Bævre-Jensen
- Department of Medical Microbiology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Marit H Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Karianne W Gammelsrud
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anja D Guleng
- Centre for Laboratory Medicine, Østfold Hospital Trust, Kalnes, Norway
| | - Nina Handal
- Department of Microbiology and Infection control, Akershus University Hospital, Lørenskog, Norway
| | - Aleksandra Jakovljev
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Microbiology, St. Olav's Hospital, Trondheim University hospital, Trondheim, Norway
| | - Simreen K Johal
- Department of Medical Microbiology, Nordland Hospital Trust, Bodø, Norway
| | - Åshild Marvik
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Ane Natvik
- Department of Medical Microbiology, Vestre Viken Hospital Trust, Bærum, Norway
| | - Rolf-Arne Sandnes
- Department of Medical Microbiology, Innlandet Hospital Trust, Lillehammer, Norway
| | - Ståle Tofteland
- Department of Microbiology, Hospital of Southern Norway Trust, Kristiansand, Norway
| | - Jørgen V Bjørnholt
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Iren H Löhr
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
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Wang X, Liu J, Li A. Incidence and risk factors for subsequent infections among rectal carriers with carbapenem-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. J Hosp Infect 2024; 145:11-21. [PMID: 38092302 DOI: 10.1016/j.jhin.2023.12.002] [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: 10/06/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a major pathogen causing nosocomial infections with a high mortality and poor prognosis. Gastrointestinal carriage has been acknowledged as the primary reservoir of CRKp infections. AIM To explore the incidence and risk factors associated with CRKp infection following colonization. METHODS The PubMed, Web of Science, and Cochrane Library databases were searched for relevant articles published between December 1998 and June 2023. Pooled estimates with a 95% confidence interval (CI) were calculated for the incidence rate, whereas pooled odds ratios (ORs) were calculated for the risk factors for which the OR was reported in three or more studies. FINDINGS Fourteen studies were included in the review with 5483 patients for the assessment of incidence, whereas seven of these studies with 2170 patients were included for the analysis of risk factors. In the meta-analysis, the incidence of CRKp infections after colonization was 23.2% (17.9-28.5). Additionally, three independent risk factors for subsequent CRKp infections were identified as admission to the intensive care unit (ICU) (2.59; 95% CI: 1.64-4.11), invasive procedures (2.53; 95% CI: 1.59-4.03), and multi-site colonization (6.24; 95% CI: 2.38-16.33). CONCLUSION This review reveals the incidence of CRKp infections in rectal carriers in different countries, emphasizing the role of rectal colonization with CRKp as an important source of nosocomial infections. Significantly, the risk factors indicated in this review can assist clinicians in identifying CRKp carriers with an elevated risk of subsequent infections, thereby enabling further measures to be taken to prevent nosocomial infections.
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Affiliation(s)
- X Wang
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - J Liu
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - A Li
- Department of Critical Care Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing, China.
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Wantuch PL, Rosen DA. Klebsiella pneumoniae: adaptive immune landscapes and vaccine horizons. Trends Immunol 2023; 44:826-844. [PMID: 37704549 DOI: 10.1016/j.it.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023]
Abstract
Klebsiella pneumoniae is among the most common antibiotic-resistant pathogens causing nosocomial infections. Additionally, it is a leading cause of neonatal sepsis and childhood mortality across the globe. Despite its clinical importance, we are only beginning to understand how the mammalian adaptive immune system responds to this pathogen. Further, many studies investigating potential K. pneumoniae vaccine candidates or alternative therapies have been launched in recent years. Here, we review the current state of knowledge on the adaptive immune response to K. pneumoniae infections and progress towards developing vaccines and other therapies to combat these infections.
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Affiliation(s)
- Paeton L Wantuch
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David A Rosen
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F. The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLoS Genet 2023; 19:e1010842. [PMID: 37531401 PMCID: PMC10395866 DOI: 10.1371/journal.pgen.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Affiliation(s)
- Judit Burgaya
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, UMR CNRS 6047, Université Paris-Cité, Paris, France
| | | | | | | | | | | | - Agnès Lefort
- Université Paris Cité, INSERM, IAME, Paris, France
| | | | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR7241 / INSERM U1050, PSL Research University, Paris, France
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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.
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Affiliation(s)
- Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, USA
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Silva I, Rodrigues ET, Tacão M, Henriques I. Microplastics accumulate priority antibiotic-resistant pathogens: Evidence from the riverine plastisphere. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121995. [PMID: 37302790 DOI: 10.1016/j.envpol.2023.121995] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Microplastics (MPs) might accumulate and transport antibiotic-resistant bacteria (ARB) in aquatic systems. We determined the abundance and diversity of culturable ciprofloxacin- and cefotaxime-resistant bacteria in biofilms covering MPs placed in river water, and characterized priority pathogens from these biofilms. Our results showed that the abundance of ARB colonizing MPs tends to be higher compared to sand particles. Also, higher numbers were cultivated from a mixture of polypropylene (PP), polyethylene (PE) and polyethylene terephthalate (PET), compared to PP and PET alone. Aeromonas and Pseudomonas isolates were the most frequently retrieved from MPs placed before a WWTP discharge while Enterobacteriaceae dominated the culturable plastisphere 200 m after the WWTP discharge. Ciprofloxacin- and/or cefotaxime-resistant Enterobacteriaceae (n = 54 unique isolates) were identified as Escherichia coli (n = 37), Klebsiella pneumoniae (n = 3), Citrobacter spp. (n = 9), Enterobacter spp. (n = 4) and Shigella sp. (n = 1). All isolates presented at least one of the virulence features tested (i.e. biofilm formation, haemolytic activity and production of siderophores), 70% carried the intI1 gene and 85% exhibited a multi-drug resistance phenotype. Plasmid-mediated quinolone resistance genes were detected in ciprofloxacin-resistant Enterobacteriaceae [aacA4-cr (40% of the isolates), qnrS (30%), qnrB (25%), and qnrVC (8%)], along with mutations in gyrA (70%) and parC (72%). Cefotaxime-resistant strains (n = 23) harbored blaCTX-M (70%), blaTEM (61%) and blaSHV (39%). Among CTX-M producers, high-risk clones of E. coli (e.g. ST10 or ST131) and K. pneumoniae (ST17) were identified, most of which carrying blaCTX-M-15. Ten out of 16 CTX-M producers were able to transfer blaCTX-M to a recipient strain. Our results demonstrated the occurrence of multidrug resistant Enterobacteriaceae in the riverine plastisphere, harboring ARGs of clinical concern and exhibiting virulence traits, suggesting a contribution of MPs to the dissemination of antibiotic-resistant priority pathogens. The type of MPs and especially water contamination (e.g. by WWTPs discharges) seem to determine the resistome of the riverine plastisphere.
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Affiliation(s)
- Isabel Silva
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal; CESAM (Centre for Environmental and Marine Studies) University of Aveiro, 3810-193, Aveiro, Portugal
| | - Elsa T Rodrigues
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Marta Tacão
- CESAM (Centre for Environmental and Marine Studies) University of Aveiro, 3810-193, Aveiro, Portugal; Department of Biology University of Aveiro, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal.
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Coleman S, Unterhauser K, Rezaul K, Ledala N, Lesmes S, Caimano MJ, Zhou Y, Jackson E, Gratalo D, Driscoll MD, Matson AP. High-resolution microbiome analysis reveals exclusionary Klebsiella species competition in preterm infants at risk for necrotizing enterocolitis. Sci Rep 2023; 13:7893. [PMID: 37193703 DOI: 10.1038/s41598-023-34735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023] Open
Abstract
Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~ 2500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiella species colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichia in NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecalis was co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiella strains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.
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Affiliation(s)
- Spencer Coleman
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Stephanie Lesmes
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa J Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Adam P Matson
- Department of Pediatrics, UConn Health, Farmington, CT, USA.
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.
- Department of Immunology, UConn Health, Farmington, CT, USA.
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Vornhagen J, Rao K, Bachman MA. Gut community structure as a risk factor for infection in Klebsiella -colonized patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.18.23288742. [PMID: 37131824 PMCID: PMC10153327 DOI: 10.1101/2023.04.18.23288742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The primary risk factor for infection with members of the Klebsiella pneumoniae species complex is prior gut colonization, and infection is often caused by the colonizing strain. Despite the importance of the gut as a reservoir for infectious Klebsiella , little is known about the association between the gut microbiome and infection. To explore this relationship, we undertook a case-control study comparing the gut community structure of Klebsiella -colonized intensive care and hematology/oncology patients. Cases were Klebsiella -colonized patients infected by their colonizing strain (N = 83). Controls were Klebsiella -colonized patients that remained asymptomatic (N = 149). First, we characterized the gut community structure of Klebsiella -colonized patients agnostic to case status. Next, we determined that gut community data is useful for classifying cases and controls using machine learning models and that the gut community structure differed between cases and controls. Klebsiella relative abundance, a known risk factor for infection, had the greatest feature importance but other gut microbes were also informative. Finally, we show that integration of gut community structure with bacterial genotype or clinical variable data enhanced the ability of machine learning models to discriminate cases and controls. This study demonstrates that including gut community data with patient- and Klebsiella -derived biomarkers improves our ability to predict infection in Klebsiella -colonized patients. Importance Colonization is generally the first step in pathogenesis for bacteria with pathogenic potential. This step provides a unique window for intervention since a given potential pathogen has yet to cause damage to its host. Moreover, intervention during the colonization stage may help alleviate the burden of therapy failure as antimicrobial resistance rises. Yet, to understand the therapeutic potential of interventions that target colonization, we must first understand the biology of colonization and if biomarkers at the colonization stage can be used to stratify infection risk. The bacterial genus Klebsiella includes many species with varying degrees of pathogenic potential. Members of the K. pneumoniae species complex have the highest pathogenic potential. Patients colonized in their gut by these bacteria are at higher risk of subsequent infection with their colonizing strain. However, we do not understand if other members of the gut microbiota can be used as a biomarker to predict infection risk. In this study, we show that the gut microbiota differs between colonized patients that develop an infection versus those that do not. Additionally, we show that integrating gut microbiota data with patient and bacterial factors improves the ability to predict infections. As we continue to explore colonization as an intervention point to prevent infections in individuals colonized by potential pathogens, we must develop effective means for predicting and stratifying infection risk.
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A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain. Pathogens 2022; 11:pathogens11121394. [PMID: 36558729 PMCID: PMC9781218 DOI: 10.3390/pathogens11121394] [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: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of K. pneumoniae is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICEKp, iuc, rmpADC/2) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 K. pneumoniae genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 K. pneumoniae, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.
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