1
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Lai X, Chow SH, Le Brun AP, Muir BW, Bergen PJ, White J, Yu HH, Wang J, Danne J, Jiang JH, Short FL, Han ML, Strugnell RA, Song J, Cameron NR, Peleg AY, Li J, Shen HH. Polysaccharide-Targeting Lipid Nanoparticles to Kill Gram-Negative Bacteria. Small 2024; 20:e2305052. [PMID: 37798622 DOI: 10.1002/smll.202305052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/16/2023] [Indexed: 10/07/2023]
Abstract
The rapid increase and spread of Gram-negative bacteria resistant to many or all existing treatments threaten a return to the preantibiotic era. The presence of bacterial polysaccharides that impede the penetration of many antimicrobials and protect them from the innate immune system contributes to resistance and pathogenicity. No currently approved antibiotics target the polysaccharide regions of microbes. Here, describe monolaurin-based niosomes, the first lipid nanoparticles that can eliminate bacterial polysaccharides from hypervirulent Klebsiella pneumoniae, are described. Their combination with polymyxin B shows no cytotoxicity in vitro and is highly effective in combating K. pneumoniae infection in vivo. Comprehensive mechanistic studies have revealed that antimicrobial activity proceeds via a multimodal mechanism. Initially, lipid nanoparticles disrupt polysaccharides, then outer and inner membranes are destabilized and destroyed by polymyxin B, resulting in synergistic cell lysis. This novel lipidic nanoparticle system shows tremendous promise as a highly effective antimicrobial treatment targeting multidrug-resistant Gram-negative pathogens.
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Affiliation(s)
- Xiangfeng Lai
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Seong Hoong Chow
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, New South Wales, 2232, Australia
| | | | - Phillip J Bergen
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jacinta White
- CSIRO Manufacturing, Clayton, Victoria, 3168, Australia
| | - Heidi H Yu
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jiping Wang
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jill Danne
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, A Node of Microscopy Australia, Monash University, Clayton, Victoria, 3800, Australia
| | - Jhih-Hang Jiang
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Francesca L Short
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Mei-Ling Han
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
| | - Neil R Cameron
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Anton Y Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Jian Li
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
| | - Hsin-Hui Shen
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, Victoria, 3800, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia
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2
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Wang N, Scott TA, Kupz A, Shreenivas MM, Peres NG, Hocking DM, Yang C, Jebeli L, Beattie L, Groom JR, Pierce TP, Wakim LM, Bedoui S, Strugnell RA. Vaccine-induced inflammation and inflammatory monocytes promote CD4+ T cell-dependent immunity against murine salmonellosis. PLoS Pathog 2023; 19:e1011666. [PMID: 37733817 PMCID: PMC10547166 DOI: 10.1371/journal.ppat.1011666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/03/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Prior infection can generate protective immunity against subsequent infection, although the efficacy of such immunity can vary considerably. Live-attenuated vaccines (LAVs) are one of the most effective methods for mimicking this natural process, and analysis of their efficacy has proven instrumental in the identification of protective immune mechanisms. Here, we address the question of what makes a LAV efficacious by characterising immune responses to a LAV, termed TAS2010, which is highly protective (80-90%) against lethal murine salmonellosis, in comparison with a moderately protective (40-50%) LAV, BRD509. Mice vaccinated with TAS2010 developed immunity systemically and were protected against gut-associated virulent infection in a CD4+ T cell-dependent manner. TAS2010-vaccinated mice showed increased activation of Th1 responses compared with their BRD509-vaccinated counterparts, leading to increased Th1 memory populations in both lymphoid and non-lymphoid organs. The optimal development of Th1-driven immunity was closely correlated with the activation of CD11b+Ly6GnegLy6Chi inflammatory monocytes (IMs), the activation of which can be modulated proportionally by bacterial load in vivo. Upon vaccination with the LAV, IMs expressed T cell chemoattractant CXCL9 that attracted CD4+ T cells to the foci of infection, where IMs also served as a potent source of antigen presentation and Th1-promoting cytokine IL-12. The expression of MHC-II in IMs was rapidly upregulated following vaccination and then maintained at an elevated level in immune mice, suggesting IMs may have a role in sustained antigen stimulation. Our findings present a longitudinal analysis of CD4+ T cell development post-vaccination with an intracellular bacterial LAV, and highlight the benefit of inflammation in the development of Th1 immunity. Future studies focusing on the induction of IMs may reveal key strategies for improving vaccine-induced T cell immunity.
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Affiliation(s)
- Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy A. Scott
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Andreas Kupz
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Meghanashree M. Shreenivas
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Newton G. Peres
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Dianna M. Hocking
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Chenying Yang
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lynette Beattie
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Joanna R. Groom
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P. Pierce
- Ludwig Institute for Cancer Research, Melbourne-Parkville Branch, Parkville, Victoria, Australia
| | - Linda M. Wakim
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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3
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Rosas NC, Wilksch J, Barber J, Li J, Wang Y, Sun Z, Rocker A, Webb CT, Perlaza-Jiménez L, Stubenrauch CJ, Dhanasekaran V, Song J, Taiaroa G, Davies M, Strugnell RA, Bao Q, Zhou T, McDonald MJ, Lithgow T. The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp. eLife 2023; 12:e83107. [PMID: 37410078 DOI: 10.7554/elife.83107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/16/2023] [Indexed: 07/07/2023] Open
Abstract
Antibiotic resistance is driven by selection, but the degree to which a bacterial strain's evolutionary history shapes the mechanism and strength of resistance remains an open question. Here, we reconstruct the genetic and evolutionary mechanisms of carbapenem resistance in a clinical isolate of Klebsiella quasipneumoniae. A combination of short- and long-read sequencing, machine learning, and genetic and enzymatic analyses established that this carbapenem-resistant strain carries no carbapenemase-encoding genes. Genetic reconstruction of the resistance phenotype confirmed that two distinct genetic loci are necessary in order for the strain to acquire carbapenem resistance. Experimental evolution of the carbapenem-resistant strains in growth conditions without the antibiotic revealed that both loci confer a significant cost and are readily lost by de novo mutations resulting in the rapid evolution of a carbapenem-sensitive phenotype. To explain how carbapenem resistance evolves via multiple, low-fitness single-locus intermediates, we hypothesised that one of these loci had previously conferred adaptation to another antibiotic. Fitness assays in a range of drug concentrations show how selection in the antibiotic ceftazidime can select for one gene (blaDHA-1) potentiating the evolution of carbapenem resistance by a single mutation in a second gene (ompK36). These results show how a patient's treatment history might shape the evolution of antibiotic resistance and could explain the genetic basis of carbapenem-resistance found in many enteric-pathogens.
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Affiliation(s)
- Natalia C Rosas
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Jonathan Wilksch
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Jake Barber
- Centre to Impact AMR, Monash University, Clayton, Australia
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Jiahui Li
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanan Wang
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- School of Biological Sciences, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Zhewei Sun
- Wenzhou Medical University, Wenzhou, China
| | - Andrea Rocker
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Chaille T Webb
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Laura Perlaza-Jiménez
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Vijaykrishna Dhanasekaran
- Centre to Impact AMR, Monash University, Clayton, Australia
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jiangning Song
- Centre to Impact AMR, Monash University, Clayton, Australia
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - George Taiaroa
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Mark Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Qiyu Bao
- Wenzhou Medical University, Wenzhou, China
| | - Tieli Zhou
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Michael J McDonald
- Centre to Impact AMR, Monash University, Clayton, Australia
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
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4
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Engel S, Bachem A, Strugnell RA, Strasser A, Herold MJ, Bedoui S. Functional flexibility and plasticity in immune control of systemic Salmonella infection. Curr Opin Immunol 2023; 83:102343. [PMID: 37245415 DOI: 10.1016/j.coi.2023.102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/30/2023]
Abstract
Immunity to systemic Salmonella infection depends on multiple effector mechanisms. Lymphocyte-derived interferon gamma (IFN-γ) enhances cell-intrinsic bactericidal capabilities to antagonize the hijacking of phagocytes as replicative niches for Salmonella. Programmed cell death (PCD) provides another means through which phagocytes fight against intracellular Salmonella. We describe remarkable levels of flexibility with which the host coordinates and adapts these responses. This involves interchangeable cellular sources of IFN-γ regulated by innate and adaptive cues, and the rewiring of PCD pathways in previously unknown ways. We discuss that such plasticity is likely the consequence of host-pathogen coevolution and raise the possibility of further functional overlap between these seemingly distinct processes.
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Affiliation(s)
- Sven Engel
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia.
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5
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Mu A, Klare WP, Baines SL, Ignatius Pang CN, Guérillot R, Harbison-Price N, Keller N, Wilksch J, Nhu NTK, Phan MD, Keller B, Nijagal B, Tull D, Dayalan S, Chua HHC, Skoneczny D, Koval J, Hachani A, Shah AD, Neha N, Jadhav S, Partridge SR, Cork AJ, Peters K, Bertolla O, Brouwer S, Hancock SJ, Álvarez-Fraga L, De Oliveira DMP, Forde B, Dale A, Mujchariyakul W, Walsh CJ, Monk I, Fitzgerald A, Lum M, Correa-Ospina C, Roy Chowdhury P, Parton RG, De Voss J, Beckett J, Monty F, McKinnon J, Song X, Stephen JR, Everest M, Bellgard MI, Tinning M, Leeming M, Hocking D, Jebeli L, Wang N, Ben Zakour N, Yasar SA, Vecchiarelli S, Russell T, Zaw T, Chen T, Teng D, Kassir Z, Lithgow T, Jenney A, Cole JN, Nizet V, Sorrell TC, Peleg AY, Paterson DL, Beatson SA, Wu J, Molloy MP, Syme AE, Goode RJA, Hunter AA, Bowland G, West NP, Wilkins MR, Djordjevic SP, Davies MR, Seemann T, Howden BP, Pascovici D, Tyagi S, Schittenhelm RB, De Souza DP, McConville MJ, Iredell JR, Cordwell SJ, Strugnell RA, Stinear TP, Schembri MA, Walker MJ. Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nat Commun 2023; 14:1530. [PMID: 36934086 PMCID: PMC10024524 DOI: 10.1038/s41467-023-37200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Wellcome Sanger Institute, Hinxton, UK
| | - William P Klare
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - C N Ignatius Pang
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nichaela Harbison-Price
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nadia Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nguyen Thi Khanh Nhu
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bernhard Keller
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brunda Nijagal
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Hwa Huat Charlie Chua
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dominik Skoneczny
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Nitika Neha
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Snehal Jadhav
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kate Peters
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Olivia Bertolla
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Hancock
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Álvarez-Fraga
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Brian Forde
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ashleigh Dale
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Warasinee Mujchariyakul
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ian Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Mabel Lum
- Bioplatforms Australia Ltd., Sydney, NSW, Australia
| | - Carolina Correa-Ospina
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Piklu Roy Chowdhury
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - James De Voss
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - James Beckett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Francois Monty
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Jessica McKinnon
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Xiaomin Song
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - John R Stephen
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Marie Everest
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Matt I Bellgard
- Office of eResearch, Queensland University of Technology, Brisbane, QLD, Australia
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Matthew Tinning
- Australian Genome Research Facility Ltd., Melbourne, VIC, Australia
| | - Michael Leeming
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nouri Ben Zakour
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Serhat A Yasar
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Stefano Vecchiarelli
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Tonia Russell
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Thiri Zaw
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Tyrone Chen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Don Teng
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Zena Kassir
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Trevor Lithgow
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Adam Jenney
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Jason N Cole
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
- Centre to Impact AMR and Infection Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - David L Paterson
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jemma Wu
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Anna E Syme
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J A Goode
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, Australia
| | - Adam A Hunter
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Grahame Bowland
- Center for Comparative Genomics, Murdoch University, Perth, WA, Australia
| | - Nicholas P West
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Marc R Wilkins
- Ramaciotti Centre for Genomics, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Sonika Tyagi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Hospital/ Westmead Institute, and Sydney ID, University of Sydney, Sydney, NSW, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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6
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Strugnell RA. When secretion turns into excretion - the different roles of IgA. Front Immunol 2022; 13:1076312. [PMID: 36618388 PMCID: PMC9812643 DOI: 10.3389/fimmu.2022.1076312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
IgA deficiency is the commonest immunodeficiency affecting up to 1 in 700 individuals. The effects of IgA deficiency are difficult to see in many individuals, are mild in many fewer and severe in fewer still. While monovalent IgA is found in serum, dimeric IgA is secreted through mucosal surfaces where it helps to maintain epithelial homeostasis. Studies with knockout mice have taught us that there are subtle inflammatory consequences of removing secretory IgA (sIgA), and the best explanation for these changes can be related by the loss of the 'excretory' immune system. The excretion of antigens is a logical process in regulating the immune system, given the long half-life of complement fixing antibodies. But the function of IgA as an immune or inflammation regulator may go beyond antigen removal.
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7
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Singh S, Wilksch JJ, Dunstan RA, Mularski A, Wang N, Hocking D, Jebeli L, Cao H, Clements A, Jenney AWJ, Lithgow T, Strugnell RA. LPS O Antigen Plays a Key Role in Klebsiella pneumoniae Capsule Retention. Microbiol Spectr 2022; 10:e0151721. [PMID: 35913154 PMCID: PMC9431683 DOI: 10.1128/spectrum.01517-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/14/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the importance of encapsulation in bacterial pathogenesis, the biochemical mechanisms and forces that underpin retention of capsule by encapsulated bacteria are poorly understood. In Gram-negative bacteria, there may be interactions between lipopolysaccharide (LPS) core and capsule polymers, between capsule polymers with retained acyl carriers and the outer membrane, and in some bacteria, between the capsule polymers and Wzi, an outer membrane protein lectin. Our transposon studies in Klebsiella pneumoniae B5055 identified additional genes that, when insertionally inactivated, resulted in reduced encapsulation. Inactivation of the gene waaL, which encodes the ligase responsible for attaching the repeated O antigen of LPS to the LPS core, resulted in a significant reduction in capsule retention, measured by atomic force microscopy. This reduction in encapsulation was associated with increased sensitivity to human serum and decreased virulence in a murine model of respiratory infection and, paradoxically, with increased biofilm formation. The capsule in the WaaL mutant was physically smaller than that of the Wzi mutant of K. pneumoniae B5055. These results suggest that interactions between surface carbohydrate polymers may enhance encapsulation, a key phenotype in bacterial virulence, and provide another target for the development of antimicrobials that may avoid resistance issues associated with growth inhibition. IMPORTANCE Bacterial capsules, typically comprised of complex sugars, enable pathogens to avoid key host responses to infection, including phagocytosis. These capsules are synthesized within the bacteria, exported through the outer envelope, and then secured to the external surface of the organism by a force or forces that are incompletely described. This study shows that in the important hospital pathogen Klebsiella pneumoniae, the polysaccharide capsule is retained by interactions with other surface sugars, especially the repeated sugar molecule of the LPS molecule in Gram-negative bacteria known as "O antigen." This O antigen is joined to the LPS molecule by ligation, and loss of the enzyme responsible for ligation, a protein called WaaL, results in reduced encapsulation. Since capsules are essential to the virulence of many pathogens, WaaL might provide a target for new antimicrobial development, critical to the control of pathogens like K. pneumoniae that have become highly drug resistant.
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Affiliation(s)
- Shweta Singh
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jonathan J. Wilksch
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Rhys A. Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Anna Mularski
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Dianna Hocking
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Abigail Clements
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adam W. J. Jenney
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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8
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Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. Lancet Reg Health West Pac 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
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Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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9
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Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, Abbott IJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, Pilcher DV, McGloughlin SA, Spelman DW, Wyres KL, Jenney AWJ, Holt KE. Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nat Commun 2022; 13:3017. [PMID: 35641522 PMCID: PMC9156735 DOI: 10.1038/s41467-022-30717-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022] Open
Abstract
Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p < 0.001). Virulence plasmid-encoded features (aerobactin, hypermucoidy) are observed at low-prevalence (<3%), mostly in community-onset cases. WGS-confirmed nosocomial transmission is implicated in just 10% of cases, but strongly associated with ESBLs (OR 21, p < 1 × 10−11). We estimate 28% risk of onward nosocomial transmission for ESBL-positive strains vs 1.7% for ESBL-negative strains. These data indicate that K. pneumoniae infections in hospitalised patients are due largely to opportunistic infections with diverse strains, with an additional burden from nosocomially-transmitted AMR strains and community-acquired hypervirulent strains. Klebsiella pneumoniae is an opportunistic pathogen of increasing public health concern due to the prevalence of antimicrobial resistance. Here, the authors provide insight into the resistance profiles, bacterial genome features and virulence genes, in a year-long prospective study of K. pneumoniae clinical isolates.
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Affiliation(s)
- Claire L Gorrie
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia.
| | - Mirjana Mirčeta
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia.,Doherty Applied Microbial Genomics (DAMG), Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Ryota Gomi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Iain J Abbott
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, Cambs, UK.,Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Kerrie M Watson
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Vic, Australia
| | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia.,Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia.,Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Denis W Spelman
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Adam W J Jenney
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia.,Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia. .,Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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10
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Strobel AG, Airs S, Nguyen C, Vadei TR, Matanitobua S, Kama M, Watson CH, Crump JA, Mulholland EK, Strugnell RA, Parry CM. Assessment of Rapid Diagnostic Tests for Typhoid Diagnosis and Assessment of Febrile Illness Outbreaks in Fiji. Am J Trop Med Hyg 2021; 106:543-549. [PMID: 34844208 PMCID: PMC8832939 DOI: 10.4269/ajtmh.21-0771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/10/2021] [Indexed: 12/02/2022] Open
Abstract
Typhoid is an endemic in Fiji with increases observed since the early 2000s and frequent outbreaks reported. We assessed the diagnostic accuracy of currently available typhoid rapid diagnostic tests (RDTs) (TUBEX, Typhidot Rapid, and Test-It assay) to establish their performance against blood culture in Fiji and to examine their suitability for rapid typhoid outbreak identification. The performance of RDTs was assessed in the public health reference laboratory in Suva, Fiji, according to the manufacturers’ instructions. A simulation was used to examine the potential use of RDTs for attribution of a febrile illness outbreak to typhoid. For the diagnostic evaluation, 179 patients were included; 49 had blood culture–confirmed typhoid, 76 had fever as a result of non-typhoid etiologies, and 54 were age-matched community controls. The median (interquartile range) age was 29 (20–46) years. Of the participants, 92 (51.4%) were male and 131 (73.2%) were indigenous Fijians. The sensitivities of the tests were 77.6% for TUBEX, 75.5% for Typhidot Rapid, and 57.1% for Test-It assay. The Test-It assay had the highest specificity of 93.4%, followed by Typhidot Rapid 85.5% and TUBEX 60.5%. Typhidot Rapid had the best performance in the simulation for attribution of a febrile illness outbreak to typhoid. Typhoid RDTs performed suboptimally for individual patient diagnosis due to low sensitivity and variable specificity. We demonstrate that RDTs could be useful in the field for rapid attribution of febrile illness outbreaks to typhoid. Typhidot Rapid had the best combination of sensitivity, specificity, positive and negative predictive values, cost, and ease of use for this purpose.
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Affiliation(s)
- Aneley Getahun Strobel
- School of Public Health and Primary Care, College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji.,Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Stephanie Airs
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Cattram Nguyen
- Murdoch Children's Research Institute, Melbourne, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, Australia
| | | | | | - Mike Kama
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Conall H Watson
- London School of Hygiene and Tropical Medicine, London, United Kingdom.,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool United Kingdom
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - E Kim Mulholland
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A Strugnell
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Christopher M Parry
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan.,Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool United Kingdom
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11
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Dunstan RA, Bamert RS, Belousoff MJ, Short FL, Barlow CK, Pickard DJ, Wilksch JJ, Schittenhelm RB, Strugnell RA, Dougan G, Lithgow T. Mechanistic Insights into the Capsule-Targeting Depolymerase from a Klebsiella pneumoniae Bacteriophage. Microbiol Spectr 2021; 9:e0102321. [PMID: 34431721 PMCID: PMC8552709 DOI: 10.1128/spectrum.01023-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
The production of capsular polysaccharides by Klebsiella pneumoniae protects the bacterial cell from harmful environmental factors such as antimicrobial compounds and infection by bacteriophages (phages). To bypass this protective barrier, some phages encode polysaccharide-degrading enzymes referred to as depolymerases to provide access to cell surface receptors. Here, we characterized the phage RAD2, which infects K. pneumoniae strains that produce the widespread, hypervirulence-associated K2-type capsular polysaccharide. Using transposon-directed insertion sequencing, we have shown that the production of capsule is an absolute requirement for efficient RAD2 infection by serving as a first-stage receptor. We have identified the depolymerase responsible for recognition and degradation of the capsule, determined that the depolymerase forms globular appendages on the phage virion tail tip, and present the cryo-electron microscopy structure of the RAD2 capsule depolymerase at 2.7-Å resolution. A putative active site for the enzyme was identified, comprising clustered negatively charged residues that could facilitate the hydrolysis of target polysaccharides. Enzymatic assays coupled with mass spectrometric analyses of digested oligosaccharide products provided further mechanistic insight into the hydrolase activity of the enzyme, which, when incubated with K. pneumoniae, removes the capsule and sensitizes the cells to serum-induced killing. Overall, these findings expand our understanding of how phages target the Klebsiella capsule for infection, providing a framework for the use of depolymerases as antivirulence agents against this medically important pathogen. IMPORTANCE Klebsiella pneumoniae is a medically important pathogen that produces a thick protective capsule that is essential for pathogenicity. Phages are natural predators of bacteria, and many encode diverse "capsule depolymerases" which specifically degrade the capsule of their hosts, an exploitable trait for potential therapies. We have determined the first structure of a depolymerase that targets the clinically relevant K2 capsule and have identified its putative active site, providing hints to its mechanism of action. We also show that Klebsiella cells treated with a recombinant form of the depolymerase are stripped of capsule, inhibiting their ability to grow in the presence of serum, demonstrating the anti-infective potential of these robust and readily producible enzymes against encapsulated bacterial pathogens such as K. pneumoniae.
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Affiliation(s)
- Rhys A. Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Rebecca S. Bamert
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Matthew J. Belousoff
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Francesca L. Short
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christopher K. Barlow
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Derek J. Pickard
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J. Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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12
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Erazo AB, Wang N, Standke L, Semeniuk AD, Fülle L, Cengiz SC, Thiem M, Weighardt H, Strugnell RA, Förster I. CCL17-expressing dendritic cells in the intestine are preferentially infected by Salmonella but CCL17 plays a redundant role in systemic dissemination. Immun Inflamm Dis 2021; 9:891-904. [PMID: 33945673 PMCID: PMC8342217 DOI: 10.1002/iid3.445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Introduction Salmonella spp. are a recognized and global cause of serious health issues from gastroenteritis to invasive disease. The mouse model of human typhoid fever, which uses Salmonella enterica serovar Typhimurium (STM) in susceptible mouse strains, has revealed that the bacteria gain access to extraintestinal tissues from the gastrointestinal tract to cause severe systemic disease. Previous analysis of the immune responses against Salmonella spp. revealed the crucial role played by dendritic cells (DCs) in carrying STM from the intestinal mucosa to the mesenteric lymph nodes (mLNs), a key site for antigen presentation and T cell activation. In this study, we investigated the influence of chemokine CCL17 on the dissemination of STM. Methods WT, CCL17/EGFP reporter, or CCL17‐deficient mice were infected orally with STM (SL1344) or mCherry‐expressing STM for 1–3 days. Colocalization of STM with CCL17‐expressing DCs in Peyer's patches (PP) and mLN was analyzed by fluorescence microscopy. In addition, DCs and myeloid cell populations from naïve and Salmonella‐infected mice were analyzed by flow cytometry. Bacterial load was determined in PP, mLN, spleen, and liver 1 and 3 days after infection. Results Histological analysis revealed that CCL17‐expressing cells are located in close proximity to STM in the dome area of PP. We show that, in mLN, STM were preferentially located within CCL17+ rather than CCL17− DCs, besides other mononuclear phagocytes, and identified the CD103+ CD11b− DC subset as the main STM‐carrying DC population in the intestine. STM infection triggered upregulation of CCL17 expression in specific intestinal DC subsets in a tissue‐specific manner. The dissemination of STM from the gut to the mLN, however, was only moderately influenced by the presence of CCL17. Conclusion CCL17‐expressing DCs were preferentially infected by Salmonella in the intestine in comparison to other DC. Nevertheless, the production of CCL17 was not essential for the early dissemination of Salmonella from the gut to systemic organs.
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Affiliation(s)
- Anna B Erazo
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lena Standke
- Department for Innate Immunity and Metaflammation, Institute of Innate Immunity, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Adrian D Semeniuk
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lorenz Fülle
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Sevgi C Cengiz
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Manja Thiem
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Heike Weighardt
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Irmgard Förster
- Immunology and Environment, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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13
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Zhang H, Wang H, Wilksch JJ, Strugnell RA, Gee ML, Feng XQ. Measurement of the interconnected turgor pressure and envelope elasticity of live bacterial cells. Soft Matter 2021; 17:2042-2049. [PMID: 33592087 DOI: 10.1039/d0sm02075c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Turgor pressure and envelope elasticity of bacterial cells are two mechanical parameters that play a dominant role in cellular deformation, division, and motility. However, a clear understanding of these two properties is lacking because of their strongly interconnected mechanisms. This study established a nanoindentation method to precisely measure the turgor pressure and envelope elasticity of live bacteria. The indentation force-depth curves of Klebsiella pneumoniae bacteria were recorded with atomic force microscopy. Through combination of dimensional analysis and numerical simulations, an explicit expression was derived to decouple the two properties of individual bacteria from the nanoindentation curves. We show that the Young's modulus of bacterial envelope is sensitive to the external osmotic environment, and the turgor pressure is significantly dependent on the external osmotic stress. This method can not only quantify the turgor pressure and envelope elasticity of bacteria, but also help resolve the mechanical behaviors of bacteria in different environments.
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Affiliation(s)
- Huanxin Zhang
- Institute of Biomechanics and Medical Engineering, AML, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
| | - Huabin Wang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China and Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing 400714, China
| | - Jonathan J Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michelle L Gee
- School of Aerospace Engineering and Aviation, RMIT University, Bundoora, Victoria 3083, Australia
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, AML, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
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14
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Nguyen K, Bui D, Hashemi M, Hocking DM, Mendis P, Strugnell RA, Dharmage SC. The Potential Use of Hypochlorous Acid and a Smart Prefabricated Sanitising Chamber to Reduce Occupation-Related COVID-19 Exposure. Risk Manag Healthc Policy 2021; 14:247-252. [PMID: 33519249 PMCID: PMC7837568 DOI: 10.2147/rmhp.s284897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 02/04/2023] Open
Abstract
This work is part of a project on the development of a smart prefabricated sanitising chamber (SPSC) to provide extra measures against the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Stabilised hypochlorous acid (HOCl) is an approved disinfectant against SARS-CoV-2 by the Environmental Protection Association US in its liquid form on non-porous surfaces. This review is extended to cover its viricidal/bactericidal efficacy in aerosolised or sprayed form which showed an effective dose of as low as 20 ppm and the exposure duration of at least 60 s. The aerosolised application was also recommended with particle size of less than 200 μm to increase the contact with pathogens. The review also includes the safety and toxicity of HOCl with different concentrations. The review calls for more investigations into the effect of HOCl in mist and fog form on the respiratory system when transitioning through the proposed SPSC.
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Affiliation(s)
- Kate Nguyen
- School of Engineering, RMIT University, Melbourne, Victoria, Australia
| | - Dinh Bui
- Centre of Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mahak Hashemi
- School of Engineering, RMIT University, Melbourne, Victoria, Australia.,ARC Training Centre on Advanced Manufacturing of Prefabricated Housing, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dianna M Hocking
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Priyan Mendis
- ARC Training Centre on Advanced Manufacturing of Prefabricated Housing, The University of Melbourne, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Shyamali C Dharmage
- Centre of Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
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15
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Nothling MD, Cao H, McKenzie TG, Hocking DM, Strugnell RA, Qiao GG. Bacterial Redox Potential Powers Controlled Radical Polymerization. J Am Chem Soc 2021; 143:286-293. [PMID: 33373526 DOI: 10.1021/jacs.0c10673] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbes employ a remarkably intricate electron transport system to extract energy from the environment. The respiratory cascade of bacteria culminates in the terminal transfer of electrons onto higher redox potential acceptors in the extracellular space. This general and inducible mechanism of electron efflux during normal bacterial proliferation leads to a characteristic fall in bulk redox potential (Eh), the degree of which is dependent on growth phase, the microbial taxa, and their physiology. Here, we show that the general reducing power of bacteria can be subverted to induce the abiotic production of a carbon-centered radical species for targeted bioorthogonal molecular synthesis. Using two species, Escherichia coli and Salmonella enterica serovar Typhimurium as model microbes, a common redox active aryldiazonium salt is employed to intervene in the terminal respiratory electron flow, affording radical production that is mediated by native redox-active molecular shuttles and active bacterial metabolism. The aryl radicals are harnessed to initiate and sustain a bioorthogonal controlled radical polymerization via reversible addition-fragmentation chain transfer (BacRAFT), yielding a synthetic extracellular matrix of "living" vinyl polymers with predetermined molecular weight and low dispersity. The ability to interface the ubiquitous reducing power of bacteria into synthetic materials design offers a new means for creating engineered living materials with promising adaptive and self-regenerative capabilities.
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Affiliation(s)
- Mitchell D Nothling
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thomas G McKenzie
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dianna M Hocking
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Greg G Qiao
- Department of Chemical Engineering, University of Melbourne, Melbourne, VIC 3010, Australia
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16
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Abstract
With the implementation of strict quarantine and adjunct health measures, Fiji was largely spared from the COVID-19 pandemic in 2020. In April 2021, the arrival of the delta variant of SARS-CoV-2 resulted in a major outbreak that is only now under control. The country enacted swift countermeasures to reduce population movement, but the delta variant gained a foothold in the peri-urban areas of the largest city, Suva, and from there spread to other major urban centres of the largest island, Viti Levu. A very effective vaccination campaign has since been implemented resulting in a rate of two-dose vaccination, above 70%, that exceeds many higher income countries and, as of late October 2021, the numbers of COVID-19 cases were in decline. Fijian life, especially in rural settings, is based on hierarchical but supportive community structures and the responsibilities that flow from community membership, for example, attending large funerals, mitigated against the organised and systematic control response instituted by the Fijian Ministry of Health and Medical Services, including vaccination, and the other Government agencies. A positive consequence of the outbreak has been the development of new capabilities, and the distribution of molecular diagnostic technologies that can be exploited to help control other infectious diseases.
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17
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Hancock SJ, Phan MD, Luo Z, Lo AW, Peters KM, Nhu NTK, Forde BM, Whitfield J, Yang J, Strugnell RA, Paterson DL, Walsh TR, Kobe B, Beatson SA, Schembri MA. Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB. Nat Microbiol 2020; 5:1340-1348. [PMID: 32807890 DOI: 10.1038/s41564-020-0775-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 07/16/2020] [Indexed: 01/05/2023]
Abstract
The IncC family of broad-host-range plasmids enables the spread of antibiotic resistance genes among human enteric pathogens1-3. Although aspects of IncC plasmid conjugation have been well studied4-9, many roles of conjugation genes have been assigned based solely on sequence similarity. We applied hypersaturated transposon mutagenesis and transposon-directed insertion-site sequencing to determine the set of genes required for IncC conjugation. We identified 27 conjugation genes, comprising 19 that were previously identified (including two regulatory genes, acaDC) and eight not previously associated with conjugation. We show that one previously unknown gene, acaB, encodes a transcriptional regulator that has a crucial role in the regulation of IncC conjugation. AcaB binds upstream of the acaDC promoter to increase acaDC transcription; in turn, AcaDC activates the transcription of IncC conjugation genes. We solved the crystal structure of AcaB at 2.9-Å resolution and used this to guide functional analyses that reveal how AcaB binds to DNA. This improved understanding of IncC conjugation provides a basis for the development of new approaches to reduce the spread of these multi-drug-resistance plasmids.
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Affiliation(s)
- Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Zhenyao Luo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Jason Whitfield
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David L Paterson
- The University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
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18
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Getahun Strobel A, Parry CM, Crump JA, Rosa V, Jenney A, Naidu R, Mulholland K, Strugnell RA. A retrospective study of patients with blood culture-confirmed typhoid fever in Fiji during 2014-2015: epidemiology, clinical features, treatment and outcome. Trans R Soc Trop Med Hyg 2020; 113:764-770. [PMID: 31638153 PMCID: PMC6907003 DOI: 10.1093/trstmh/trz075] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/25/2019] [Accepted: 07/15/2019] [Indexed: 01/22/2023] Open
Abstract
Background Typhoid fever is endemic in Fiji. We sought to describe the epidemiology, clinical features and case fatality risk of blood culture-confirmed typhoid fever from January 2014 through December 2015. Methods Blood culture-positive patients were identified from a typhoid surveillance line list. A standardised case investigation form was used to record data from patients’ medical records. Results Of 542 patients, 518 (95.6%) were indigenous Fijians (iTaukei) and 285 (52.6%) were male. The median (IQR) age was 25 (16–38) y. Mean (SD) time from the onset of illness to admission was 11.1 (6.9) d. Of 365 patients with clinical information, 346 (96.9%) had fever, 239 (66.9%) diarrhoea, 113 (33.5%) vomiting, and 72 (30.2%) abdominal pain. There were 40 (11.0%) patients with complications, including 17 (4.7%) with shock, and 11 (3.0%) with hepatitis. Nine patients died for a case fatality risk of 1.7%. Of the 544 Salmonella Typhi isolates tested, none were resistant to first line antimicrobials; 3(0.8%) were resistant to ciprofloxacin and 5(1.4%) to nalidixic acid. Conclusions In Fiji, most blood culture-confirmed typhoid fever cases were in young adults. Common clinical manifestations were fever and gastrointestinal symptoms. Further studies are required to elucidate the factors associated with complications and death.
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Affiliation(s)
- Aneley Getahun Strobel
- School of Public Health and Primary Care, College of Medicine, Nursing and Health Sciences, Fiji National University, Private mail bag, Suva, Fiji.,Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Christopher M Parry
- Institute of Infection and Global Health, University of Liverpool, The Ronald Ross Building, 8 West Derby Street, Liverpool, L69 7BE UK.,School of Tropical Medicine and Global Health, University of Nagasaki, 12, Nagasaki, 852-8102, Japan
| | - John A Crump
- Centre for International Health, University of Otago, 55 Hanover Street, Dunedin 9016, New Zealand
| | - Varanisese Rosa
- Fiji Centre for Communicable Diseases Control, Fiji Ministry of Health and Medical Services, Tamavua, Suva, Fiji
| | - Adam Jenney
- School of Medical Science, College of Medicine, Nursing and Health Sciences, Fiji National University, Private mail bag, Suva, Fiji
| | - Ravi Naidu
- Colonial War Memorial Hospital, Fiji Ministry of Health and Medical Services, Waimanu Road, Suva, Fiji
| | - Kim Mulholland
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Melbourne VIC 3052, Australia.,London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT UK
| | - Richard A Strugnell
- Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne VIC 3000, Australia
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19
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Doerflinger M, Deng Y, Whitney P, Salvamoser R, Engel S, Kueh AJ, Tai L, Bachem A, Gressier E, Geoghegan ND, Wilcox S, Rogers KL, Garnham AL, Dengler MA, Bader SM, Ebert G, Pearson JS, De Nardo D, Wang N, Yang C, Pereira M, Bryant CE, Strugnell RA, Vince JE, Pellegrini M, Strasser A, Bedoui S, Herold MJ. Flexible Usage and Interconnectivity of Diverse Cell Death Pathways Protect against Intracellular Infection. Immunity 2020; 53:533-547.e7. [PMID: 32735843 PMCID: PMC7500851 DOI: 10.1016/j.immuni.2020.07.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/12/2020] [Accepted: 07/02/2020] [Indexed: 12/31/2022]
Abstract
Programmed cell death contributes to host defense against pathogens. To investigate the relative importance of pyroptosis, necroptosis, and apoptosis during Salmonella infection, we infected mice and macrophages deficient for diverse combinations of caspases-1, -11, -12, and -8 and receptor interacting serine/threonine kinase 3 (RIPK3). Loss of pyroptosis, caspase-8-driven apoptosis, or necroptosis had minor impact on Salmonella control. However, combined deficiency of these cell death pathways caused loss of bacterial control in mice and their macrophages, demonstrating that host defense can employ varying components of several cell death pathways to limit intracellular infections. This flexible use of distinct cell death pathways involved extensive cross-talk between initiators and effectors of pyroptosis and apoptosis, where initiator caspases-1 and -8 also functioned as executioners when all known effectors of cell death were absent. These findings uncover a highly coordinated and flexible cell death system with in-built fail-safe processes that protect the host from intracellular infections. Mice lacking pyroptosis and apoptosis cannot control Salmonella infection Macrophages lacking pyroptosis and apoptosis resist Salmonella-induced killing Caspase-1 kills Salmonella-infected cells by activating GSDMD, BID, or other caspases Caspase-1 and -8 act as cell death executioners when all cell death effectors are lost
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Affiliation(s)
- Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yexuan Deng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Paul Whitney
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Ranja Salvamoser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Sven Engel
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Annabell Bachem
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Elise Gressier
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Niall D Geoghegan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kelly L Rogers
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Michael A Dengler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Stefanie M Bader
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Gregor Ebert
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia; Department of Molecular and Translational Research, Monash University, Clayton, VIC, Australia; Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Dominic De Nardo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nancy Wang
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Chenying Yang
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Milton Pereira
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA; University of Cambridge, Cambridge, UK
| | | | - Richard A Strugnell
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Sammy Bedoui
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia.
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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20
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Wang H, Kjer-Nielsen L, Shi M, D'Souza C, Pediongco TJ, Cao H, Kostenko L, Lim XY, Eckle SBG, Meehan BS, Zhu T, Wang B, Zhao Z, Mak JYW, Fairlie DP, Teng MWL, Rossjohn J, Yu D, de St Groth BF, Lovrecz G, Lu L, McCluskey J, Strugnell RA, Corbett AJ, Chen Z. IL-23 costimulates antigen-specific MAIT cell activation and enables vaccination against bacterial infection. Sci Immunol 2020; 4:4/41/eaaw0402. [PMID: 31732518 DOI: 10.1126/sciimmunol.aaw0402] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/09/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are activated in a TCR-dependent manner by antigens derived from the riboflavin synthesis pathway, including 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), bound to MHC-related protein-1 (MR1). However, MAIT cell activation in vivo has not been studied in detail. Here, we have found and characterized additional molecular signals required for optimal activation and expansion of MAIT cells after pulmonary Legionella or Salmonella infection in mice. We show that either bone marrow-derived APCs or non-bone marrow-derived cells can activate MAIT cells in vivo, depending on the pathogen. Optimal MAIT cell activation in vivo requires signaling through the inducible T cell costimulator (ICOS), which is highly expressed on MAIT cells. Subsequent expansion and maintenance of MAIT-17/1-type responses are dependent on IL-23. Vaccination with IL-23 plus 5-OP-RU augments MAIT cell-mediated control of pulmonary Legionella infection. These findings reveal cellular and molecular targets for manipulating MAIT cell function under physiological conditions.
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Affiliation(s)
- Huimeng Wang
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Mai Shi
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,School of Medicine, Tsinghua University, Beijing, China
| | - Criselle D'Souza
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia
| | - Troi J Pediongco
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Xin Yi Lim
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Tianyuan Zhu
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.,School of Medicine, Tsinghua University, Beijing, China
| | - Bingjie Wang
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Zhe Zhao
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Saint Lucia, QLD 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Saint Lucia, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Saint Lucia, QLD 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Saint Lucia, QLD 4072, Australia
| | - Michele W L Teng
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, CF14 4XN Wales, UK
| | - Di Yu
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601 Australia
| | - Barbara Fazekas de St Groth
- Discipline of Pathology, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - George Lovrecz
- Biomedical Manufacturing, CSIRO, Parkville, VIC, 3052, Australia
| | - Louis Lu
- Biomedical Manufacturing, CSIRO, Parkville, VIC, 3052, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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21
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Chen Z, Wang H, D'Souza C, Koay HF, Meehan B, Zhao Z, Pediongco T, Shi M, Zhu T, Wang B, Kjer-Nielsen L, Eckle SBG, Rossjohn J, Fairlie DP, Godfrey DI, Strugnell RA, McCluskey J, Corbett AJ. Characterization and Purification of Mouse Mucosal-Associated Invariant T (MAIT) Cells. ACTA ACUST UNITED AC 2020; 127:e89. [PMID: 31763782 DOI: 10.1002/cpim.89] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This unit describes the utility of various mouse models of infection and immunization for studying mucosal-associated invariant T (MAIT) cell immunity: MAIT cells can be isolated from the lungs (or from other tissues/organs) and then identified and characterized by flow cytometry using MR1 tetramers in combination with a range of antibodies. The response kinetics, cytokine profiles, and functional differentiation of lung MAIT cells are studied following infection with the bacterial pathogen Legionella longbeachae or Salmonella enterica Typhimurium or immunization with synthetic MAIT cell antigen plus Toll-like receptor agonist. MAIT cells enriched or expanded during the process can be used for further studies. A step-by-step protocol is provided for MAIT cell sorting and adoptive transfer. Mice can then be challenged and MAIT cells tracked and further examined. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zhenjun Chen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Criselle D'Souza
- Human Immunology Translational Research Lab (HITRL), Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Bronwyn Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Zhe Zhao
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Troi Pediongco
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mai Shi
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,School of Medicine, Tsinghua University, Beijing, China
| | - Tianyuan Zhu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Bingjie Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Wales, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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22
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Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T, Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T. The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane. Cell Rep 2019; 23:2782-2794. [PMID: 29847806 DOI: 10.1016/j.celrep.2018.04.093] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/05/2018] [Accepted: 04/23/2018] [Indexed: 01/28/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is essential for localization of surface proteins on bacterial cells, but the mechanism by which it functions is unclear. We developed a direct stochastic optical reconstruction microscopy (dSTORM) methodology to view the BAM complex in situ. Single-cell analysis showed that discrete membrane precincts housing several BAM complexes are distributed across the E. coli surface, with a nearest neighbor distance of ∼200 nm. The auxiliary lipoprotein subunit BamB was crucial for this spatial distribution, and in situ crosslinking shows that BamB makes intimate contacts with BamA and BamB in neighboring BAM complexes within the precinct. The BAM complex precincts swell when outer membrane protein synthesis is maximal, visual proof that the precincts are active in protein assembly. This nanoscale interrogation of the BAM complex in situ suggests a model whereby bacterial outer membranes contain highly organized assembly precincts to drive integral protein assembly.
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Affiliation(s)
- Sachith D Gunasinghe
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Takuya Shiota
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Christopher J Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Keith E Schulze
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Chaille T Webb
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Alex J Fulcher
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Iain D Hay
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Thomas Naderer
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Donna R Whelan
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Kirstin D Elgass
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Hudson Institute of Medical Research, Clayton, VIC 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
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23
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Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T. The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre. Mol Microbiol 2019; 112:1831-1846. [PMID: 31556164 DOI: 10.1111/mmi.14396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
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Affiliation(s)
- Rhys A Dunstan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sam Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Claire Cormie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joshua Hardy
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Fuyi Li
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Rhys Grinter
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, 3800, Australia
| | | | - Lu Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jiangning Song
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | | | - Jyoti Choudhary
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fasseli Coulibaly
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, 3052, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
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24
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Wang N, Knodler LA, Strugnell RA. Typhoid Fever: The More We Learn, the Less We Know (Apologies, Albert Einstein). Cell Host Microbe 2019; 26:303-306. [PMID: 31513767 DOI: 10.1016/j.chom.2019.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In this issue of Cell Host & Microbe, Karlinsey et al. (2019) combine TraDIS with humanized mice to identify genes required for early replication of Salmonella Typhi in vivo. Surprisingly, some expected virulence traits and genes appear dispensable in the replication of S. Typhi, supporting findings from a recent human challenge study by Gibani et al. (2019).
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Affiliation(s)
- Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leigh A Knodler
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Washington State University Paul G. Allen School for Global Animal Health, Pullman, WA, USA
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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25
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Nang SC, Morris FC, McDonald MJ, Han ML, Wang J, Strugnell RA, Velkov T, Li J. Fitness cost of mcr-1-mediated polymyxin resistance in Klebsiella pneumoniae. J Antimicrob Chemother 2019. [PMID: 29514208 DOI: 10.1093/jac/dky061] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Objectives The discovery of mobile colistin resistance mcr-1, a plasmid-borne polymyxin resistance gene, highlights the potential for widespread resistance to the last-line polymyxins. In the present study, we investigated the impact of mcr-1 acquisition on polymyxin resistance and biological fitness in Klebsiella pneumoniae. Methods K. pneumoniae B5055 was used as the parental strain for the construction of strains carrying vector only (pBBR1MCS-5) and mcr-1 recombinant plasmids (pmcr-1). Plasmid stability was determined by serial passaging for 10 consecutive days in antibiotic-free LB broth, followed by patching on gentamicin-containing and antibiotic-free LB agar plates. Lipid A was analysed using LC-MS. The biological fitness was examined using an in vitro competition assay analysed with flow cytometry. The in vivo fitness cost of mcr-1 was evaluated in a neutropenic mouse thigh infection model. Results Increased polymyxin resistance was observed following acquisition of mcr-1 in K. pneumoniae B5055. The modification of lipid A with phosphoethanolamine following mcr-1 addition was demonstrated by lipid A profiling. The plasmid stability assay revealed the instability of the plasmid after acquiring mcr-1. Reduced in vitro biological fitness and in vivo growth were observed with the mcr-1-carrying K. pneumoniae strain. Conclusions Although mcr-1 confers a moderate level of polymyxin resistance, it is associated with a significant biological fitness cost in K. pneumoniae. This indicates that mcr-1-mediated resistance in K. pneumoniae could be attenuated by limiting the usage of polymyxins.
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Affiliation(s)
- Sue C Nang
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria, Australia
| | - Faye C Morris
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria, Australia
| | - Michael J McDonald
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Victoria, Australia
| | - Mei-Ling Han
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria, Australia
| | - Jiping Wang
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria, Australia
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26
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Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T. Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinformatics 2019; 34:2546-2555. [PMID: 29547915 DOI: 10.1093/bioinformatics/bty155] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022] Open
Abstract
Motivation Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data. Results We extracted a wide range of features from T6SE protein sequences and comprehensively analyzed the prediction performance of these features through unsupervised and supervised learning. By integrating these features, we subsequently developed a two-layer SVM-based ensemble model with fine-grain optimized parameters, to identify potential T6SEs. We further validated the predictive model using an independent dataset, which showed that the proposed model achieved an impressive performance in terms of ACC (0.943), F-value (0.946), MCC (0.892) and AUC (0.976). To demonstrate applicability, we employed this method to correctly identify two very recently validated T6SE proteins, which represent challenging prediction targets because they significantly differed from previously known T6SEs in terms of their sequence similarity and cellular function. Furthermore, a genome-wide prediction across 12 bacterial species, involving in total 54 212 protein sequences, was carried out to distinguish 94 putative T6SE candidates. We envisage both this information and our publicly accessible web server will facilitate future discoveries of novel T6SEs. Availability and implementation http://bastion6.erc.monash.edu/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiawei Wang
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Bingjiao Yang
- Bioinformatics Group, School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Morihiro Hayashida
- National Institute of Technology, Matsue College, Matsue, Shimane, Japan
| | - Andrea Rocker
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Yanju Zhang
- Bioinformatics Group, School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, China
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard A Strugnell
- Department of Microbiology and Immunology and Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology.,Monash Centre for Data Science, Faculty of Information Technolog, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Trevor Lithgow
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
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27
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Zhao Y, Zhang X, Torres VVL, Liu H, Rocker A, Zhang Y, Wang J, Chen L, Bi W, Lin J, Strugnell RA, Zhang S, Lithgow T, Zhou T, Cao J. An Outbreak of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae in an Intensive Care Unit of a Major Teaching Hospital in Wenzhou, China. Front Public Health 2019; 7:229. [PMID: 31552210 PMCID: PMC6736603 DOI: 10.3389/fpubh.2019.00229] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Carbapenem-resistant, hypervirulent Klebsiella pneumoniae (CR-hvKP) has recently emerged as a significant threat to public health. In this study, 29 K. pneumoniae isolates were isolated from eight patients admitted to the intensive care unit (ICU) of a comprehensive teaching hospital located in China from March 2017 to January 2018. Clinical information of patients was the basis for the further analyses of the isolates including antimicrobial susceptibility tests, identification of antibiotic resistance and virulence gene determinants, multilocus sequence typing (MLST), XbaI-macrorestriction by pulsed-field gel electrophoresis (PFGE). Selected isolates representing distinct resistance profiles and virulence phenotypes were screened for hypervirulence in a Galleria mellonella larvae infection model. In the course of the outbreak, the overall mortality rate of patients was 100% (n = 8) attributed to complications arising from CR-hvKP infections. All isolates except one (28/29, 96.6%) were resistant to multiple antimicrobial agents, and harbored diverse resistance determinants that included the globally prevalent carbapenemase blaKPC−2. Most isolates had hypervirulent genotypes being positive for 19 virulence-associated genes, including iutA (25/29, 86.2%), rmpA (27/29, 93.1%), ybtA (27/29, 93.1%), entB (29/29, 100%), fimH (29/29, 100%), and mrkD (29/29, 100%). MLST revealed ST11 for the majority of isolates (26/29, 89,7%). Infection assays demonstrated high mortality in the Galleria mellonella model with the highest LD50 values for three isolates (<105 CFU/mL) demonstrating the degree of hypervirulence of these CR-hvKP isolates, and is discussed relative to previous outbreaks of CR-hvKP.
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Affiliation(s)
- Yajie Zhao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xiucai Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Von Vergel L Torres
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Haiyang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Andrea Rocker
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Yizhi Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jiawei Wang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenzi Bi
- School of Medicine, The Fourth Affiliated Hospital of Zhejiang University, Jinhua, China
| | - Jie Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Siqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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28
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Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ. Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nat Genet 2019; 51:1295. [DOI: 10.1038/s41588-019-0482-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Newson JPM, Scott NE, Yeuk Wah Chung I, Wong Fok Lung T, Giogha C, Gan J, Wang N, Strugnell RA, Brown NF, Cygler M, Pearson JS, Hartland EL. Salmonella Effectors SseK1 and SseK3 Target Death Domain Proteins in the TNF and TRAIL Signaling Pathways. Mol Cell Proteomics 2019; 18:1138-1156. [PMID: 30902834 PMCID: PMC6553940 DOI: 10.1074/mcp.ra118.001093] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/13/2019] [Indexed: 01/09/2023] Open
Abstract
Strains of Salmonella utilize two distinct type three secretion systems to deliver effector proteins directly into host cells. The Salmonella effectors SseK1 and SseK3 are arginine glycosyltransferases that modify mammalian death domain containing proteins with N-acetyl glucosamine (GlcNAc) when overexpressed ectopically or as recombinant protein fusions. Here, we combined Arg-GlcNAc glycopeptide immunoprecipitation and mass spectrometry to identify host proteins GlcNAcylated by endogenous levels of SseK1 and SseK3 during Salmonella infection. We observed that SseK1 modified the mammalian signaling protein TRADD, but not FADD as previously reported. Overexpression of SseK1 greatly broadened substrate specificity, whereas ectopic co-expression of SseK1 and TRADD increased the range of modified arginine residues within the death domain of TRADD. In contrast, endogenous levels of SseK3 resulted in modification of the death domains of receptors of the mammalian TNF superfamily, TNFR1 and TRAILR, at residues Arg376 and Arg293 respectively. Structural studies on SseK3 showed that the enzyme displays a classic GT-A glycosyltransferase fold and binds UDP-GlcNAc in a narrow and deep cleft with the GlcNAc facing the surface. Together our data suggest that salmonellae carrying sseK1 and sseK3 employ the glycosyltransferase effectors to antagonise different components of death receptor signaling.
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Affiliation(s)
- Joshua P M Newson
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nichollas E Scott
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ivy Yeuk Wah Chung
- §Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tania Wong Fok Lung
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Cristina Giogha
- ¶Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Jiyao Gan
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- ¶Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Nancy Wang
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nathaniel F Brown
- **Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Miroslaw Cygler
- §Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jaclyn S Pearson
- ¶Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Elizabeth L Hartland
- From the ‡Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia;
- ¶Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- ‖Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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30
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Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nat Genet 2019; 51:1035-1043. [PMID: 31133745 DOI: 10.1038/s41588-019-0417-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 04/10/2019] [Indexed: 11/09/2022]
Abstract
Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia. .,The Wellcome Trust Sanger Institute, Hinxton, UK. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Liam McIntyre
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ankur Mutreja
- The Wellcome Trust Sanger Institute, Hinxton, UK.,GSK Vaccines Institute for Global Health, Siena, Italy
| | - Jake A Lacey
- Doherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Rebecca J Towers
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Sebastián Duchêne
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Pierre R Smeesters
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pediatrics, Queen Fabiola Childrens University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Hannah R Frost
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pediatrics, Queen Fabiola Childrens University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - David J Price
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Hinxton, UK.,School of Medicine, University of St Andrews, St Andrews, UK
| | - Sophia David
- The Wellcome Trust Sanger Institute, Hinxton, UK
| | - Philip M Giffard
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Kate A Worthing
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - James A Berkley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tania Rivera-Hernandez
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Olga Berking
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda J Cork
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Rosângela S L A Torres
- Laboratory of Bacteriology, Epidemiology Laboratory and Disease Control Division, Laboratório Central do Estado do Paraná, Curitiba, Brazil.,Department of Medicine, Universidade Positivo, Curitiba, Brazil
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Rene Bergmann
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | | | - John D Fraser
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jonathan R Carapetis
- Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, Western Australia, Australia
| | - Andrew C Steer
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | | | - Allan Saul
- GSK Vaccines Institute for Global Health, Siena, Italy
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Bart J Currie
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Steven Y C Tong
- Doherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Menzies School of Health Research, Darwin, Northern Territory, Australia.,Victorian Infectious Disease Service, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
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31
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Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T. Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Brief Bioinform 2019; 20:931-951. [PMID: 29186295 PMCID: PMC6585386 DOI: 10.1093/bib/bbx164] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/08/2017] [Indexed: 12/13/2022] Open
Abstract
In the course of infecting their hosts, pathogenic bacteria secrete numerous effectors, namely, bacterial proteins that pervert host cell biology. Many Gram-negative bacteria, including context-dependent human pathogens, use a type IV secretion system (T4SS) to translocate effectors directly into the cytosol of host cells. Various type IV secreted effectors (T4SEs) have been experimentally validated to play crucial roles in virulence by manipulating host cell gene expression and other processes. Consequently, the identification of novel effector proteins is an important step in increasing our understanding of host-pathogen interactions and bacterial pathogenesis. Here, we train and compare six machine learning models, namely, Naïve Bayes (NB), K-nearest neighbor (KNN), logistic regression (LR), random forest (RF), support vector machines (SVMs) and multilayer perceptron (MLP), for the identification of T4SEs using 10 types of selected features and 5-fold cross-validation. Our study shows that: (1) including different but complementary features generally enhance the predictive performance of T4SEs; (2) ensemble models, obtained by integrating individual single-feature models, exhibit a significantly improved predictive performance and (3) the 'majority voting strategy' led to a more stable and accurate classification performance when applied to predicting an ensemble learning model with distinct single features. We further developed a new method to effectively predict T4SEs, Bastion4 (Bacterial secretion effector predictor for T4SS), and we show our ensemble classifier clearly outperforms two recent prediction tools. In summary, we developed a state-of-the-art T4SE predictor by conducting a comprehensive performance evaluation of different machine learning algorithms along with a detailed analysis of single- and multi-feature selections.
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Affiliation(s)
- Jiawei Wang
- Biomedicine Discovery Institute and the Department of Microbiology at Monash University, Australia
| | - Bingjiao Yang
- National Engineering Research Center for Equipment and Technology of Cold Strip Rolling, College of Mechanical Engineering from Yanshan University, China
| | - Yi An
- College of Information Engineering, Northwest A&F University, China
| | - Tatiana Marquez-Lago
- Department of Genetics, University of Alabama at Birmingham (UAB) School of Medicine, USA
| | - André Leier
- Department of Genetics and the Informatics Institute, University of Alabama at Birmingham (UAB) School of Medicine, USA
| | - Jonathan Wilksch
- Department of Microbiology and Immunology at the University of Melbourne, Australia
| | | | - Yang Zhang
- Computer Science and Engineering in 2015 fromNorthwestern Polytechnical University, China
| | | | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash Centre for Data Science, Monash University
| | - Richard A Strugnell
- Department of Microbiology and Immunology, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Australia
| | - Trevor Lithgow
- Department of Microbiology at Monash University, Australia
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32
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Simpfendorfer KR, Wang N, Tull DL, De Souza DP, Nahid A, Mu A, Hocking DM, Pedersen JS, Wijburg OLC, McConville MJ, Strugnell RA. Mus musculus deficient for secretory antibodies show delayed growth with an altered urinary metabolome. Mol Med 2019; 25:12. [PMID: 30943912 PMCID: PMC6446318 DOI: 10.1186/s10020-019-0077-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
Background The polymeric immunoglobulin receptor (pIgR) maintains the integrity of epithelial barriers by transporting polymeric antibodies and antigens through the epithelial mucosa into the lumen. In this study, we examined the role of pIgR in maintaining gut barrier integrity, which is important for the normal development in mice. Methods Cohorts of pIgR−/− mice and their wildtype controls were housed under Specific Pathogen Free (SPF) conditions and monitored for weight gain as an indicator of development over time. The general physiology of the gastrointestinal tract was analysed using immunohistochemistry in young (8–12 weeks of age) and aged mice (up to 18 months of age), and the observed immunopathology in pIgR−/− mice was further characterised using flow cytometry. Urinary metabolites were analysed using gas chromatography-mass spectrometry (GC-MS), which revealed changes in metabolites that correlated with age-related increase in gut permeability in pIgR−/− mice. Results We observed that pIgR−/− mice exhibited delayed growth, and this phenomenon is associated with low-grade gut inflammation that increased with ageing. The gross intraepithelial lymphocytic (IEL) infiltration characteristic of pIgR−/− mice was redefined as CD8α+αβ+ T cells, the majority of which expressed high levels of CD103 and CD69 consistent with tissue resident memory T cells (TRM). Comparison of the urinary metabolome between pIgR−/− and wild-type mice revealed key changes in urinary biomarkers fucose, glycine and Vitamin B5, suggestive of altered mucosal permeability. A significant increase in gut permeability was confirmed by analysing the site-specific uptake of sugar probes in different parts of the intestine. Conclusion Our data show that loss of the secretory antibody system in mice results in enhanced accumulation of inflammatory IELs in the gut, which likely reflects ongoing inflammation in reaction to gut microbiota or food antigens, leading to delayed growth in pIgR−/− mice. We demonstrate that this leads to the presence of a unique urinary metabolome profile, which may provide a biomarker for altered gut permeability. Electronic supplementary material The online version of this article (10.1186/s10020-019-0077-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim R Simpfendorfer
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Present address: The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Nancy Wang
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Dedreia L Tull
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Amsha Nahid
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Andre Mu
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Dianna M Hocking
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Odilia L C Wijburg
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Parkville, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Parkville, Australia
| | - Richard A Strugnell
- The Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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33
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Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D, Wilksch J, Cao H, Haq IU, Dougan G, Strugnell RA. Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep 2019; 9:2392. [PMID: 30787414 PMCID: PMC6382945 DOI: 10.1038/s41598-019-38943-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/11/2019] [Indexed: 11/25/2022] Open
Abstract
Klebsiella pneumoniae is a major threat to public health with the emergence of isolates resistant to most, if not all, useful antibiotics. We present an in-depth analysis of 178 extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae collected from patients resident in a region of Pakistan, during the period 2010–2012, when the now globally-distributed carbapenemase bla-NDM-1 was being acquired by Klebsiella. We observed two dominant lineages, but neither the overall resistance profile nor virulence-associated factors, explain their evolutionary success. Phenotypic analysis of resistance shows few differences between the acquisition of resistance genes and the phenotypic resistance profile, including beta-lactam antibiotics that were used to treat ESBL-positive strains. Resistance against these drugs could be explained by inhibitor-resistant beta-lactamase enzymes, carbapenemases or ampC type beta-lactamases, at least one of which was detected in most, but not all relevant strains analysed. Complete genomes for six selected strains are reported, these provide detailed insights into the mobile elements present in these isolates during the initial spread of NDM-1. The unexplained success of some lineages within this pool of highly resistant strains, and the discontinuity between phenotypic resistance and genotype at the macro level, indicate that intrinsic mechanisms contribute to competitive advantage and/or resistance.
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Affiliation(s)
- Eva Heinz
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, CAMS, Jouf University, Al-Jouf, Saudi Arabia.,Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology, The Children's Hospital & The Institute of Child Health, Lahore, Pakistan
| | | | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Shruti Gujaran
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Derek Pickard
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ikram-Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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34
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Grinter R, Hay ID, Song J, Wang J, Teng D, Dhanesakaran V, Wilksch JJ, Davies MR, Littler D, Beckham SA, Henderson IR, Strugnell RA, Dougan G, Lithgow T. FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants. PLoS Biol 2018; 16:e2006026. [PMID: 30071011 PMCID: PMC6071955 DOI: 10.1371/journal.pbio.2006026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/29/2018] [Indexed: 11/19/2022] Open
Abstract
Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Reports of iron-bearing proteins being used as a source of iron indicate specific protein import reactions across the bacterial outer membrane. The molecular mechanism by which a folded protein can be imported in this way had remained mysterious, as did the evolutionary process that could lead to such a protein import pathway. How does the bacterium evolve the specificity factors that would be required to select and import a protein encoded on another organism's genome? We describe here a model whereby the plant iron-bearing protein ferredoxin can be imported across the outer membrane of the plant pathogen Pectobacterium by means of a Brownian ratchet mechanism, thereby liberating iron into the bacterium to enable its growth in plant tissues. This import pathway is facilitated by FusC, a member of the same protein family as the mitochondrial processing peptidase (MPP). The Brownian ratchet depends on binding sites discovered in crystal structures of FusC that engage a linear segment of the plant protein ferredoxin. Sequence relationships suggest that the bacterial gene encoding FusC has previously unappreciated homologues in plants and that the protein import mechanism employed by the bacterium is an evolutionary echo of the protein import pathway in plant mitochondria and plastids.
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Affiliation(s)
- Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Iain D. Hay
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Jiangning Song
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
| | - Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Don Teng
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Vijay Dhanesakaran
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Jonathan J. Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Mark R. Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Dene Littler
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
| | - Simone A. Beckham
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Clayton, Australia
| | - Ian R. Henderson
- Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
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35
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Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. Clin Infect Dis 2018; 67:161-170. [PMID: 29340588 PMCID: PMC6030810 DOI: 10.1093/cid/ciy027] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk. Methods We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Results K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type [ST] 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital. Conclusions The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.
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Affiliation(s)
- Claire L Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mirjana Mirceta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kerrie M Watson
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Victoria, Australia
| | | | - Denis W Spelman
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
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Prasad N, Jenkins AP, Naucukidi L, Rosa V, Sahu-Khan A, Kama M, Jenkins KM, Jenney AWJ, Jack SJ, Saha D, Horwitz P, Jupiter SD, Strugnell RA, Mulholland EK, Crump JA. Epidemiology and risk factors for typhoid fever in Central Division, Fiji, 2014-2017: A case-control study. PLoS Negl Trop Dis 2018; 12:e0006571. [PMID: 29883448 PMCID: PMC6010302 DOI: 10.1371/journal.pntd.0006571] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/20/2018] [Accepted: 05/29/2018] [Indexed: 11/26/2022] Open
Abstract
Background Typhoid fever is endemic in Fiji, with high reported annual incidence. We sought to identify the sources and modes of transmission of typhoid fever in Fiji with the aim to inform disease control. Methodology/Principal findings We identified and surveyed patients with blood culture-confirmed typhoid fever from January 2014 through January 2017. For each typhoid fever case we matched two controls by age interval, gender, ethnicity, and residential area. Univariable and multivariable analysis were used to evaluate associations between exposures and risk for typhoid fever. We enrolled 175 patients with typhoid fever and 349 controls. Of the cases, the median (range) age was 29 (2–67) years, 86 (49%) were male, and 84 (48%) lived in a rural area. On multivariable analysis, interrupted water availability (odds ratio [OR] = 2.17; 95% confidence interval [CI] 1.18–4.00), drinking surface water in the last 2 weeks (OR = 3.61; 95% CI 1.44–9.06), eating unwashed produce (OR = 2.69; 95% CI 1.48–4.91), and having an unimproved or damaged sanitation facility (OR = 4.30; 95% CI 1.14–16.21) were significantly associated with typhoid fever. Frequent handwashing after defecating (OR = 0.57; 95% CI 0.35–0.93) and using soap for handwashing (OR = 0.61; 95% CI 0.37–0.95) were independently associated with a lower odds of typhoid fever. Conclusions Poor sanitation facilities appear to be a major source of Salmonella Typhi in Fiji, with transmission by drinking contaminated surface water and consuming unwashed produce. Improved sanitation facilities and protection of surface water sources and produce from contamination by human feces are likely to contribute to typhoid control in Fiji. Modeling suggests that Oceania has surpassed Asia and sub-Saharan Africa as the region with the highest typhoid fever incidence. While Pacific Islands are often neglected due to small population sizes, there is an urgent need to understand the epidemiology of typhoid fever in the region. Fiji, an upper-middle income country in Oceania, has reported an increase in typhoid fever notifications over the last decade. However, the epidemiology of typhoid fever in Fiji is incompletely understood due to gaps in surveillance and lack of epidemiological research on local risk factors. We conducted a case-control study in the Central Division of Fiji to help inform prevention and control strategies. We found unimproved sanitation facilities to be major source of typhoid fever in Fiji, with transmission by drinking contaminated surface water and consumption of unwashed produce. We also found an association between poor water availability and poor hygiene with typhoid fever. Improvements in sanitation facilities to protect surface water and produce from contamination are likely to contribute to improved typhoid control in Fiji. Because of the distinct socio-demographic and environmental conditions found in Oceania, our findings may reflect sources and modes of transmission predominant elsewhere in the region.
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Affiliation(s)
- Namrata Prasad
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail: (NP); (JAC)
| | - Aaron P. Jenkins
- School of Science, Edith Cowan University, Joondalup, Australia
- School of Public Health, University of Sydney, Sydney, Australia
| | - Lanieta Naucukidi
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Aalisha Sahu-Khan
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Mike Kama
- Fiji Centre for Communicable Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Kylie M. Jenkins
- Fiji Health Sector Support Program, Suva, Fiji
- Telethon Kids Institute, Perth, Western Australia
| | - Adam W. J. Jenney
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Susan J. Jack
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Debasish Saha
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Pierre Horwitz
- School of Science, Edith Cowan University, Joondalup, Australia
| | - Stacy D. Jupiter
- Wildlife Conservation Society, Melanesia Regional Program, Suva, Fiji
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - E. Kim Mulholland
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - John A. Crump
- Centre for International Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail: (NP); (JAC)
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Torres VVL, Heinz E, Stubenrauch CJ, Wilksch JJ, Cao H, Yang J, Clements A, Dunstan RA, Alcock F, Webb CT, Dougan G, Strugnell RA, Hay ID, Lithgow T. An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis. Mol Microbiol 2018; 109:584-599. [PMID: 29873128 DOI: 10.1111/mmi.13990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2018] [Indexed: 12/29/2022]
Abstract
Members of the Omp85 protein superfamily have important roles in Gram-negative bacteria, with the archetypal protein BamA being ubiquitous given its essential function in the assembly of outer membrane proteins. In some bacterial lineages, additional members of the family exist and, in most of these cases, the function of the protein is unknown. We detected one of these Omp85 proteins in the pathogen Klebsiella pneumoniae B5055, and refer to the protein as BamK. Here, we show that bamK is a conserved element in the core genome of Klebsiella, and its expression rescues a loss-of-function ∆bamA mutant. We developed an E. coli model system to measure and compare the specific activity of BamA and BamK in the assembly reaction for the critical substrate LptD, and find that BamK is as efficient as BamA in assembling the native LptDE complex. Comparative structural analysis revealed that the major distinction between BamK and BamA is in the external facing surface of the protein, and we discuss how such changes may contribute to a mechanism for resistance against infection by bacteriophage.
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Affiliation(s)
- Von Vergel L Torres
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Eva Heinz
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Christopher J Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Jonathan J Wilksch
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia.,Department of Microbiology & Immunology, University of Melbourne, Parkville, 3052, Australia
| | - Hanwei Cao
- Department of Microbiology & Immunology, University of Melbourne, Parkville, 3052, Australia
| | - Ji Yang
- Department of Microbiology & Immunology, University of Melbourne, Parkville, 3052, Australia
| | - Abigail Clements
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Felicity Alcock
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia.,Department of Biochemistry, Oxford University, Oxford, UK
| | - Chaille T Webb
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, 3052, Australia
| | - Iain D Hay
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, 3800, Australia
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38
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Husna AU, Wang N, Cobbold SA, Newton HJ, Hocking DM, Wilksch JJ, Scott TA, Davies MR, Hinton JC, Tree JJ, Lithgow T, McConville MJ, Strugnell RA. Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium. J Biol Chem 2018; 293:9506-9519. [PMID: 29720401 PMCID: PMC6005444 DOI: 10.1074/jbc.ra118.002592] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/28/2018] [Indexed: 11/06/2022] Open
Abstract
Methionine (Met) is an amino acid essential for many important cellular and biosynthetic functions, including the initiation of protein synthesis and S-adenosylmethionine–mediated methylation of proteins, RNA, and DNA. The de novo biosynthetic pathway of Met is well conserved across prokaryotes but absent from vertebrates, making it a plausible antimicrobial target. Using a systematic approach, we examined the essentiality of de novo methionine biosynthesis in Salmonella enterica serovar Typhimurium, a bacterial pathogen causing significant gastrointestinal and systemic diseases in humans and agricultural animals. Our data demonstrate that Met biosynthesis is essential for S. Typhimurium to grow in synthetic medium and within cultured epithelial cells where Met is depleted in the environment. During systemic infection of mice, the virulence of S. Typhimurium was not affected when either de novo Met biosynthesis or high-affinity Met transport was disrupted alone, but combined disruption in both led to severe in vivo growth attenuation, demonstrating a functional redundancy between de novo biosynthesis and acquisition as a mechanism of sourcing Met to support growth and virulence for S. Typhimurium during infection. In addition, our LC-MS analysis revealed global changes in the metabolome of S. Typhimurium mutants lacking Met biosynthesis and also uncovered unexpected interactions between Met and peptidoglycan biosynthesis. Together, this study highlights the complexity of the interactions between a single amino acid, Met, and other bacterial processes leading to virulence in the host and indicates that disrupting the de novo biosynthetic pathway alone is likely to be ineffective as an antimicrobial therapy against S. Typhimurium.
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Affiliation(s)
- Asma Ul Husna
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Nancy Wang
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia,
| | - Simon A Cobbold
- the Department of Biochemistry and Molecular Biology, University of Melbourne at the Bio21 Institute, Parkville, Victoria 3052, Australia
| | - Hayley J Newton
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Dianna M Hocking
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Jonathan J Wilksch
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Timothy A Scott
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Mark R Davies
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Jay C Hinton
- the Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jai J Tree
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia.,the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia, and
| | - Trevor Lithgow
- the Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Malcolm J McConville
- the Department of Biochemistry and Molecular Biology, University of Melbourne at the Bio21 Institute, Parkville, Victoria 3052, Australia
| | - Richard A Strugnell
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia,
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D'Souza C, Pediongco T, Wang H, Scheerlinck JPY, Kostenko L, Esterbauer R, Stent AW, Eckle SBG, Meehan BS, Strugnell RA, Cao H, Liu L, Mak JYW, Lovrecz G, Lu L, Fairlie DP, Rossjohn J, McCluskey J, Every AL, Chen Z, Corbett AJ. Mucosal-Associated Invariant T Cells Augment Immunopathology and Gastritis in Chronic Helicobacter pylori Infection. J Immunol 2018; 200:1901-1916. [PMID: 29378910 DOI: 10.4049/jimmunol.1701512] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/29/2017] [Indexed: 11/19/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells produce inflammatory cytokines and cytotoxic granzymes in response to by-products of microbial riboflavin synthesis. Although MAIT cells are protective against some pathogens, we reasoned that they might contribute to pathology in chronic bacterial infection. We observed MAIT cells in proximity to Helicobacter pylori bacteria in human gastric tissue, and so, using MR1-tetramers, we examined whether MAIT cells contribute to chronic gastritis in a mouse H. pylori SS1 infection model. Following infection, MAIT cells accumulated to high numbers in the gastric mucosa of wild-type C57BL/6 mice, and this was even more pronounced in MAIT TCR transgenic mice or in C57BL/6 mice where MAIT cells were preprimed by Ag exposure or prior infection. Gastric MAIT cells possessed an effector memory Tc1/Tc17 phenotype, and were associated with accelerated gastritis characterized by augmented recruitment of neutrophils, macrophages, dendritic cells, eosinophils, and non-MAIT T cells and by marked gastric atrophy. Similarly treated MR1-/- mice, which lack MAIT cells, showed significantly less gastric pathology. Thus, we demonstrate the pathogenic potential of MAIT cells in Helicobacter-associated immunopathology, with implications for other chronic bacterial infections.
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Affiliation(s)
- Criselle D'Souza
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.,Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences,The University of Melbourne, Victoria 3010, Australia
| | - Troi Pediongco
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jean-Pierre Y Scheerlinck
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences,The University of Melbourne, Victoria 3010, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Andrew W Stent
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences,The University of Melbourne, Victoria 3010, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - George Lovrecz
- BioMedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria 3052, Australia
| | - Louis Lu
- BioMedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria 3052, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Alison L Every
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences,The University of Melbourne, Victoria 3010, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia;
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia;
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40
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Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, ul-Haq I, Dougan G, Strugnell RA, Heinz E. Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan. Emerg Infect Dis 2017; 23:1872-1875. [PMID: 29048298 PMCID: PMC5652443 DOI: 10.3201/eid2311.170833] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Klebsiella pneumoniae shows increasing emergence of multidrug-resistant lineages, including strains resistant to all available antimicrobial drugs. We conducted whole-genome sequencing of 178 highly drug-resistant isolates from a tertiary hospital in Lahore, Pakistan. Phylogenetic analyses to place these isolates into global context demonstrate the expansion of multiple independent lineages, including K. quasipneumoniae.
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Affiliation(s)
| | | | - Jonathan J. Wilksch
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Andrew J. Page
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Hanwei Cao
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Shruti Gujaran
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Jacqueline A. Keane
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Trevor Lithgow
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Ikram ul-Haq
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
| | - Gordon Dougan
- CAMS, Aljouf University, Aljouf, Saudi Arabia; The Children’s Hospital, Lahore, Pakistan (H. Ejaz)
- The University of Melbourne, Melbourne, Victoria, Australia (H. Ejaz, N. Wang, J.J. Wilksch, H. Cao, S. Gujaran, R.A. Strugnell)
- Wellcome Trust Sanger Institute, Hinxton, UK (A.J. Page, J.A. Keane, G. Dougan, E. Heinz)
- Monash University, Melbourne (T. Lithgow, E. Heinz); Government College University, Lahore (I.ul-Haq)
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Webb CT, Chandrapala D, Oslan SN, Bamert RS, Grinter RD, Dunstan RA, Gorrell RJ, Song J, Strugnell RA, Lithgow T, Kwok T. Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori. Microbiologyopen 2017; 6. [PMID: 29055967 PMCID: PMC5727368 DOI: 10.1002/mbo3.513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/19/2017] [Accepted: 05/25/2017] [Indexed: 12/18/2022] Open
Abstract
Helicobacter pylori is a gram‐negative bacterial pathogen that chronically inhabits the human stomach. To survive and maintain advantage, it has evolved unique host–pathogen interactions mediated by Helicobacter‐specific proteins in the bacterial outer membrane. These outer membrane proteins (OMPs) are anchored to the cell surface via a C‐terminal β‐barrel domain, which requires their assembly by the β‐barrel assembly machinery (BAM). Here we have assessed the complexity of the OMP C‐terminal β‐barrel domains employed by H. pylori, and characterized the H. pyloriBAM complex. Around 50 Helicobacter‐specific OMPs were assessed with predictive structural algorithms. The data suggest that H. pylori utilizes a unique β‐barrel architecture that might constitute H. pylori‐specific Type V secretions system. The structural and functional diversity in these proteins is encompassed by their extramembrane domains. Bioinformatic and biochemical characterization suggests that the low β‐barrel‐complexity requires only minimalist assembly machinery. The H. pylori proteins BamA and BamD associate to form a BAM complex, with features of BamA enabling an oligomerization that might represent a mechanism by which a minimalist BAM complex forms a larger, sophisticated machinery capable of servicing the outer membrane proteome of H. pylori.
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Affiliation(s)
- Chaille T. Webb
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Dilini Chandrapala
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Siti Nurbaya Oslan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Department of BiochemistryFaculty of Biotechnology and Biomolecular SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Enzyme and Microbial Technology Research CenterUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Rebecca S. Bamert
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rhys D. Grinter
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rhys A. Dunstan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rebecca J. Gorrell
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Jiangning Song
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Centre for Data ScienceFaculty of Information TechnologyMonash UniversityMelbourneAustralia
| | - Richard A. Strugnell
- Department of Microbiology & ImmunologyUniversity of MelbourneParkvilleAustralia
| | - Trevor Lithgow
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Terry Kwok
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
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Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients. Clin Infect Dis 2017; 65:208-215. [PMID: 28369261 PMCID: PMC5850561 DOI: 10.1093/cid/cix270] [Citation(s) in RCA: 283] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/21/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is an opportunistic pathogen and leading cause of hospital-associated infections. Intensive care unit (ICU) patients are particularly at risk. Klebsiella pneumoniae is part of the healthy human microbiome, providing a potential reservoir for infection. However, the frequency of gut colonization and its contribution to infections are not well characterized. METHODS We conducted a 1-year prospective cohort study in which 498 ICU patients were screened for rectal and throat carriage of K. pneumoniae shortly after admission. Klebsiella pneumoniae isolated from screening swabs and clinical diagnostic samples were characterized using whole genome sequencing and combined with epidemiological data to identify likely transmission events. RESULTS Klebsiella pneumoniae carriage frequencies were estimated at 6% (95% confidence interval [CI], 3%-8%) among ICU patients admitted direct from the community, and 19% (95% CI, 14%-51%) among those with recent healthcare contact. Gut colonization on admission was significantly associated with subsequent infection (infection risk 16% vs 3%, odds ratio [OR] = 6.9, P < .001), and genome data indicated matching carriage and infection isolates in 80% of isolate pairs. Five likely transmission chains were identified, responsible for 12% of K. pneumoniae infections in ICU. In sum, 49% of K. pneumoniae infections were caused by the patients' own unique strain, and 48% of screened patients with infections were positive for prior colonization. CONCLUSIONS These data confirm K. pneumoniae colonization is a significant risk factor for infection in ICU, and indicate ~50% of K. pneumoniae infections result from patients' own microbiota. Screening for colonization on admission could limit risk of infection in the colonized patient and others.
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Affiliation(s)
- Claire L Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne
| | - Mirjana Mirceta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne
| | | | | | | | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital
- Australian and New Zealand Intensive Care - Research Centre, School of Public Health and Preventive Medicine, Monash University
| | - Denis W Spelman
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute
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43
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Bi W, Liu H, Dunstan RA, Li B, Torres VVL, Cao J, Chen L, Wilksch JJ, Strugnell RA, Lithgow T, Zhou T. Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes. Front Microbiol 2017; 8:1230. [PMID: 28713357 PMCID: PMC5492486 DOI: 10.3389/fmicb.2017.01230] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/19/2017] [Indexed: 01/05/2023] Open
Abstract
The rise in diversity of antimicrobial resistance phenotypes seen in Klebsiella pneumoniae is becoming a serious antibiotic management problem. We sought to investigate the molecular characteristics and clinical implications of extensively drug-resistant (XDR) K. pneumoniae isolated from different nosocomial bloodstream infections (BSIs) patients from July 2013 to November 2015. Even in combination treatment, meropenem did not protect against mortality of BSIs patients (P = 0.015). In contrast, tigecycline in combination with other antimicrobial agents significantly protected against mortality (P = 0.016). Antimicrobial susceptibility tests, molecular detection of antibiotic resistance determinants, conjugation experiments, multilocus sequence typing (MLST), S1-PFGE, Southern blot, SDS-PAGE, immunoblot analysis, and pulsed-field gel electrophoresis (PFGE) were used to characterize these isolates. These XDR K. pneumoniae strains were resistant to conventional antimicrobials except tigecycline and polymyxin B and co-harbored diverse resistance determinants. rmtB, blaKPC−2 as well as blaCTX−M−9 were located on a transferable plasmid of ~54.2 kb and the most predominant replicon type was IncF. 23 of the 35 isolates belonging the predominant clone were found to incorporate the globally-disseminated sequence type ST11, but others including a unique, previously undiscovered lineage ST2281 (allelic profile: 4-1-1-22-7-4-35) were also found and characterized. The porins OmpK35 and OmpK36 were deficient in two carbapenemase-negative carbapenem-resistant strains, suggesting decreased drug uptake as a mechanism for carbapenem resistance. This study highlights the importance of tracking hospital acquired infections, monitoring modes of antibiotic resistance to improve health outcomes of BSIs patients and to highlight the problems of XDR K. pneumoniae dissemination in healthcare settings.
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Affiliation(s)
- Wenzi Bi
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical UniversityWenzhou, China
| | - Haiyang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
| | - Rhys A Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityMelbourne, VIC, Australia
| | - Bin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
| | - Von Vergel L Torres
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityMelbourne, VIC, Australia
| | - Jianming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical UniversityWenzhou, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
| | - Jonathan J Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityMelbourne, VIC, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of MelbourneParkville, VIC, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityMelbourne, VIC, Australia
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
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44
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Wang H, Wilksch JJ, Chen L, Tan JWH, Strugnell RA, Gee ML. Influence of Fimbriae on Bacterial Adhesion and Viscoelasticity and Correlations of the Two Properties with Biofilm Formation. Langmuir 2017; 33:100-106. [PMID: 27959542 DOI: 10.1021/acs.langmuir.6b03764] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The surface polymers of bacteria determine the ability of bacteria to adhere to a substrate for colonization, which is an essential step for a variety of microbial processes, such as biofilm formation and biofouling. Capsular polysaccharides and fimbriae are two major components on a bacterial surface, which are critical for mediating cell-surface interactions. Adhesion and viscoelasticity of bacteria are two major physical properties related to bacteria-surface interactions. In this study, we employed atomic force microscopy (AFM) to interrogate how the adhesion work and the viscoelasticity of a bacterial pathogen, Klebsiella pneumoniae, influence biofilm formation. To do this, the wild-type, type 3 fimbriae-deficient, and type 3 fimbriae-overexpressed K. pneumoniae strains have been investigated in an aqueous environment. The results show that the measured adhesion work is positively correlated to biofilm formation; however, the viscoelasticity is not correlated to biofilm formation. This study indicates that AFM-based adhesion measurements of bacteria can be used to evaluate the function of bacterial surface polymers in biofilm formation and to predict the ability of bacterial biofilm formation.
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Affiliation(s)
- Huabin Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714, China
- Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences , Shanghai 201800, China
| | | | - Ligang Chen
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714, China
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45
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Mularski A, Wilksch JJ, Wang H, Hossain MA, Wade JD, Separovic F, Strugnell RA, Gee ML. Correction to "Atomic Force Microscopy Reveals the Mechanobiology of Lytic Peptide Action on Bacteria". Langmuir 2016; 32:6010. [PMID: 27263366 DOI: 10.1021/acs.langmuir.6b01939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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46
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Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G, Lithgow T. Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. Genome Biol Evol 2016; 8:1690-705. [PMID: 27190006 PMCID: PMC4943183 DOI: 10.1093/gbe/evw112] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bacterial cell surface proteins intimin and invasin are virulence factors that share a common domain structure and bind selectively to host cell receptors in the course of bacterial pathogenesis. The β-barrel domains of intimin and invasin show significant sequence and structural similarities. Conversely, a variety of proteins with sometimes limited sequence similarity have also been annotated as “intimin-like” and “invasin” in genome datasets, while other recent work on apparently unrelated virulence-associated proteins ultimately revealed similarities to intimin and invasin. Here we characterize the sequence and structural relationships across this complex protein family. Surprisingly, intimins and invasins represent a very small minority of the sequence diversity in what has been previously the “intimin/invasin protein family”. Analysis of the assembly pathway for expression of the classic intimin, EaeA, and a characteristic example of the most prevalent members of the group, FdeC, revealed a dependence on the translocation and assembly module as a common feature for both these proteins. While the majority of the sequences in the grouping are most similar to FdeC, a further and widespread group is two-partner secretion systems that use the β-barrel domain as the delivery device for secretion of a variety of virulence factors. This comprehensive analysis supports the adoption of the “inverse autotransporter protein family” as the most accurate nomenclature for the family and, in turn, has important consequences for our overall understanding of the Type V secretion systems of bacterial pathogens.
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Affiliation(s)
- Eva Heinz
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Christopher J Stubenrauch
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rhys Grinter
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Trevor Lithgow
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
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47
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Mularski A, Wilksch JJ, Hanssen E, Strugnell RA, Separovic F. Atomic force microscopy of bacteria reveals the mechanobiology of pore forming peptide action. Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:1091-8. [DOI: 10.1016/j.bbamem.2016.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/26/2022]
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48
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Stubenrauch C, Belousoff MJ, Hay ID, Shen HH, Lillington J, Tuck KL, Peters KM, Phan MD, Lo AW, Schembri MA, Strugnell RA, Waksman G, Lithgow T. Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine. Nat Microbiol 2016; 1:16064. [DOI: 10.1038/nmicrobiol.2016.64] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
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49
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McWilliam HEG, Eckle SBG, Theodossis A, Liu L, Chen Z, Wubben JM, Fairlie DP, Strugnell RA, Mintern JD, McCluskey J, Rossjohn J, Villadangos JA. The intracellular pathway for the presentation of vitamin B-related antigens by the antigen-presenting molecule MR1. Nat Immunol 2016; 17:531-7. [PMID: 27043408 DOI: 10.1038/ni.3416] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/18/2016] [Indexed: 02/08/2023]
Abstract
The antigen-presenting molecule MR1 presents vitamin B-related antigens (VitB antigens) to mucosal-associated invariant T (MAIT) cells through an uncharacterized pathway. We show that MR1, unlike other antigen-presenting molecules, does not constitutively present self-ligands. In the steady state it accumulates in a ligand-receptive conformation within the endoplasmic reticulum. VitB antigens reach this location and form a Schiff base with MR1, triggering a 'molecular switch' that allows MR1-VitB antigen complexes to traffic to the plasma membrane. These complexes are endocytosed with kinetics independent of the affinity of the MR1-ligand interaction and are degraded intracellularly, although some MR1 molecules acquire new ligands during passage through endosomes and recycle back to the surface. MR1 antigen presentation is characterized by a rapid 'off-on-off' mechanism that is strictly dependent on antigen availability.
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Affiliation(s)
- Hamish E G McWilliam
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Alex Theodossis
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jacinta M Wubben
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Justine D Mintern
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Jose A Villadangos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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50
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Han JX, Ng GZ, Cecchini P, Chionh YT, Saeed MA, Næss LM, Joachim M, Blandford LE, Strugnell RA, Colaco CA, Sutton P. Heat shock protein complex vaccines induce antibodies against Neisseria meningitidis via a MyD88-independent mechanism. Vaccine 2016; 34:1704-11. [DOI: 10.1016/j.vaccine.2016.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 01/14/2016] [Accepted: 02/02/2016] [Indexed: 12/17/2022]
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