1
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Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C, Frentzas S, Michael M, Gao B, Palmer J, Cebon J, Behren A, Adams DJ, Lawley TD. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat Med 2024; 30:797-809. [PMID: 38429524 PMCID: PMC10957475 DOI: 10.1038/s41591-024-02823-z] [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: 06/23/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.
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Affiliation(s)
- Ashray Gunjur
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Rozday
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bastiaan W Haak
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ben Markman
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Alfred Health, Melbourne, Victoria, Australia
- School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
- Melanoma Institute of Australia, University of Sydney, Sydney, New South Wales, Australia
| | - Craig Underhill
- Border Medical Oncology and Haematology Research Unit, Albury-Wodonga Regional Cancer Centre, Albury-Wodonga, New South Wales, Australia
- Rural Medical School, University of New South Wales, Albury, New South Wales, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Michael Michael
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bo Gao
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
| | - Jodie Palmer
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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2
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Boslem E, Reibe S, Carlessi R, Smeuninx B, Tegegne S, Egan CL, McLennan E, Terry LV, Nobis M, Mu A, Nowell C, Horadagoda N, Mellett NA, Timpson P, Jones M, Denisenko E, Forrest AR, Tirnitz-Parker JE, Meikle PJ, Rose-John S, Karin M, Febbraio MA. Therapeutic blockade of ER stress and inflammation prevents NASH and progression to HCC. Sci Adv 2023; 9:eadh0831. [PMID: 37703359 PMCID: PMC10499313 DOI: 10.1126/sciadv.adh0831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
The incidence of hepatocellular carcinoma (HCC) is rapidly rising largely because of increased obesity leading to nonalcoholic steatohepatitis (NASH), a known HCC risk factor. There are no approved treatments to treat NASH. Here, we first used single-nucleus RNA sequencing to characterize a mouse model that mimics human NASH-driven HCC, the MUP-uPA mouse fed a high-fat diet. Activation of endoplasmic reticulum (ER) stress and inflammation was observed in a subset of hepatocytes that was enriched in mice that progress to HCC. We next treated MUP-uPA mice with the ER stress inhibitor BGP-15 and soluble gp130Fc, a drug that blocks inflammation by preventing interleukin-6 trans-signaling. Both drugs have progressed to phase 2/3 human clinical trials for other indications. We show that this combined therapy reversed NASH and reduced NASH-driven HCC. Our data suggest that these drugs could provide a potential therapy for NASH progression to HCC.
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Affiliation(s)
- Ebru Boslem
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Saskia Reibe
- Garvan Institute of Medical Research, Sydney, Australia
| | - Rodrigo Carlessi
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Benoit Smeuninx
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Surafel Tegegne
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Casey L. Egan
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Emma McLennan
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Lauren V. Terry
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Max Nobis
- Garvan Institute of Medical Research, Sydney, Australia
| | - Andre Mu
- Wellcome Sanger Institute, Cambridge, UK
- EMBL's European Bioinformatics Institute, Cambridge UK
| | - Cameron Nowell
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Neil Horadagoda
- Faculty of Veterinary Science, University of Sydney, Camden, Australia
| | | | - Paul Timpson
- Garvan Institute of Medical Research, Sydney, Australia
| | - Matthew Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Alistair R. R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Janina E. E. Tirnitz-Parker
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Peter J. Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stefan Rose-John
- Department of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Michael Karin
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mark A. Febbraio
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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3
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Naderer T, Mu A, Monteith AJ, Wong Fok Lung T. Editorial: Understanding the effects of metabolites and trace minerals on microbes during infection. Front Cell Infect Microbiol 2023; 13:1276271. [PMID: 37712062 PMCID: PMC10499517 DOI: 10.3389/fcimb.2023.1276271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Thomas Naderer
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory (EMBL)– European Bioinformatics Institute, Hinxton, United Kingdom
| | - Andrew J. Monteith
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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4
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Cattò C, Mu A, Moreau JW, Wang N, Cappitelli F, Strugnell R. Biofilm colonization of stone materials from an Australian outdoor sculpture: Importance of geometry and exposure. J Environ Manage 2023; 339:117948. [PMID: 37080094 DOI: 10.1016/j.jenvman.2023.117948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
The safeguarding of Australian outdoor stone heritage is currently limited by a lack of information concerning mechanisms responsible for the degradation of the built heritage. In this study, the bacterial community colonizing the stone surface of an outdoor sculpture located at the Church of St. John the Evangelist in Melbourne was analysed, providing an overview of the patterns of microbial composition associated with stone in an anthropogenic context. Illumina MiSeq 16S rRNA gene sequencing together with confocal laser microscope investigations highlighted the bacterial community was composed of both phototrophic and chemotrophic microorganisms characteristic of stone and soil, and typical of arid, salty and urban environments. Cardinal exposure, position and surface geometry were the most important factors in determining the structure of the microbial community. The North-West exposed areas on the top of the sculpture with high light exposure gave back the highest number of sequences and were dominated by Cyanobacteria. The South and West facing in middle and lower parts of the sculpture received significantly lower levels of radiation and were dominated by Actinobacteria. Proteobacteria were observed as widespread on the sculpture. This pioneer research provided an in-depth investigation of the microbial community structure on a deteriorated artistic stone in the Australian continent and provides information for the identification of deterioration-associated microorganisms and/or bacteria beneficial for stone preservation.
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Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy; Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Andre Mu
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom; School of Geographical, Atmospheric and Earth Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Nancy Wang
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy.
| | - Richard Strugnell
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
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5
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Affiliation(s)
- Andre Mu
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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6
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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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7
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Soares A, Edwards A, An D, Bagnoud A, Bradley J, Barnhart E, Bomberg M, Budwill K, Caffrey SM, Fields M, Gralnick J, Kadnikov V, Momper L, Osburn M, Mu A, Moreau JW, Moser D, Purkamo L, Rassner SM, Sheik CS, Sherwood Lollar B, Toner BM, Voordouw G, Wouters K, Mitchell AC. A global perspective on bacterial diversity in the terrestrial deep subsurface. Microbiology (Reading) 2023; 169:001172. [PMID: 36748549 PMCID: PMC9993121 DOI: 10.1099/mic.0.001172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/07/2022] [Indexed: 01/19/2023]
Abstract
While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.
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Affiliation(s)
- A. Soares
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
- Present address: Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Campus Essen - Environmental Microbiology and Biotechnology, Universitätsstr. 5, 45141 Essen, Germany
| | - A. Edwards
- Institute of Biology, Environmental and Rural Sciences (IBERS), AU, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - D. An
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - A. Bagnoud
- Institut de Génie Thermique (IGT), Haute École d'Ingénierie et de Gestion du Canton de Vaud (HEIG-VD), Yverdon-les-Bains, Switzerland
| | - J. Bradley
- School of Geography, Queen Mary University of London, London, UK
| | - E. Barnhart
- U.S. Geological Survey (USGS), USA, Reston, VA, USA
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
| | - M. Bomberg
- VTT Technical Research Centre of Finland, Finland
| | | | | | - M. Fields
- Center for Biofilm Engineering (CBE), Montana State University, Bozeman, MT, USA
- Department of Microbiology & Immunology, MSU, Bozeman, MT, USA
| | - J. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
| | - V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Russia
| | - L. Momper
- Department of Earth, Atmospheric and Planetary Sciences (DEAPS), The Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - M. Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - A. Mu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - J. W. Moreau
- School of Earth Sciences, The University of Melbourne, Parkville, Australia
| | - D. Moser
- Division of Hydrologic Sciences, Desert Research Institute (DRI), Las Vegas, NV, USA
| | - L. Purkamo
- VTT Technical Research Centre of Finland, Finland
- School of Earth and Environmental Sciences (SEES), University of St. Andrews, St. Andrews, UK
- Geological Survey of Finland (GTK), Finland
| | - S. M. Rassner
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
| | - C. S. Sheik
- Large Lakes Observatory, University of Minnesota, Duluth, MN, USA
| | | | - B. M. Toner
- Department of Soil, Water & Climate, University of Minnesota, Minneapolis/Saint Paul, MN, USA
| | - G. Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - K. Wouters
- Institute for Environment, Health and Safety (EHS), Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - A. C. Mitchell
- Department of Geography and Earth Sciences (DGES), Aberystwyth University (AU), Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), AU, Aberystwyth, UK
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8
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Wong Fok Lung T, Charytonowicz D, Beaumont KG, Shah SS, Sridhar SH, Gorrie CL, Mu A, Hofstaedter CE, Varisco D, McConville TH, Drikic M, Fowler B, Urso A, Shi W, Fucich D, Annavajhala MK, Khan IN, Oussenko I, Francoeur N, Smith ML, Stockwell BR, Lewis IA, Hachani A, Upadhyay Baskota S, Uhlemann AC, Ahn D, Ernst RK, Howden BP, Sebra R, Prince A. Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection. Cell Metab 2022; 34:761-774.e9. [PMID: 35413274 PMCID: PMC9081115 DOI: 10.1016/j.cmet.2022.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 03/22/2022] [Indexed: 12/21/2022]
Abstract
K. pneumoniae sequence type 258 (Kp ST258) is a major cause of healthcare-associated pneumonia. However, it remains unclear how it causes protracted courses of infection in spite of its expression of immunostimulatory lipopolysaccharide, which should activate a brisk inflammatory response and bacterial clearance. We predicted that the metabolic stress induced by the bacteria in the host cells shapes an immune response that tolerates infection. We combined in situ metabolic imaging and transcriptional analyses to demonstrate that Kp ST258 activates host glutaminolysis and fatty acid oxidation. This response creates an oxidant-rich microenvironment conducive to the accumulation of anti-inflammatory myeloid cells. In this setting, metabolically active Kp ST258 elicits a disease-tolerant immune response. The bacteria, in turn, adapt to airway oxidants by upregulating the type VI secretion system, which is highly conserved across ST258 strains worldwide. Thus, much of the global success of Kp ST258 in hospital settings can be explained by the metabolic activity provoked in the host that promotes disease tolerance.
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Affiliation(s)
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Shivang S Shah
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Claire L Gorrie
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andre Mu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Casey E Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | - David Varisco
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | | | - Marija Drikic
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Brandon Fowler
- Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Andreacarola Urso
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Wei Shi
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Dario Fucich
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Medini K Annavajhala
- Department of Medicine, Columbia University, New York, NY 10032, USA; Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Ibrahim N Khan
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Irina Oussenko
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | | | - Anne-Catrin Uhlemann
- Department of Medicine, Columbia University, New York, NY 10032, USA; Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Danielle Ahn
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA; Sema4: A Mount Sinai Venture, Stamford, CT 06902, USA
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY 10032, USA.
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9
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Romero AR, Mu A, Ayres JS. Adipose triglyceride lipase mediates lipolysis and lipid mobilization in response to iron-mediated negative energy balance. iScience 2022; 25:103941. [PMID: 35265813 PMCID: PMC8899412 DOI: 10.1016/j.isci.2022.103941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/13/2021] [Revised: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Maintenance of energy balance is essential for overall organismal health. Mammals have evolved complex regulatory mechanisms that control energy intake and expenditure. Traditionally, studies have focused on understanding the role of macronutrient physiology in energy balance. In the present study, we examined the role of the essential micronutrient iron in regulating energy balance. We found that a short course of dietary iron caused a negative energy balance resulting in a severe whole body wasting phenotype. This disruption in energy balance was because of impaired intestinal nutrient absorption. In response to dietary iron-induced negative energy balance, adipose triglyceride lipase (ATGL) was necessary for wasting of subcutaneous white adipose tissue and lipid mobilization. Fat-specific ATGL deficiency protected mice from fat wasting, but caused a severe cachectic response in mice when fed iron. Our work reveals a mechanism for micronutrient control of lipolysis that is necessary for regulating mammalian energy balance.
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Affiliation(s)
- Alicia R. Romero
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Gene Expression Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andre Mu
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Gene Expression Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Janelle S. Ayres
- Molecular and Systems Physiology Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Gene Expression Lab, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA,Corresponding author
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10
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Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022; 30:853-865. [DOI: 10.1016/j.tim.2022.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
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11
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Mu A, McDonald D, Jarmusch AK, Martino C, Brennan C, Bryant M, Humphrey GC, Toronczak J, Schwartz T, Nguyen D, Ackermann G, D'Onofrio A, Strathdee SA, Schooley RT, Dorrestein PC, Knight R, Aslam S. Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection. Microbiome 2021; 9:92. [PMID: 33853672 PMCID: PMC8048313 DOI: 10.1186/s40168-021-01026-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 06/09/2020] [Accepted: 02/05/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood. RESULTS Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum. CONCLUSION Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.
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Affiliation(s)
- Andre Mu
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mackenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Julia Toronczak
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Dominic Nguyen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, USA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Robert T Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Sciences and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, USA
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12
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Lee YM, Mu A, Wallace M, Gengatharan JM, Furst AJ, Bode L, Metallo CM, Ayres JS. Microbiota control of maternal behavior regulates early postnatal growth of offspring. Sci Adv 2021; 7:7/5/eabe6563. [PMID: 33514556 PMCID: PMC7846171 DOI: 10.1126/sciadv.abe6563] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/08/2020] [Indexed: 05/28/2023]
Abstract
Maternal behavior is necessary for optimal development and growth of offspring. The intestinal microbiota has emerged as a critical regulator of growth and development in the early postnatal period life. Here, we describe the identification of an intestinal Escherichia coli strain that is pathogenic to the maternal-offspring system during the early postnatal stage of life and results in growth stunting of the offspring. However, rather than having a direct pathogenic effect on the infant, we found that this particular E. coli strain was pathogenic to the dams by interfering with the maturation of maternal behavior. This resulted in malnourishment of the pups and impaired insulin-like growth factor 1 (IGF-1) signaling, leading to the consequential stunted growth. Our work provides a new understanding of how the microbiota regulates postnatal growth and an additional variable that must be considered when studying the regulation of maternal behavior.
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Affiliation(s)
- Yujung Michelle Lee
- Molecular and Systems Physiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andre Mu
- Molecular and Systems Physiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martina Wallace
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92092, USA
| | - Jivani M Gengatharan
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92092, USA
| | - Annalee J Furst
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California San Diego, La Jolla, CA 92092, USA
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California San Diego, La Jolla, CA 92092, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92092, USA
| | - Janelle S Ayres
- Molecular and Systems Physiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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13
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Mu A, Thomas BC, Banfield JF, Moreau JW. Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph. Environ Microbiol Rep 2020; 12:525-533. [PMID: 32633030 DOI: 10.1111/1758-2229.12868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2 ) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilizing anaerobe Carboxydocella, which decreased in relative abundance post-scCO2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO).
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Affiliation(s)
- Andre Mu
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Melbourne, Australia
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14
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Simpson CA, Mu A, Haslam N, Schwartz OS, Simmons JG. Feeling down? A systematic review of the gut microbiota in anxiety/depression and irritable bowel syndrome. J Affect Disord 2020; 266:429-446. [PMID: 32056910 DOI: 10.1016/j.jad.2020.01.124] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/24/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
Background Anxiety/depression and irritable bowel syndrome (IBS) are highly prevalent and burdensome conditions, whose co-occurrence is estimated between 44 and 84%. Shared gut microbiota alterations have been identified in these separate disorders relative to controls; however, studies have not adequately considered their comorbidity. This review set out to identify case-control studies comparing the gut microbiota in anxiety/depression, IBS, and both conditions comorbidly relative to each other and to controls, as well as gut microbiota investigations including measures of both IBS and anxiety/depression. Methods Four databases were systematically searched using comprehensive search terms (OVID Medline, Embase, PsycINFO, and PubMed), following PRISMA guidelines. Results Systematic review identified 17 studies (10 human, 7 animal). Most studies investigated the gut microbiota and anxiety/depression symptoms in IBS cohorts. Participants with IBS and high anxiety/depression symptoms had lower alpha diversity compared to controls and IBS-only cohorts. Machine learning and beta diversity distinguished between IBS participants with and without anxiety/depression by their gut microbiota. Comorbid IBS and anxiety/depression also had higher abundance of Proteobacteria, Prevotella/Prevotellaceae, Bacteroides and lower Lachnospiraceae relative to controls. Limitations A large number of gut microbiota estimation methods and statistical techniques were utilized; therefore, meta-analysis was not possible. Conclusions Well-designed case-control and longitudinal studies are required to disentangle whether the gut microbiota is predicted as a continuum of gastrointestinal and anxiety/depression symptom severity, or whether reported dysbiosis is unique to IBS and anxiety/depression comorbidity. These findings may inform the development of targeted treatment through the gut microbiota for individuals with both anxiety/depression and IBS.
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Affiliation(s)
- Carra A Simpson
- Melbourne School of Psychological Sciences, The University of Melbourne, 12th floor Redmond Barry Building, Parkville, VIC, Australia; Melbourne Neuropsychiatry Centre, The University of Melbourne and Melbourne Health, VIC, Australia.
| | - Andre Mu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia; Microbiological Diagnostic Unit Public Health Laboratory, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, VIC, Australia
| | - Nick Haslam
- Melbourne School of Psychological Sciences, The University of Melbourne, 12th floor Redmond Barry Building, Parkville, VIC, Australia
| | - Orli S Schwartz
- Orygen, The National Centre of Excellence in Youth Mental Health; Centre for Youth Mental Health, The University of Melbourne, VIC, Australia
| | - Julian G Simmons
- Melbourne School of Psychological Sciences, The University of Melbourne, 12th floor Redmond Barry Building, Parkville, VIC, Australia; Melbourne Neuropsychiatry Centre, The University of Melbourne and Melbourne Health, VIC, Australia
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15
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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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16
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Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. Engineering the microbiome for animal health and conservation. Exp Biol Med (Maywood) 2019; 244:494-504. [PMID: 30776908 DOI: 10.1177/1535370219830075] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPACT STATEMENT Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.
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Affiliation(s)
- Se Jin Song
- 1 Department of Pediatrics, University of California, San Diego, CA 92093, USA
| | - Douglas C Woodhams
- 2 Biology Department, University of Massachusetts Boston, Boston, MA 02125, USA.,3 Smithsonian Tropical Research Institute, Panama city 0843-03092, Panama
| | - Cameron Martino
- 4 Bioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA
| | - Celeste Allaband
- 5 Biomedical Sciences Graduate Program, University of California, San Diego, CA 92093, USA
| | - Andre Mu
- 6 Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville 3010, Australia.,7 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Australia
| | - Sandrine Javorschi-Miller-Montgomery
- 8 Department of Bioengineering, University of California, San Diego, CA 92093, USA.,9 Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | - Jan S Suchodolski
- 10 Gastrointestinal Laboratory, Texas A&M University, College Station, TX 77843, USA
| | - Rob Knight
- 1 Department of Pediatrics, University of California, San Diego, CA 92093, USA.,8 Department of Bioengineering, University of California, San Diego, CA 92093, USA.,9 Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA.,11 Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA
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17
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Wardle M, Mu A, Tong SYC. Streptococcus gallolyticus subsp. pasteurianus meningitis complicated by venous sinus thrombosis: A case report. Int J Infect Dis 2018; 71:30-32. [PMID: 29656136 DOI: 10.1016/j.ijid.2018.04.005] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022] Open
Abstract
A case of Streptococcus gallolyticus subsp. pasteurianus meningitis, unusually occurring in a splenectomized patient and complicated by cerebral venous thrombosis, is described. Following presentation with meningism and diagnosis and management of S. gallolyticus meningitis, the patient presented again with a further 4days of fevers and subsequently developed left-sided paresthesias. Cerebral imaging revealed a venous thrombus in the right frontal cortical veins and left sigmoid sinus. The patient recovered following 4 weeks of intravenous ceftriaxone and anticoagulation with enoxaparin and then warfarin. Apart from the splenectomy, no underlying cause was found. The patient was commenced on life-long prophylactic amoxicillin, given appropriate vaccinations, and anticoagulated with warfarin. After initial difficulties, identification of the causative organism to the subspecies level was confirmed by analysis of short-read whole genome sequencing data. This case demonstrates two features that have not previously been reported for S. gallolyticus subsp. pasteurianus infections: splenectomy as a potential risk factor and that infection may be complicated by cerebral venous thrombosis. The resolution provided by whole genome sequencing was valuable in accurately identifying the bacterial subspecies.
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Affiliation(s)
- Martin Wardle
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Victoria, Australia.
| | - Andre Mu
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, and The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia; Menzies School of Health Research, Darwin, Australia.
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18
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Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M, Cronin K, Waters MJ, Tomita T, Stevens K, Schultz MB, Baines SL, Sherry NL, Carter GP, Mu A, Sait M, Ballard SA, Seemann T, Stinear TP, Howden BP. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 2018; 6:e4210. [PMID: 29312831 PMCID: PMC5756455 DOI: 10.7717/peerj.4210] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 10/12/2017] [Accepted: 12/09/2017] [Indexed: 12/21/2022] Open
Abstract
Background Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks. Methods All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Results Initial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation. Conclusion A real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management.
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Affiliation(s)
- Jason C Kwong
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Health Protection Branch, Department of Health and Human Services, Victoria State Government, Melbourne, VIC, Australia
| | - Finn Romanes
- Health Protection Branch, Department of Health and Human Services, Victoria State Government, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marion Easton
- Health Protection Branch, Department of Health and Human Services, Victoria State Government, Melbourne, VIC, Australia
| | - Katie Cronin
- Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, VIC, Australia
| | - Mary Jo Waters
- Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, VIC, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mark B Schultz
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia
| | - Glen P Carter
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Andre Mu
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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19
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Mu A, Moreau JW. The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection. Front Microbiol 2015; 6:263. [PMID: 25914677 PMCID: PMC4391042 DOI: 10.3389/fmicb.2015.00263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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] [Received: 11/26/2014] [Accepted: 03/16/2015] [Indexed: 11/13/2022] Open
Abstract
Our primary research paper (Mu et al., 2014) demonstrated selective changes to a deep subsurface prokaryotic community as a result of CO2 stress. Analyzing geochemical and microbial 16S rRNA gene profiles, we evaluated how in situ prokaryotic communities responded to increased CO2 and the presence of trace organic compounds, and related temporal shifts in phylogeny to changes in metabolic potential. In this focused review, we extend upon our previous discussion to present analysis of taxonomic unit co-occurrence profiles from the same field experiment, to attempt to describe dynamic community behavior within the deep subsurface. Understanding the physiology of the subsurface microbial biosphere, including how key functional groups integrate into the community, will be critical to determining the fate of injected CO2. For example, community-wide network analyses may provide insights to whether microbes cooperatively produce biofilm biomass, and/or biomineralize the CO2, and hence, induce changes to formation porosity or changes in electron flow. Furthermore, we discuss potential impacts to the feasibility of subsurface CO2 storage of selectively enriching for particular metabolic functions (e.g., methanogenesis) as a result of CO2 injection.
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Affiliation(s)
- Andre Mu
- Moreau Lab, School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne Melbourne, VIC, Australia
| | - John W Moreau
- Moreau Lab, School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia
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20
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Mu A, Boreham C, Leong HX, Haese RR, Moreau JW. Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment. Front Microbiol 2014; 5:209. [PMID: 24860559 PMCID: PMC4030138 DOI: 10.3389/fmicb.2014.00209] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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] [Received: 02/03/2014] [Accepted: 04/19/2014] [Indexed: 01/08/2023] Open
Abstract
Subsurface microorganisms may respond to increased CO2 levels in ways that significantly affect pore fluid chemistry. Changes in CO2 concentration or speciation may result from the injection of supercritical CO2 (scCO2) into deep aquifers. Therefore, understanding subsurface microbial responses to scCO2, or unnaturally high levels of dissolved CO2, will help to evaluate the use of geosequestration to reduce atmospheric CO2 emissions. This study characterized microbial community changes at the 16S rRNA gene level during a scCO2 geosequestration experiment in the 1.4 km-deep Paaratte Formation of the Otway Basin, Australia. One hundred and fifty tons of mixed scCO2 and groundwater was pumped into the sandstone Paaratte aquifer over 4 days. A novel U-tube sampling system was used to obtain groundwater samples under in situ pressure conditions for geochemical analyses and DNA extraction. Decreases in pH and temperature of 2.6 log units and 5.8°C, respectively, were observed. Polyethylene glycols (PEGs) were detected in the groundwater prior to scCO2 injection and were interpreted as residual from drilling fluid used during the emplacement of the CO2 injection well. Changes in microbial community structure prior to scCO2 injection revealed a general shift from Firmicutes to Proteobacteria concurrent with the disappearance of PEGs. However, the scCO2 injection event, including changes in response to the associated variables (e.g., pH, temperature and salinity), resulted in increases in the relative abundances of Comamonadaceae and Sphingomonadaceae suggesting the potential for enhanced scCO2 tolerance of these groups. This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.
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Affiliation(s)
- Andre Mu
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Chris Boreham
- Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia ; Geoscience Australia Canberra, NSW, Australia
| | - Henrietta X Leong
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - Ralf R Haese
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
| | - John W Moreau
- School of Earth Sciences, Faculty of Science, University of Melbourne Melbourne, VIC, Australia ; Cooperative Research Centre for Greenhouse Gas Technologies Canberra, NSW, Australia
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21
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Vu H, Mu A, Moreau J. Biodegradation of thiocyanate by a novel strain of Burkholderia phytofirmans
from soil contaminated by gold mine tailings. Lett Appl Microbiol 2013; 57:368-72. [DOI: 10.1111/lam.12123] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/15/2013] [Accepted: 06/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- H.P. Vu
- Geomicrobiology Lab; School of Earth Sciences; University of Melbourne; Parkville Vic. Australia
| | - A. Mu
- Geomicrobiology Lab; School of Earth Sciences; University of Melbourne; Parkville Vic. Australia
- Department of Microbiology and Immunology; University of Melbourne; Parkville Vic. Australia
| | - J.W. Moreau
- Geomicrobiology Lab; School of Earth Sciences; University of Melbourne; Parkville Vic. Australia
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22
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Welsh DC, Dipla K, McNulty PH, Mu A, Ojamaa KM, Klein I, Houser SR, Margulies KB. Preserved contractile function despite atrophic remodeling in unloaded rat hearts. Am J Physiol Heart Circ Physiol 2001; 281:H1131-6. [PMID: 11514279 DOI: 10.1152/ajpheart.2001.281.3.h1131] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study was designed to determine whether myocardial atrophy is necessarily associated with changes in cardiac contractility. Myocardial unloading of normal hearts was produced via heterotopic transplantation in rats. Contractions of isolated myocytes (1.2 mM Ca2+; 37 degrees C) were assessed during field stimulation (0.5, 1.0, and 2.0 Hz), and papillary muscle contractions were assessed during direct stimulation (2.0 mM Ca2+; 37 degrees C; 0.5 Hz). Hemodynamic unloading was associated with a 41% decrease in median myocyte volume and proportional decreases in myocyte length and width. Nevertheless, atrophic myocytes had normal fractional shortening, time to peak contraction, and relaxation times. Despite decreases in absolute maximal force generation (F(max)), there were no differences in F(max)/ area in papillary muscles isolated from unloaded transplanted hearts. Therefore, atrophic remodeling after unloading is associated with intact contractile function in isolated myocytes and papillary muscles when contractile indexes are normalized to account for reductions in cell length and cross-sectional area, respectively. Nevertheless, in the absence of compensatory increases in contractile function, reductions in myocardial mass will lead to impaired overall work capacity.
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Affiliation(s)
- D C Welsh
- Cardiovascular Research Group, Temple University Medical Center, Philadelphia, Pennsylvania 19140, USA
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23
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Autieri MV, Carbone C, Mu A. Expression of allograft inflammatory factor-1 is a marker of activated human vascular smooth muscle cells and arterial injury. Arterioscler Thromb Vasc Biol 2000; 20:1737-44. [PMID: 10894811 DOI: 10.1161/01.atv.20.7.1737] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The cytokine-induced activation and proliferation of medial vascular smooth muscle cells (VSMCs) leading to intimal hyperplasia is one of the most critical cellular events in the formation of transplant arteriopathy and balloon angioplasty-induced restenosis. Allograft inflammatory factor-1 (AIF-1) is a calcium-binding protein that we have previously shown to be expressed in balloon angioplasty-injured rat carotid arteries. We hypothesized that AIF-1 expression may be associated with the VSMC response to injury. In this study, we examined AIF-1 expression in immunologic and mechanical models of arterial injury. Reverse transcription-polymerase chain reaction and Western analysis demonstrated that AIF-1 is acutely and transiently expressed in aortic medial smooth muscle cells of rat cardiac allografts, with mRNA and protein peaking at 3 to 7 days after transplant and declining by 10 days after transplant. Immunohistochemical analysis identified abundant AIF-1 in the medial VSMCs of these vessels. Immunohistochemical analysis of balloon angioplasty-injured swine coronary arteries also demonstrates an acute AIF-1 expression detectable by 24 hours and continuing up to 14 days after the procedure. AIF-1 in these vessels also localizes to the medial VSMCs and cells of the developing neointima. AIF-1 protein is not expressed in quiescent cultured human VSMCs but is induced in cells challenged with various inflammatory cytokines, primarily by interferon-gamma, interleukin-1beta, and T-cell-conditioned media. Transfection and overexpression of AIF-1 in human VSMCs result in enhanced growth of these cells. Taken together, these data indicate that AIF-1 expression is associated with vascular trauma and suggest that this protein may play a role in VSMC activation subsequent to arterial injury.
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MESH Headings
- Amino Acid Sequence
- Angioplasty, Balloon/adverse effects
- Animals
- Aorta/pathology
- Aorta/transplantation
- Arteriosclerosis/immunology
- Biomarkers
- Calcium-Binding Proteins/analysis
- Calcium-Binding Proteins/genetics
- Cell Division/immunology
- Cells, Cultured
- Cytokines/immunology
- DNA-Binding Proteins
- Femoral Artery/immunology
- Femoral Artery/injuries
- Gene Expression/immunology
- Heart Transplantation/immunology
- Humans
- Hyperplasia
- Microfilament Proteins
- Molecular Sequence Data
- Muscle, Smooth, Vascular/chemistry
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/immunology
- RNA, Messenger/analysis
- Rats
- Rats, Inbred Lew
- Rats, Inbred WF
- Swine
- Transplantation, Homologous
- Tunica Intima/immunology
- Tunica Intima/injuries
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Affiliation(s)
- M V Autieri
- Department of Physiology and Cardiology, Heart Failure Research Group, Temple University School of Medicine, Philadelphia, PA 19140, USA.
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Abstract
A survey of women in two highly developed rural counties of China, Sichuan and Jiangsu Provinces, was carried out in late 1991, to gain information about demographic and economic change between 1980 and 1990. Three separate surveys were conducted: the first a questionnaire administered to married women aged 30-39, eliciting information about childbearing and contraception, as well as the social and economic background of the respondents; the second, focus group interviews emphasizing the motivation for childbearing. Official information about the selected villages, townships and counties was also collected. National level data in 1987 show that individual reproductive behaviour in China failed to conform to a universal, effectively implemented, population policy. They imply either a spatial range of policies, or great diversity in the demand for children, or perhaps a combination of both. Such diversity in reproductive behaviour is also found in the study area. The purpose of the analysis was to examine the diversity in reproductive behaviour and contraceptive practice, and to discover whether differentials are influenced by area, or else exist between individuals within areas. If the former, then the explanation may be found in differences in policy formulation and implementation between areas: and if the latter, to demand for children, or else differential application of policy restrictions. The main findings were that: (1) the explanation of the pattern of fertility and contraceptive use is to be found at the individual level (within locations) rather than in policy differences between administrative units; (2) the association between income and number of children is negative, as is that between income and the propensity for uniparous women to remain unsterilized. The theory that privilege may be exercised to gain concessions from birth planning cadres is therefore not supported; (3) ideal family size differentials are largely absent, showing that social (education) and economic (income, occupation) characteristics are not responsible for differences in reproductive motivations, and implying that the nature of the demand for children is very different from that in most rural areas of the Third World; (4) data on ideal family size by sex of the existing offspring indicate only a weak preference for sons. The low demand for children, and the weak son preference, may both be explained by the social acceptability of uxorilocal marriages, and of village endogamy, together with the prohibitive costs of children, and especially of sons. This partly results from the expense of education, but most mothers emphasize marriage costs. It is speculated that the circumstances responsible for the escalating costs of children in the two countries are likely to pertain in growing areas of the country, with the privatization of education and health services, the declining support of collective institutions, and the replacement of this function by kinship networks. These on-going changes imply that any policy of reproductive restriction for the purposes of population control is likely soon to meet with diminishing resistance; and it may later be rendered unnecessary in the eyes of government officials, as fulfilled reproductive intentions lead to a fertility level below replacement level.
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Affiliation(s)
- N H Thomas
- Department of City and Regional Planning, University of Wales, Cardiff
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Mu A. [Clinical analysis of pulmonary infection in patients with acquired immunodeficiency syndrome (AIDS)]. Zhonghua Jie He He Hu Xi Za Zhi 1998; 21:526-7. [PMID: 11360501] [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] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
OBJECTIVE This clinical analysis is made to achieve a better understanding of the opportunistic infection of patients with AIDS, especially pulmonary infection. METHOD 32 cases of patients with AIDS are analyzed. RESULT The clinical manifestations of the 32 cases are: fever, tiredness, loss of weight, night sweat, cough, sputum, and generalized pain. Among the 32 cases, 24 suffered for tuberculosis, constituting 78% of the total. The other patients suffered for bacterial infection and pneumocystis carinii pneumonia. These patients are complicated with skin infection and impairment of the heart, liver, kidney and other organs. CONCLUSION Pulmonary infection is a major opportunistic infection of AIDS patients at late stage. Patients with AIDS can be easily infected with tuberculosis and complicated with multi-organ impairments, which are very difficult to treat.
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Affiliation(s)
- A Mu
- Respiratory Department, Affiliated Hospital of Shandong Medical University, Jinan, 250012
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