MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profilingElectronic supplementary information (ESI) available. See DOI: 10.1039/c6an02486f

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectio...

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Main Authors Burnum-Johnson, Kristin E, Kyle, Jennifer E, Eisfeld, Amie J, Casey, Cameron P, Stratton, Kelly G, Gonzalez, Juan F, Habyarimana, Fabien, Negretti, Nicholas M, Sims, Amy C, Chauhan, Sadhana, Thackray, Larissa B, Halfmann, Peter J, Walters, Kevin B, Kim, Young-Mo, Zink, Erika M, Nicora, Carrie D, Weitz, Karl K, Webb-Robertson, Bobbie-Jo M, Nakayasu, Ernesto S, Ahmer, Brian, Konkel, Michael E, Motin, Vladimir, Baric, Ralph S, Diamond, Michael S, Kawaoka, Yoshihiro, Waters, Katrina M, Smith, Richard D, Metz, Thomas O
Format Journal Article
LanguageEnglish
Published 26.01.2017
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Abstract The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis , Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis , Campylobacter jejuni , and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus , Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes. The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines.
AbstractList The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis , Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis , Campylobacter jejuni , and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus , Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes. The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines.
Author Weitz, Karl K
Waters, Katrina M
Casey, Cameron P
Sims, Amy C
Motin, Vladimir
Konkel, Michael E
Nicora, Carrie D
Thackray, Larissa B
Ahmer, Brian
Smith, Richard D
Chauhan, Sadhana
Kim, Young-Mo
Webb-Robertson, Bobbie-Jo M
Metz, Thomas O
Stratton, Kelly G
Negretti, Nicholas M
Zink, Erika M
Eisfeld, Amie J
Habyarimana, Fabien
Walters, Kevin B
Kyle, Jennifer E
Baric, Ralph S
Gonzalez, Juan F
Nakayasu, Ernesto S
Kawaoka, Yoshihiro
Burnum-Johnson, Kristin E
Halfmann, Peter J
Diamond, Michael S
AuthorAffiliation Pathology & Immunology
Ohio State University
Departments of Medicine
University of Wisconsin-Madison
University of Texas Medical Branch
Department of Pathobiological Sciences
Department of Epidemiology
Molecular Microbiology
School of Veterinary Medicine
Department of Microbial Infection and Immunity
School of Molecular Biosciences
College of Veterinary Medicine
Washington State University
Computational and Statistical Analytics Division
Department of Pathology
Biological Sciences Division
Influenza Research Institute
Washington University School of Medicine
University of North Carolina at Chapel Hill
Pacific Northwest National Laboratory
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  publication-title: Disinfection, sterilization, and preservation
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  publication-title: Classification of bacteriophages, in The Bacteriophages
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  publication-title: Bergey's manual of systematic bacteriology
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