Main description:

This detailed volume presents a diverse set of methodological approaches designed to improve our understanding of bacterial infections from a wide range of bacterial species. Beginning with biofilms and subcellular compartments, the book explores transcriptional analysis, methods for studying plasmid dynamics, and tools for phylogenetic analysis of bacterial genomes, as well as bacterial effector proteins interfering with host systems, host response analysis, and in vivo and in vitro infection models. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and up-to-date, Bacterial Pathogenesis: Methods and Protocols, Second Edition is a vital resource for researchers in the area of infection biology, as well as but not limited to, those working in the fields of microbiology, immunology, structural biology, molecular biology, genetics, imaging, and computational study.

Contents:

Part I: Biofilms and Subcellular Compartments

1. Measuring Niche-Associated Metabolic Activity in Planktonic and Biofilm Bacteria

Supradipta De and Anders P. Hakansson

2. Formation and Analysis of Mono-Species and Polymicrobial Oral Biofilms in Flow-Cell Models

Jessica Neilands, Gunnel Svensater, Gabriella Boisen, Carolina Robertsson, Claes Wickstroem, and Julia R. Davies

3. Isolation and Purification of Mycobacterial Extracellular Vesicles (EVs)

Komal Umashankar Rao and Gabriela Godaly

4. Strategies to Isolate Extracellular Vesicles from Gram - and Gram + Bacteria

Ana Rita Narciso and Marie-Stephanie Aschtgen

Part II: Bacterial Genetics, Genomics, and Phylogenetics

5. Total Bacterial RNA Isolation and Northern Blotting Analysis

Jens Karlsson, Hannes Eichner, and Edmund Loh

6. Phylogenetic Analysis of Bacterial Pathogen Genomes

Xavier Didelot

7. Determination of Growth Rate and Virulence Plasmid Copy Number during Yersinia pseudotuberculosis Infection Using Droplet Digital PCR

Tifaine Hechard and Helen Wang

Part III: Identification and Characterization of Bacterial Effector Proteins

8. Methods to Analyze the Contribution of Complement Evasion Factor (CEF) to Streptococcus pyogenes Virulence

Haniyeh Aghababa, Jacelyn M.S. Loh, and Thomas Proft

9. Expression of the Bacterial Enzyme IdeS Using a GFP Fusion in the Yeast Saccharomyces cerevisiae

Tova Lindh, Mattias Collin, Rolf Lood, and Magnus Carlquist

10. Mass Spectrometry-Based Methods to Determine the Substrate Specificities and Kinetics of N-Linked Glycan Hydrolysis by Endo- -N-Acetylglucosaminidases

Jonathan J. Du, Diego Sastre, Beatriz Trastoy, Blaine Roberts, Daniel Deredge, Erik H. Klontz, Maria W. Flowers, Nazneen Sultana, Marcelo E. Guerin, and Eric J. Sundberg

11. Identification of Substrates of Secreted Bacterial Protease by APEX2-Based Proximity Labeling

Yanxuan Xie, Yang Mao, Zong-Wan Mao, and Wei Xia

12. Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host-Pathogen Protein-Protein Complexes

Lotta J. Happonen

13. Elucidating the Stoichiometries of Host-Pathogen Protein Interactions with Mass Photometry

Emma-Jayne Proctor, Sandeep Satapathy, and Martina Sanderson-Smith

Part IV: Analysis of Host Responses to Bacteria

14. Analysis of Neutrophil and Monocyte Inflammation Markers in Response to Gram-Positive Anaerobic Cocci

Tobias Schmidt and Ariane Neumann

15. Quantification of Phagocytosis Using Flow Cytometry

Therese de Neergaard and Pontus Nordenfelt

16. Anti-Bacterial Neutrophil Effector Response: Ex Vivo Quantification of Regulated Cell Death Associated with Extracellular Trap Release

Tiziano A. Schweizer, Sanne Hertegonne, Clement Vulin, Annelies S. Zinkernagel, and Srikanth Mairpady Shambat

17. Measurement of Antibody Binding Affinity on Bacterial Surfaces Using Flow Cytometry

Vibha Kumra Ahnlide and Pontus Nordenfelt

18. Detection of Inflammasome Activation in Murine Bone Marrow-Derived Macrophages Infected with Group A Streptococcus

Christine Valfridsson, Elsa Westerlund, Dora Hancz, and Jenny J. Persson

Part V: In Vivo and In Vitro Infection Models

19. In Vivo Profiling of the Vascular Cell Surface Proteome in Murine Models of Bacteremia

Charlotte Spliid, Jeffrey D. Esko, Johan Malmstroem, and Alejandro Gomez Toledo

20. Barcoded Consortium Infections: A Scalable, Internally Controlled Method to Study Host Cell Binding and Invasion by Pathogenic Bacteria

Maria Letizia Di Martino and Mikael E. Sellin

21. A Murine Mycobacterium marinum Infection Model for Longitudinal Analyses of Disease Development and the Inflammatory Response

Julia Lienard, Kristina Munke, and Fredric Carlsson

22. In Vitro Approaches for the Study of Pneumococcal-Neuronal Interaction and Pathogenesis

Kristine Farmen and Miguel Tofino-Vian