Bacterial Persistence Methods and Protocols

This volume presents a collection of methods that have contributed to the current understanding of bacterial persisters. Chapters in the book detail general guidelines for measuring persister levels in bacterial cultures, strategies to enrich and resuscitate persister subpopulations, single-cell approaches for visualizing and characterizing persisters, omics techniques and cellular and animal models for studying persistence. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Bacterial Persistence: Methods and Protocols, Second Edition aims to be a useful practical guide to researchers to help further their study in this field.

PART I: Introduction

1.     Studying [NV1] Bacterial Persistence: Established Methods And Current Advances

Elen Louwagie, Laure Verstraete, Jan Michiels, and Natalie Verstraeten

PART II: Quantification and enrichment of persister cells

2.     Antibiotic Tolerance and Persistence Studied Throughout Bacterial Growth Phases

Enea Maffei, Cinzia Fino, and Alexander Harms

3.     A Robust Method For Generating, Quantifying, and Testing Large Numbers of Escherichia coli persisters

Silke R. Vedelaar, Jakub L. Radzikowski, and Matthias Heinemann

4.     Enrichment of Persister Cells through ß-lactam-induced Filamentation and Size Separation

Etthel Windels, Bram Van den Bergh, and Jan Michiels

5.     Methods for Enrichment of Bacterial Persister Populations For Phenotypic Screens And Genomic Studies

Samantha Adikari, Elizabeth Hong-Geller, and Sofiya Micheva-Viteva

PART III : Single-cell analysis of persister cells

6.     Observing Bacterial Persistence at Single-Cell Resolution

Emma Dawson, Emrah Simsek, and Minsu Kim

7.     Phenotypic Characterization of Antibiotic Persisters at the Single-Cell Level: From Data Acquisition to Data Analysis

Nathan Fraikin, Laurence Van Melderen, and Frédéric Goormaghtigh

8.     Microfluidics for Single-Cell Study of Antibiotic Tolerance and Persistence Induced by Nutrient Limitation

Stefany Moreno-Gámez, Alma Dal Co, Simon van Vliet, and Martin Ackermann

9.     Counting Chromosomes in Individual Bacteria to Quantify their Impacts on Persistence

Allison M. Murawski, Katherine Rittenbach, Christina J. DeCoste, Gary Laevsky, and Mark P. Brynildsen

PART IV: Omics approaches in persistence research

10.  Analyzing PERSISTER PROTEOMES with SILAC and Label-Free Methods

Bork A. Berghoff

11.  Defining Proteomic Signatures To Predict Multi-Drug Persistence in Pseudomonas aeruginosa

Pablo Manfredi, Isabella Santi, Enea Maffei, Emmanuelle Lezan, Alexander Schmidt, and Urs Jenal

12.  The use of Experimental Evolution to Study The Response of Pseudomonas aeruginosa to Single or Double Antibiotic Treatment

Isabella Santi, Pablo Manfredi, Urs Jenal

PART V: Persister cell resuscitation and eradication

13.  Detecting persister awakening determinants

Dorien Wilmaerts, Jan Michiels, and Natalie Verstraeten

14.  Monitoring Persister Resuscitation with Flow Cytometry

Sayed Golam Mohiuddin and Mehmet A. Orman

15.  Stimulating Aminoglycoside Uptake to Kill Staphylococcus aureus persisters

Ashelyn E. Sidders, Lauren C. Radlinski, Sarah E. Rowe, and Brian P. Conlon

PART VI: Cellular and animal model systems for studying persistence

16.  In vitro Models for the Study of the Intracellular Activity Of Antibiotics

Frédéric Peyrusson, Tiep K. Nguyen, Julien M. Buyck, Sandrine Lemaire, Gang W. Wang, Cristina Seral, Paul M. Tulkens, and Van Bambeke

17.  Analysis of Salmonella Persister Population Sizes, Dynamics Of Gut Luminal Seeding, And Plasmid Transfer In Mouse Models Of Salmonellosis

Erik Bakkeren, Joshua P. M. Newson, and Wolf-Dietrich Hardt

18.  Studying Antibiotic Persistence During Infection

Charlotte Michaux, Severin Ronneau, and Sophie Helaine