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phenotype and gene expression pattern are different in the persister isolated under
various stresses. For example, the size of starvation induced persisters were smaller
than the ciprofloxacin induced persisters, and more sensitive to heat and oxidative
stress (Paranjape and Shashidhar 2019). The reduction of growth rate has been
shown to be correlated with persistence both in vitro (Aldridge et al. 2012; Balaban
et al. 2004; Shah et al. 2006) and in vivo (Levin and Rozen 2006). Most antibiotics
are only active against growing cells by targeting the ribosome, cell wall synthesizing enzymes and deoxyribonucleic acid (DNA) gyrase or DNA topoisomerase etc.
These antibiotics are not effective against slow growing or non replicating bacteria
(Lewis 2010).
Persisters have been characterized in both Gram positive and Gram negative bacteria. In addition, persisters have been described in the fungal pathogen Candida
albicans (Van den Bergh et al. 2017). The regulatory mechanisms involved in bacterial persister formation have been identified, including SOS response (Bernier et al.
2013; Dorr et al. 2009), toxin antitoxin systems (Page and Peti 2016), stringent
response (Germain et al. 2013; Kaspy et al. 2013; Khakimova et al. 2013), quorum
sensing (Leung and Levesque 2012; Moker et al. 2010) and intracellular adenosine
triphosphate (ATP) level (Conlon et al. 2016; Pu et al. 2019; Shan et al. 2017).
Several excellent reviews on persister physiology (Helaine and Kugelberg 2014;
Van den Bergh et al. 2017), formation (Balaban et al. 2019; Cohen et al. 2013;
Fisher et al. 2017; Harms et al. 2016; Lewis 2007; Maisonneuve and Gerdes 2014),
resuscitation (Jõers et al. 2019; Matilla 2018; Wilmaerts et al. 2019) mechanisms
and strategies used to combating persisters (Allison et al. 2011; Defraine et al. 2018;
Keren et al. 2012; Wood 2016) have been published in recent years. In this article,
we review current approaches to study persister cells and provide information on
some emerging technologies which are likely be applied in persister cell research.
5.2 Classical Approaches
Colony forming unit (CFU) count is one of the most basic method to quantify viable
bacteria in a sample. In 1944, Joseph Bigger treated pathogenic Staphylococcus
aureus with penicillin which resulted in lysis. He plated this transparent liquid and
found one in a million S. aureus persister cells within the cell culture by means of
CFU count (Bigger 1944). This simple and useful method provides a very straightforward result for us to analyse the proportion of persister cells within the population. However, CFU assay failed to measure the deep dormant bacteria that wouldn’t
start to regrow in a short time (Pu et al. 2019).
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…
phenotype and gene expression pattern are different in the persister isolated under
various stresses. For example, the size of starvation induced persisters were smaller
than the ciprofloxacin induced persisters, and more sensitive to heat and oxidative
stress (Paranjape and Shashidhar 2019). The reduction of growth rate has been
shown to be correlated with persistence both in vitro (Aldridge et al. 2012; Balaban
et al. 2004; Shah et al. 2006) and in vivo (Levin and Rozen 2006). Most antibiotics
are only active against growing cells by targeting the ribosome, cell wall synthesizing enzymes and deoxyribonucleic acid (DNA) gyrase or DNA topoisomerase etc.
These antibiotics are not effective against slow growing or non replicating bacteria
(Lewis 2010).
Persisters have been characterized in both Gram positive and Gram negative bacteria. In addition, persisters have been described in the fungal pathogen Candida
albicans (Van den Bergh et al. 2017). The regulatory mechanisms involved in bacterial persister formation have been identified, including SOS response (Bernier et al.
2013; Dorr et al. 2009), toxin antitoxin systems (Page and Peti 2016), stringent
response (Germain et al. 2013; Kaspy et al. 2013; Khakimova et al. 2013), quorum
sensing (Leung and Levesque 2012; Moker et al. 2010) and intracellular adenosine
triphosphate (ATP) level (Conlon et al. 2016; Pu et al. 2019; Shan et al. 2017).
Several excellent reviews on persister physiology (Helaine and Kugelberg 2014;
Van den Bergh et al. 2017), formation (Balaban et al. 2019; Cohen et al. 2013;
Fisher et al. 2017; Harms et al. 2016; Lewis 2007; Maisonneuve and Gerdes 2014),
resuscitation (Jõers et al. 2019; Matilla 2018; Wilmaerts et al. 2019) mechanisms
and strategies used to combating persisters (Allison et al. 2011; Defraine et al. 2018;
Keren et al. 2012; Wood 2016) have been published in recent years. In this article,
we review current approaches to study persister cells and provide information on
some emerging technologies which are likely be applied in persister cell research.
5.2 Classical Approaches
Colony forming unit (CFU) count is one of the most basic method to quantify viable
bacteria in a sample. In 1944, Joseph Bigger treated pathogenic Staphylococcus
aureus with penicillin which resulted in lysis. He plated this transparent liquid and
found one in a million S. aureus persister cells within the cell culture by means of
CFU count (Bigger 1944). This simple and useful method provides a very straightforward result for us to analyse the proportion of persister cells within the population. However, CFU assay failed to measure the deep dormant bacteria that wouldn’t
start to regrow in a short time (Pu et al. 2019).
5 Molecular and Systems Biology Approaches for Analyzing Drug-Tolerant Bacterial…