Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B

Abstract

Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. As a result, this phenomenon (persistence) is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. However, the precise molecular mechanisms of persistence are still unclear. To examine the key mechanisms of persistence, we used the synthetically developed minimal cell Mycoplasma mycoides JCVI-Syn3B; the genome contains <500 genes, which are mostly essential. We found that Syn3B evolves expeditiously and rapidly evolves antibiotic resistance to kasugamycin. The minimum cell also tolerates and persists against multiple antibiotics despite lacking many systems related to bacterial persistence (e.g. toxin-antitoxin systems). These results show that this minimal system is a suitable system to unravel the central regulatory mechanisms of persistence.

Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

“…We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems. Indeed, in our very recent work, we demonstrated that a bacteria population containing primarily essential genes have both antibiotic tolerant and persister subpopulations to different types of antibiotics 98 . Based on ours and others’ work, we propose that a systems biology approach would be fruitful for further study of antibiotic tolerance and persistence.…”

“…This type of systems biology approach is advantageous when compared to methods focusing on individual genes and specific mechanisms, which are susceptible to the presence of redundant systems and can often lead to contrary results. For example, toxin-antitoxins (TA) systems were once thought by many to be the primary effectors of persistence; however, several studies have suggested that they are not directly related to persistence [84][85][86] . We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems of the cell.…”

Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

“…We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems. Indeed, in our very recent work, we demonstrated that a bacteria population containing primarily essential genes have both antibiotic tolerant and persister subpopulations to different types of antibiotics 98 . Based on ours and others’ work, we propose that a systems biology approach would be fruitful for further study of antibiotic tolerance and persistence.…”

“…This type of systems biology approach is advantageous when compared to methods focusing on individual genes and specific mechanisms, which are susceptible to the presence of redundant systems and can often lead to contrary results. For example, toxin-antitoxins (TA) systems were once thought by many to be the primary effectors of persistence; however, several studies have suggested that they are not directly related to persistence [84][85][86] . We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems of the cell.…”

Blockade of endoplasmic reticulum stress‐induced cell death by Ureaplasma parvum vacuolating factor

“…We utilised near minimal bacterium JCVI-syn3A (GenBank CP016816.2) harbouring the minimal synthetic Mycoplasma mycoides genome and JCVI-syn3B harbouring dual loxP landing pad in the JCVI-syn3A genome (Hossain, Deter, Peters, & Butzin, 2021;Pelletier et al, 2020) as a mycoplasma vehicle to express U. parvum surface membrane lipoprotein multiple banded antigen (MBA) and UpVF.…”

Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

“…We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems. Indeed, in our very recent work, we demonstrated that a bacteria population containing primarily essential genes have both antibiotic tolerant and persister subpopulations to different types of antibiotics 98 . Based on ours and others’ work, we propose that a systems biology approach would be fruitful for further study of antibiotic tolerance and persistence.…”

“…This type of systems biology approach is advantageous when compared to methods focusing on individual genes and specific mechanisms, which are susceptible to the presence of redundant systems and can often lead to contrary results. For example, toxin-antitoxins (TA) systems were once thought by many to be the primary effectors of persistence; however, several studies have suggested that they are not directly related to persistence [84][85][86] . We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems of the cell.…”

Blockade of endoplasmic reticulum stress‐induced cell death by Ureaplasma parvum vacuolating factor

“…We utilised near minimal bacterium JCVI-syn3A (GenBank CP016816.2) harbouring the minimal synthetic Mycoplasma mycoides genome and JCVI-syn3B harbouring dual loxP landing pad in the JCVI-syn3A genome (Hossain, Deter, Peters, & Butzin, 2021;Pelletier et al, 2020) as a mycoplasma vehicle to express U. parvum surface membrane lipoprotein multiple banded antigen (MBA) and UpVF.…”

Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli

“…We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems. Indeed, in our very recent work, we demonstrated that a bacteria population containing primarily essential genes have both antibiotic tolerant and persister subpopulations to different types of antibiotics 98 . Based on ours and others’ work, we propose that a systems biology approach would be fruitful for further study of antibiotic tolerance and persistence.…”

“…This type of systems biology approach is advantageous when compared to methods focusing on individual genes and specific mechanisms, which are susceptible to the presence of redundant systems and can often lead to contrary results. For example, toxin-antitoxins (TA) systems were once thought by many to be the primary effectors of persistence; however, several studies have suggested that they are not directly related to persistence [84][85][86] . We instead propose that antibiotic tolerance is a multifaceted response rooted in the general stress response systems of the cell.…”

Blockade of endoplasmic reticulum stress‐induced cell death by Ureaplasma parvum vacuolating factor

“…We utilised near minimal bacterium JCVI-syn3A (GenBank CP016816.2) harbouring the minimal synthetic Mycoplasma mycoides genome and JCVI-syn3B harbouring dual loxP landing pad in the JCVI-syn3A genome (Hossain, Deter, Peters, & Butzin, 2021;Pelletier et al, 2020) as a mycoplasma vehicle to express U. parvum surface membrane lipoprotein multiple banded antigen (MBA) and UpVF.…”