Project

Back to overview

Molecular basis of Mycobacterium Abscessus heterogeneity during stress

Applicant Boeck Lucas
Number 185792
Funding scheme Ambizione
Research institution Departement Biomedizin Universität Basel
Institution of higher education University of Basel - BS
Main discipline Medical Microbiology
Start/End 01.10.2019 - 30.09.2023
Approved amount 946'409.00
Show all

All Disciplines (3)

Discipline
Medical Microbiology
Genetics
Experimental Microbiology

Keywords (10)

Single cell; Evolution; Genomics; Antimicrobials; Drug resistance; Tolerance; Persistence; CRISPR; Phenotype; Mycobacterium

Lay Summary (German)

Lead
Genetisch idente Bakterien verhalten sich insbesondere unter Stress unterschiedlich. Während die meisten Bakterien einer Population mit Antibiotika erfolgreich behandelt werden können, sprechen einzelne Bakterien ungenügend auf diese Therapie an und können dadurch zu einem Therapieversagen führen. Mit diesem Projekt untersuchen wir das zunehmend bedrohliche multiresistente Bakterium Mykobakterium abscessus. Wir werden das Verhalten einzelner Mykobakterien unter Stress (z.B. nach Antibiotikagabe) studieren und die zugrunde liegenden molekularen Mechanismen identifizieren.
Lay summary

Ziele des Forschungsprojekts 

Ziel 1: Das aktuelle mikrobiologische Wissen beruht fast ausschliesslich auf Experimenten von sehr grossen Bakterienpopulationen. Dies erlaubt uns jedoch nicht Unterschiede innerhalb der Population festzustellen. Wir gehen davon aus, dass diese Unterschiede jedoch entscheidend für das Überleben der Bakterien unter Stress sind. Mithilfe neuer Techniken werden wir tausende einzelne Bakterien studieren um eine genaue Information über das Verhalten der Population unter Stress zu bekommen. 

Ziel 2: Das unterschiedliche Verhalten von Bakterien innerhalb einer genetisch identen Population (die Heterogenität) wird genetisch festgelegt und gesteuert. Mithilfe von «Genome-wide association studies» und «Genome editing» Strategien werden wir versuchen diese Mechanismen zu identifizieren. 

Ziel 3: Die funktionellen Eigenschaften der Bakterien Subpopulationen sind schlecht charakterisiert. Ziel ist es deren Charakteristika sowie deren zugrunde liegende regulatorische Netzwerke zu eruieren. 


Wissenschaftlicher und gesellschaftlicher Kontext

Unser Wissen über die evolutionären Strategien die das Überleben von Bakterien unter Stress ermöglichen sind gering und im Fall von M. abscessus fast inexistent. Ein besseres molekulares Verständnis der Bakterien ist essentiell um wirksamere Therapien zu entwickeln. Dies könnte in Zukunft nicht nur Therapieversagen und Rückfälle verhindern, sondern potentiell auch die Entstehung von Antibiotika-Resistenzen beeinflussen. 

 

Direct link to Lay Summary Last update: 18.09.2019

Responsible applicant and co-applicants

Employees

Collaboration

Group / person Country
Types of collaboration
Prof. Sébastien Gagneux, SwissTPH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Warner Digby South Africa (Africa)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Prof. Petra Dittrich, D-BSSE Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Adrian Egli, Clinical Microbiology Switzerland (Europe)
- Research Infrastructure
Prof. Andres Floto Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Prof. Urs Jenal, Biozentrum Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Abstract

The evolutionary success of bacteria lies, to a large degree, in their adaptability; none more so than environmental mycobacteria. They have acquired multiple strategies to survive a large spectrum of stresses, and some, such as Mycobacterium tuberculosis managed to evolve from an environmental niche to become an obligate human pathogen.The focus of my proposal is Mycobacterium abscessus, a nontuberculous mycobacterium which has recently emerged as the most lethal and frequent multidrug-resistant mycobacterial infection in the developed world. M. abscessus infections are frequently impossible to treat despite prolonged combination antibiotic therapy and, at least in individuals with Cystic Fibrosis, cause accelerated lung damage and prevent safe lung transplantation. To date, the molecular strategies used by M. abscessus to resist antibiotics and escape host immune responses remain largely unknown but are likely to result from interactions between mycobacterial and non-mycobacterial virulence programmes (the latter acquired through horizontal gene transfer from other bacterial species). I have recently identified many of the critical gene networks controlling M. abscessus infection, virulence, and antimicrobial resistance through a multidimensional GWAS analysis of clinical isolates (Boeck et al in preparation). I now wish to examine how the generation of phenotypic heterogeneity by genetically identical bacteria may help M. abscessus adapt to changing environmental stresses. To do so, I will undertake three orthogonal experimental approaches (outlined below) to quantify mycobacterial heterogeneity, define the molecular basis underlying heterogeneity, and examine its functional implications during stress: Aim A: Single-cell dynamics of M. abscessus during stressOur knowledge of bacteria is almost exclusively based on the study of bulk populations. Particularly during stress (e.g. exposure to antibiotics) a large number of phenotypically different states emerge, which cannot be assessed by traditional approaches. In order to capture replication and functional dynamics I will use a custom-made microfluidic device to track millions of individual mycobacteria over time. This will allow me to characterise heterogeneity across different genetic backgrounds and during exposure to different stresses. Aim B: Genetic drivers for M. abscessus heterogeneity Phenotypic heterogeneity occurs in genetically identical individuals, mainly due to variations in transcription. The degree of phenotypic heterogeneity, however, is specified within and variable across genetic backgrounds, i.e. is a heritable genetic trait. I will combine a bacterial genome-wide association study (GWAS) approach with a forward genetic screen to identify drivers of mycobacterial heterogeneity during stress; in order to identify molecular mechanisms of involved stress pathways and heterogeneity formation. Aim C: Functional networks of stress induced M. abscessus subpopulationsThe functional properties of stress tolerant bacteria are poorly understood, and several misconceptions prevail, particularly that bacterial persistence is exclusively mediated via dormancy, a metabolically inactive state. To characterise their functional properties during stress I will define the transcriptional networks active in specific phenotypic subpopulations of M. abscessus, and develop a functional framework for how persistence is activated and maintained.
-