GenEpi-BioTrain - Virtual Training 26 - Genomic analysis of non-tuberculous mycobacteria

Topic outline

• Welcome to this training on genomic analysis of non-tuberculous mycobacteria

  Welcome to this training on genomic analysis of non-tuberculous mycobacteria

  Non-tuberculous mycobacteria (NTM) are an emerging public health concern. They include all species within the genus Mycobacterium, excluding those causing tuberculosis and leprosy. Although more than 200 NTM species have been identified, only a subset is clinically relevant. Diagnosis remains challenging, and treatment depends on accurate species identification and antimicrobial resistance profiles.

  Whole genome sequencing (WGS) has become a key tool for NTM analysis, enabling precise species identification, investigation of transmission and outbreaks, and prediction of resistance patterns.

  This course provides an overview of NTM, including classification, risk factors, clinical manifestations, diagnostics, treatment, transmission, prevalence, and global trends. In addition, participants will be introduced to bioinformatic tools for the analysis of WGS data.

  Training objective
  Participants will gain both theoretical knowledge and practical experience with open-source and commercial tools for NTM species and subspecies identification, typing, transmission analysis, and resistance profiling.

  Target audience
  This training is designed primarily for researchers, bioinformaticians, clinicians, public health professionals, PhDs,  bachelor/master students (e.g. molecular biology or infection biology). However it is open for everyone with an interest in NTM.

  Prerequisites
  No prior bioinformatics experience is required. For participants with prior bioinformatics experience (particularly command-line skills), a command-line analysis pipeline for NTM will be presented in more detail in the second session. Installation instructions and guidance for this pipeline can be provided upon request (mdiricks@fz-borstel.de).

  Practical component
  You can complete a guided step-by-step tutorial using web-based tools (e.g. Pathogenwatch and PubMLST) to analyse a real Mycobacterium abscessus outbreak (takes around 1 hour). You can complete the tutorial between the two sessions. No software installation is required to complete the task, unless you would like to try out the desktop application Ridom Typer (demo licenses can be requested via their website). 

  Sessions

  • 05 May 2026, 09:00–12:00 (CEST) - Introduction to NTM and WGS-based bioinformatic tools for NTM
  • 11 May 2026, 09:00–12:15 (CEST) - Demonstration of bioinformatic tools for NTM

  The recordings of the sessions will be made available.

  • FileInformation on the GenEpi-BioTrain programme, Code of conduct
  • PagePresenters' biography
  • PageLegal terms and conditions
• Collapse allExpand all
  Session 1 (05 May) - Introduction to NTM and WGS-based bioinformatic tools for NTM

  Session 1 (05 May) - Introduction to NTM and WGS-based bioinformatic tools for NTM

  The first session aims to provide participants with a solid foundation in non-tuberculous mycobacteria (NTM), covering their clinical relevance, epidemiology, and key challenges in diagnosis and management. In addition, it introduces the principles and tools of whole genome sequencing analysis, preparing participants for hands-on application in outbreak investigation and genomic data interpretation.

  After attending this session, participants will be able to:

  • Describe the clinical and epidemiological relevance of non-tuberculous mycobacteria (NTM)
  • Summarise key aspects of NTM classification, transmission, diagnosis, and treatment
  • Recognise the role of whole genome sequencing (WGS) in NTM analysis
  • Identify commonly used bioinformatic tools for NTM species identification, typing, and resistance profiling
  • Apply introductory knowledge to a real-case scenario (Mycobacterium abscessus outbreak tutorial)

  Agenda: 

  Time CEST	Session	Intended Learning Outcomes
  09:00-09:15	ECDC introduction	Greeting of participants, presentation of GenEpi-BioTrain, code of conduct, get to know the participants, get to know the trainer
  09:15-10:15	Lecture: Introduction to NTM	Gaining knowledge on classification, risk factors, disease manifestation, diagnosis, treatment, transmission, prevalence, global trends and population structure of clinically relevant NTM
  10:15-10:30	Coffee Break
  10:30- 11:15	Lecture: Tools for analysis of whole genome sequencing data from non-tuberculous mycobacteria	Learn about available open-source and commercial tools that can be used for NTM (sub)species identification, typing, transmission/outbreak analysis and resistance profiling
  11:15-11:30	Coffee Break
  11:30-11:45	Tutorial: M. abscessus outbreak – Case presentation & Task assignment	Getting hands-on experience with GUI-based bioinformatic tools for genomic analysis of NTM
  11:45-12:15	Q & A

  • Opening of session 1
  • Part 1 - Lecture: Introduction to NTM

    NOTE: The initial 5 minutes of this presentation are missing from the recording and will be added as soon as possible.

     

     
    

  • FilePresentation: Introduction to NTM
  • Part 2 - Lecture: Tools for analysis of whole genome sequencing data from non-tuberculous mycobacteria 

     

  • FilePresentation: Tools for analysis of whole genome sequencing data from non-tuberculous mycobacteria
  • Part 3 - Tutorial: M. abscessus outbreak – Case presentation & Task assignment 

     
    

  • FilePresentation: Tutorial: M. abscessus outbreak – Case presentation & Task assignment
• Homework between sessions

  Homework between sessions
  • Participants shall complete the tasks by following the tutorial provided in the learning portal (2026_ECDC_tutorial_NTM.pdf) until the next session.
    

  • File2026_ECDC_tutorial_NTM.pdf
  • FileTask_Exercise2026_NTM.xlsx
  • File110_Ref_Mabscessus_pubMLST.xlsx
  • • FastAFastA
      • H.fastaH.fasta
      • I.fastaI.fasta
      • J.fastaJ.fasta
      • K.fastaK.fasta
      • L.fastaL.fasta
      • M.fastaM.fasta
      • N.fastaN.fasta
      • O.fastaO.fasta
  • FileDownload all FastA files
  • • Optional: FastQ filesOptional: FastQ files
      • H_libx_R1.fastq.gzH_libx_R1.fastq.gz
      • H_libx_R2.fastq.gzH_libx_R2.fastq.gz
      • I_libx_R1.fastq.gzI_libx_R1.fastq.gz
      • I_libx_R2.fastq.gzI_libx_R2.fastq.gz
      • J_libx_R1.fastq.gzJ_libx_R1.fastq.gz
      • J_libx_R2.fastq.gzJ_libx_R2.fastq.gz
      • K_libx_R1.fastq.gzK_libx_R1.fastq.gz
      • K_libx_R2.fastq.gzK_libx_R2.fastq.gz
      • L_libx_R1.fastq.gzL_libx_R1.fastq.gz
      • L_libx_R2.fastq.gzL_libx_R2.fastq.gz
  • FileDownload all fastq files
  • FileOptional: 110_Ref_Mabscessus_Ridom.xlsx
  • FileTutorial_literature_Wuzinski2020
  • FileResults_Task_Exercise2026
• Session 2 (11 May) - Demonstration of bioinformatic tools for NTM

  Session 2 (11 May) - Demonstration of bioinformatic tools for NTM
  The second session aims to consolidate participants’ understanding of NTM genomic analysis through discussion of real outbreak results and broader case studies. It further introduces practical workflows, including a command-line pipeline for WGS data analysis, providing insight into real-world applications and challenges in detecting and investigating NTM.
  

  
  

  After attending this session, the participants will be able to:

  • Interpret and discuss results from a genomic outbreak investigation (Mycobacterium abscessus)
  • Apply GUI-based bioinformatic tools to analyse and contextualise NTM genomic data
  • Describe key characteristics and challenges of NTM outbreaks in different settings
  • Recognise common difficulties in detecting transmission and identifying sources of NTM infections
  • Understand the components of a command-line WGS analysis pipeline (e.g. NTMseq)
  • Describe the main steps involved in processing and analysing NTM whole genome sequencing data in a real-world reference laboratory setting

  Agenda: 

  Time CEST	Session	Intended Learning Outcomes
  09:00-09:15	ECDC introduction	Greeting of participants, presentation of GenEpi-BioTrain, code of conduct, get to know the participants
  09:15-10:10	Tutorial: M. abscessus outbreak – Results & Discussion	Getting hands-on experience with GUI-based bioinformatic tools for genomic analysis of NTM
  10:10-10:20	Coffee break
  10:20-10:30 10:30-10:40	Lecture: Cluster threshold selection Lecture: Other NTM outbreak investigations	Learning which genetic distance thresholds can be used to identify clusters of closely related isolates Gaining knowledge on other (global) NTM outbreaks; Learning about challenges associated with detecting NTM outbreaks and eliminating their sources
  10:40-10:50	Coffee break
  10:50-11:50	Demonstration of a command-line based pipeline for the analysis of NTM WGS data (NTMseq) used at the National Reference Center for Mycobacteria (Germany)	Getting an example of a complete WGS data processing bioinformatic workflow for NTM
  11:50-12:15	Conclusions and Q & A

  • Opening of session 2

  • Part 1: Tutorial: M. abscessus outbreak – Demo & discussion

  • FilePresentation: Tutorial: M. abscessus outbreak – Demo & discussion
  • Part 2: Cluster threshold selection 

     
    
  • FilePresentation: Cluster threshold selection
  • Part 3:  NTM outbreaks

  • FilePresentation: NTM outbreaks
  • Part 4: NTMseq - bioinformatic pipeline for WGS analysis of NTM 

     
    
  • FilePresentation: NTMseq - bioinformatic pipeline for WGS analysis of NTM
• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact the ECDC Service Desk at servicedesk@ecdc.europa.eu.