Inês Mendes
Bioinformatics PhD student.
@ines_cim
cimendes
Inês Mendes
The role of bioinformatics in clinical microbiology
MRamirez Lab - iMM
Núcleo do Curso de Bioinformática da AAIPS
October 27th, 2020
Biologia Celular e Molecular
Bioinformática e Biologia Computacional
Tecnologias da Saúde (Bioinformática)
| Clinical Microbiology
- Sample collection
- Pathogen indentification and characterization
- Colonization surveillance
| Bioinformatics
- Pathogen indentification and characterization
- Surveillance
Clinical Microbiology
| Epidemiology
John Snow (1813 - 1858)
English physician and father of modern epidemiology.
Tracing the source of a cholera outbreak in Soho, London, in 1854.
Water pump in Broad Street.
Total of 616 fatalities.
Clinical Microbiology
| Epidemiology
Epidemiology is the study and analysis of the distribution (who, when, and where), patterns and determinants of health and disease conditions in defined populations.
- risk factors for disease
- targets for preventive healthcare
Clinical Microbiology
| Epidemiology
Clinical Microbiology
| The now
Bacterial Population Genetics
Pathogenesis and Natural History of Infection
Outbreak Investigation and Control
Surveillance of Infectious Diseases
Clinical Microbiology
Didelot, X., Bowden, R., Wilson, D. et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13, 601–612 (2012). https://doi.org/10.1038/nrg3226
| The now
Clinical Microbiology
Joana Silva, MRamirez
| The now
Clinical Microbiology
| The now
Clinical Microbiology
Didelot, X., Bowden, R., Wilson, D. et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13, 601–612 (2012). https://doi.org/10.1038/nrg3226
| The now
Clinical Microbiology
https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data
| The now
Bioinformatics
| Whishful thinking
Magic box of NGS Wonders for Microbiology
Completely characterized strain:
- Identification & Typing
- Antibiotic resistance profile
- Virulence factors present
- Other information
- spa (S. aureus)
- emm (GAS)
Bioinformatics
| The role in microbiology
Read mapping
- Using a reference strain:
- Outbreak determination
- Comparative studies
- Caveats:
- Recombination/horizontal gene transfer
- Bias towards reference/reference dependent
Read mapping software
reads
reference genome
Bioinformatics
| The role in microbiology
Miguel P Machado
MRamirez -> INSA
Bioinformatics
| The role in microbiology
Gene-by-Gene
- No need for a reference strain
- "Discovery" of new features
- Caveats:
- Missing data
de novo assembly software
reads
contigs
annotation/ comparison
Bioinformatics
| The role in microbiology
Miguel P Machado
MRamirez -> INSA
Bioinformatics
| The role in microbiology
Soucy, S., Huang, J. & Gogarten, J. Horizontal gene transfer: building the web of life. Nat Rev Genet 16, 472–482 (2015). https://doi.org/10.1038/nrg3962
Pangenome:
" (...) hence, core and dispensable genes represent the essence and the diversity of the species, respectively.
Medini et al, 2005
Bioinformatics
| The role in microbiology
Mendes, CI. Pan-genome comparison between Streptococcus dysgalactiae subsp. equisimilis isolates from human and animal sources. Tese de mestrado, Bioinformática e Biologia Computacional, FCUL, 2016. http://hdl.handle.net/10451/25958
Bioinformatics
| The role in microbiology
Multilocus Sequence Typing
Why stop here?
Bioinformatics
| The role in microbiology
Whole-Genome/Core-Genome MLST
- Profile
| File | Locus 1 | Locus 2 |
|---|---|---|
| genome1.fasta | Allele 1 | Allele 2 |
| genome2.fasta | Allele 1 | Allele 6 |
- Visualization
Bioinformatics
| The role in microbiology
Whole-Genome/Core-Genome MLST
Mickael Silva - ???
Bruno Gonçalves - Lifebit
Pedro Cerqueira e Rafael Maria, MRamirez
Bioinformatics
| The role in microbiology
Mobile Genetic Elements: Plasmids
Tiago Jesus - Lifebit
Bioinformatics
| The role in microbiology
Genome Typing: Dengue Virus
Erley Lizarazo - UMCG
Bioinformatics
| The role in microbiology
Metagenomics
Who is there? - Taxonomic identification
What are they doing? - Virulome, Resistome, Functional Annotation
Who is doing what? - Functional Assignment
Bioinformatics
| The role in microbiology
Metagenomics
Natacha Couto
UMCG -> EdFeil Lab
- Highlights the potential and the limitations of shotgun metagenomics as a diagnostic tool - Lack of reproducibility
- Results are highly dependent on the tools, and specially database, chosen for the analysis - Lack of standardization and proper benchmark.
Major issues
Bioinformatics
| Reproducibility
- Do I know what is happening?
- Is it reproducible?
- Is it shareable?
Bioinformatics
| Reproducibility
Black
Box
Transparent
Box
- Commercial/Freeware
- You get what it gives you
- Ready to use
- Stealth change
- Standalone
- Freeware
- You can "tailor"
- "Major" headache
- Visible change
- Dependencies
The needs:
- Analyze a large amount of sequence data routinely
- Some computationally intensive steps
- Constantly updating/adding software
Bioinformatics
| Reproducibility
In the Paleolithic era:
Writing of pipelines in python/perl/shell scripts circa 2000, colorized.
- Custom ad-hoc scripts
- Difficult to parallelise
- Difficult to install/run
- Hard to deploy in multiple environments
- What's workflow managers?!
- What's docker?!
Bioinformatics
| Reproducibility
In the Modern days:
The game changing combination of workflow managers and containers:
- Portability
- Reproducible
- Scalability
- Multi-scale containerization
- Native cloud support
Bioinformatics
| Reproducibility
Diogo Silva - Lifebit
(and Tiago & Bruno)
Bioinformatics
| Reproducibility
With this framework, building workflows becomes simple:
flowcraft build -t 'trimmomatic fastqc spades pilon' -o my_nextflow_pipeline
Results in the following workflow DAG (direct acyclic graph)
Bioinformatics
| Public Health
Bioinformatics
| Public Health
Standardized data structures and interchangable formats - critical to the development of an open software ecosystem.
Emma Griffiths
University of British Columbia
Data Stuctures Workgroup
Algorithms
Data Structures
Interfaces
The role of bioinformatics in clinical microbiology
Mário Ramirez
head of lab
João Carriço
Rafael Mamede & Pedro Cerqueira (& me!)
Current MRamirez bioinformaticians
BioMérieux
MRamirez Lab
Thank you for your attention
Special thanks to Diogo Silva, Bruno Gonçalves, Tiago Jesus, Pedro Vila-Cerqueira, Rafael Maria Mamede, João Carriço, John Rossen, Mário Ramirez and Emma Griffiths.
Bioinformatics in clinical microbiology
By Inês Mendes
