a year in clinical bioinformaticsclinicalmetagenomics.org/wp-content/uploads/2018/... · clinical...
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A year in clinical bioinformatics
Helena Seth-Smith, PhD
October 2018
Division of Clinical Microbiology
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ICCMg
Helena Seth-Smith 18.10.2018
"…the application of next generation sequencing
to clinical samples in order to recover information
of clinical relevance"
Ruppé Microb Infect 2018
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Helena Seth-Smith 18.10.2018
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ICCMg themes
Helena Seth-Smith 18.10.2018
Quality
Speed
Applications
Communication
contamination
ISO accreditation: ISO/IEC 17025
gold standards
bottleneck of DNA extraction
sequencing platform
analysis, universal pipelines
resistance determination
metagenomic diagnosis, novel pathogens
therapeutics
transmission detection and outbreak control
reporting
data storage / sharing
interactive analysis
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Clinical microbiology and NGS:
Quality
Helena Seth-Smith 18.10.2018
ISO accreditation wet and dry lab SOPs
quality management system
Validation improvements: maintaining validity
Backwards compatibility
Reference material
External Quality Assessment
Pipelines: commercial vs open source
variant calling
Gargis J Clin Microbiol 2016
Rossen Clin Microbiol Infect 2018
Balloux Trends Microbiol 2018
Technically competent to
produce accurate and
reliable data
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NGS workflow at
6
Sample
Isolate
DNA Extraction
MALDI-TOF MS
DNA Quantification
Library Preparation
Sequencing
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Sequencing platforms
Helena Seth-Smith 18.10.2018
4-24 samples
per run
24-96 samples
per run
long reads
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QC pipeline at
Helena Seth-Smith 18.10.2018
Raw readsHigh
quality
reads
Trimming Genome
scaffolds
De novo
assemblyAnnotated
genome
assembly
Annotation
Read
quality
Meta-
genomic
analysis
rMLST16S
rRNA
gene
Remapping
Coverage,
VariantsQC
ID
Genome
size, N50
AMR
genes
Virulence
genes
Phenotype
prediction
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Clinical microbiology and NGS:
Applications
Helena Seth-Smith 18.10.2018
Species identification
Factor identification resistance determinants
virulence determinants
Outbreak and transmission analysis typing: highest discrimination
infection control and epidemiology
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Analysis software
Helena Seth-Smith 18.10.2018
Ridom SeqSphere:
cgMLST typing
CLC Genomics Workbench:
SNP analysis
Seth-Smith EID submitted
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Helena Seth-Smith 18.10.2018
First cases in Switzerland
Case histories underpinned by
genomic analysis
Higher antimicrobial resistance
(azithromycin, quinoline)
Related to known MSM
associated clades
Carry pKSR100 with macrolide
resistance determinants
Public health: Shigella sonnei as an STI
Hinic Swiss Med Weekly 2018
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Helena Seth-Smith 18.10.2018
Identifying foodborne sources by hierarchical genomic analysis
Public health: Campylobacter in Basel
Isolates
n= 685
Seth-Smith et al in preparation
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Helena Seth-Smith 18.10.2018
Public health: Campylobacter in Basel
Transmission cluster n= 20
Patient only cluster n= 26
Chicken only cluster n= 47
Seth-Smith et al in preparation
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Helena Seth-Smith 18.10.2018
Outbreaks:
Vancomycin Resistant Enterococci (VRE)
Leading multidrug resistant hospital pathogen
>400 VREs sequenced
Ridom SeqSphere: MLST (n=7) and cgMLST (n=1423) loci
Within clusters, CLC Genomics Workbench: SNP trees
Highly virulent ST796, Australia (2011)
Bern outbreak Dec-Apr (n=76)
Wassilew, Eurosurveillance, 2018
Dec-Oct, n=241 patientsBuultjens PeerJ 2017
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Helena Seth-Smith 18.10.2018
Outbreaks: VRE
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Helena Seth-Smith 18.10.2018
Outbreaks: VRE
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Helena Seth-Smith 18.10.2018
Coloured by source hospital
Outbreaks: VRE
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Helena Seth-Smith 18.10.2018
Outbreaks: VRE
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Helena Seth-Smith 18.10.2018
Coloured by patient with
repeat samples
Outbreaks: VRE
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Helena Seth-Smith 18.10.2018
Gómez-López Brief Bioinf 2017
Reporting
Carriço Clin Microbiol Infect 2018
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Reporting
Helena Seth-Smith 18.10.2018
Crisan Peer J 2017
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Helena Seth-Smith 18.10.2018
Data sharing
Tagini Eur J Clin Microbiol Infect Dis 2017
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Helena Seth-Smith 18.10.2018
Swiss Pathogen Surveillance Platform
for interpretation and
modelling
Data coordination
Emma Hodcroft, Walker Lancet ID 2018, Gagneux
Mycobacterium
tuberculosis
sublineage 4.6.2
http://spsp.ch
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Helena Seth-Smith 18.10.2018
Continuous improvement necessary
speed
resistance, mobile elements, plasmids, recombination…
data mining
machine learning
Coordination of sequence and metadata
surveillance platforms
online tools
Standardised workflows as goal
pathogens are plastic: can one size fit all?
Conclusions
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18.10.2018Helena Seth-Smith 25
[email protected]://appliedmicrobiologyresearch.net/
https://www.unispital-basel.ch/
Acknowledgements
Dr Adrian Egli PD
Dr Daniel Wüthrich
Josiane Reist
Dr Ferdinando Bonfiglio
NGS Team
Division of Clinical
Microbiology
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18.10.2018Helena Seth-Smith 26
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Helena Seth-Smith 18.10.2018
Projects: outbreaks: VRE: dynamics
Aus VSEAug 2018
Oct 2018Sep 2018
Sw
iss s
am
ple
s2018
Au
str
ali
a
2014-1
6
Buultjens PeerJ 2017
Leong Sci Rep 2018
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Helena Seth-Smith 18.10.2018
Outbreaks: VRE
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18.10.2018Helena Seth-Smith 29
Also, if you want to highlight the importance of “bioinformaticians” or “clinical
bioinformaticians", I really like the figure 1 of this
paper: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-
8-125; Sboner Genome Biol 2011
and also this paper: https://academic.oup.com/bib/advance-
article/doi/10.1093/bib/bbx144/4565521; Gómez-López Briefings in
Bioinformatics 2017
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Helena Seth-Smith 18.10.2018
Candida albicans:
typing and Echinocandin resistance detection
Aspergillus fumigatus
typing and Azole resistance detection
Description of species / cases:
Blastobotrys
Auritidibacter
Lawsonella
Mycobacterium basiliense
Projects: novel
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Helena Seth-Smith 18.10.2018
Outbreaks: VRE