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Mycobacterium tuberculosis resistance prediction fromgenome sequencing:
comparison of automated software tools
V. Schleusener S. Feuerriegel S. Niemann
Research Center Borstel, Borstel, Germany
2nd Conference Rapid Microbial NGS and Bioinformatics:Translation Into Practice, 2016
Outline
1 MotivationThe Basic ProblemState of the art
2 ComparisonVisualizationValidation datasetPerformance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 0 / 14
Outline
1 MotivationThe Basic ProblemState of the art
2 ComparisonVisualizationValidation datasetPerformance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 0 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Tuberculosis
• Worldwide occurring infection (normally of the lung)
• 1.5 million deaths annually
• 9.6 million cases (1/3 of the worlds population infected)
• Infection caused by pathogens of the Mycobacterium tuberculosisComplex (MTBC)
• Treatment impaired by increasing numbers of antibiotic resistance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 1 / 14
Molecular Drug Susceptibility Testing
PacBio RSII
Ion Torrent Proton
Illumina NextSeq
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 2 / 14
• Key to control: timely diagnosis
• Fast molecular Tests such as GeneXpert
• Highest resolution with Next-GenerationSequencing (NGS) data
• NGS analysis complex and computationallyintensive
Automated tools needed:Raw data ⇒ resistance profile
Molecular Drug Susceptibility Testing
PacBio RSII
Ion Torrent Proton
Illumina NextSeq
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 2 / 14
• Key to control: timely diagnosis
• Fast molecular Tests such as GeneXpert
• Highest resolution with Next-GenerationSequencing (NGS) data
• NGS analysis complex and computationallyintensive
Automated tools needed:Raw data ⇒ resistance profile
Molecular Drug Susceptibility Testing
PacBio RSII
Ion Torrent Proton
Illumina NextSeq
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 2 / 14
• Key to control: timely diagnosis
• Fast molecular Tests such as GeneXpert
• Highest resolution with Next-GenerationSequencing (NGS) data
• NGS analysis complex and computationallyintensive
Automated tools needed:Raw data ⇒ resistance profile
Molecular Drug Susceptibility Testing
PacBio RSII
Ion Torrent Proton
Illumina NextSeq
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 2 / 14
• Key to control: timely diagnosis
• Fast molecular Tests such as GeneXpert
• Highest resolution with Next-GenerationSequencing (NGS) data
• NGS analysis complex and computationallyintensive
Automated tools needed:Raw data ⇒ resistance profile
Molecular Drug Susceptibility Testing
PacBio RSII
Ion Torrent Proton
Illumina NextSeq
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 2 / 14
• Key to control: timely diagnosis
• Fast molecular Tests such as GeneXpert
• Highest resolution with Next-GenerationSequencing (NGS) data
• NGS analysis complex and computationallyintensive
Automated tools needed:Raw data ⇒ resistance profile
NGS Analysis
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 3 / 14
Automated analysis tools for TBavailable?
NGS Analysis
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 3 / 14
Automated analysis tools for TBavailable?
Available tools - Screening
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 4 / 14
Available tools - Screening
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 4 / 14
Available tools - Screening
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 4 / 14
Available tools - Screening
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 4 / 14
Outline
1 MotivationThe Basic ProblemState of the art
2 ComparisonVisualizationValidation datasetPerformance
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 4 / 14
Available tools-CASTBCASTB - Comprehensive Analysis Server for MTBC
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 5 / 14
Iwai et. al.,Tuberculosis (Edinb), 2015
Available tools-CASTBCASTB - Comprehensive Analysis Server for MTBC
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 5 / 14
Iwai et. al.,Tuberculosis (Edinb), 2015
Available tools-CASTBCASTB - Comprehensive Analysis Server for MTBC
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 5 / 14
Iwai et. al.,Tuberculosis (Edinb), 2015
Available tools-CASTBCASTB - Comprehensive Analysis Server for MTBC
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 5 / 14
Iwai et. al.,Tuberculosis (Edinb), 2015
Available tools-CASTBCASTB - Comprehensive Analysis Server for MTBC
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 5 / 14
Iwai et. al.,Tuberculosis (Edinb), 2015
Available tools-KvarQ
KvarQ
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 6 / 14
MTBC/phylo: lineage 4MTBC/resistance: Streptomycin resistance::SNP781687AG=rpsL.K43R;Isoniazid resistance [2155168CG=katG.S315T];Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Steiner et. al., BMC Genomics, 2014
Available tools-KvarQ
KvarQ
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 6 / 14
MTBC/phylo: lineage 4MTBC/resistance: Streptomycin resistance::SNP781687AG=rpsL.K43R;Isoniazid resistance [2155168CG=katG.S315T];Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Steiner et. al., BMC Genomics, 2014
Available tools-KvarQ
KvarQ
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 6 / 14
MTBC/phylo: lineage 4
MTBC/resistance: Streptomycin resistance::SNP781687AG=rpsL.K43R;Isoniazid resistance [2155168CG=katG.S315T];Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Steiner et. al., BMC Genomics, 2014
Available tools-KvarQ
KvarQ
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 6 / 14
MTBC/phylo: lineage 4MTBC/resistance: Streptomycin resistance::SNP781687AG=rpsL.K43R;Isoniazid resistance [2155168CG=katG.S315T];Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Steiner et. al., BMC Genomics, 2014
Available tools-KvarQ
KvarQ
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 6 / 14
MTBC/phylo: lineage 4
MTBC/resistance: Streptomycin resistance::SNP781687AG=rpsL.K43R;Isoniazid resistance [2155168CG=katG.S315T];Rifampicin resistance (RRDR) [761155CT=rpoB.S450L]
Steiner et. al., BMC Genomics, 2014
Available tools - MykrobePredictor TB
MykrobePredictor TB
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 7 / 14
Bradley et. al., Nat Commun, 2015
Available tools - MykrobePredictor TB
MykrobePredictor TB
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 7 / 14
Bradley et. al., Nat Commun, 2015
Available tools - MykrobePredictor TB
MykrobePredictor TB
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 7 / 14
Bradley et. al., Nat Commun, 2015
Available tools - MykrobePredictor TB
MykrobePredictor TB
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 7 / 14
Bradley et. al., Nat Commun, 2015
Available tools - PhyResSE
PhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - PhyResSE
PhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - PhyResSE
PhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - PhyResSEPhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - PhyResSEPhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - PhyResSEPhyResSE - Phylo-Resistance Search Engine
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 8 / 14
Feuerriegel et. al., JCM, 2015
Available tools - TBProfilerTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 9 / 14
Coll et al., Genome Medicine, 2015
Available tools - TBProfilerTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 9 / 14
Coll et al., Genome Medicine, 2015
Available tools - TBProfilerTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 9 / 14
Coll et al., Genome Medicine, 2015
Available tools - TBProfilerTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 9 / 14
Coll et al., Genome Medicine, 2015
Available tools - TBProfilerTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 9 / 14
Coll et al., Genome Medicine, 2015
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
Easiest handling with PhyResSE
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
KvarQ is a fast, mapping-free algorithm
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Feature comparison
Feature CASTB KvarQ MykrobePredictor PhyResSE TBProfiler(Version 1.1) (Version 0.12.2) (Version 0.1.3) (Version 1.0)
Web-based Yes No No Yes YesBatch mode No Yes No Yes NoPaired-end reads Yes Merged files Merged files Yes YesPipeline Velvet assembly; Python modules Stampy mapping bwa mapping (H37Rv V3), snap mapping ;
BIGSdb; with C extensions (H37Rv V2); duplicates samtools (edited H37Rv V3)MUMmer mapping; (No mapping) variant calling samtools recalibration, variant calling samtools/
custom scripts re-alignment and; vcftoolsvariant calling GATK
Modifiable No Yes Yes Yes (undocumented) Yes
Programming skills needed for KvarQ, MykrobePredictor TB andTBProfiler
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 10 / 14
Sierra Leone dataset
No (%)
Total 92 (100)Fully sensitive 44 (47.8)
Any resistance 48 (52.2)Any SM resistance 22 (23.9)Any INH resistance 30 (32.6)Any RMP resistance 15 (16.3)Any EMB resistance 14 (15.2)Any PZA resistance 9 (9.8)
Any Mono-resistance 23 (25)SM only 14 (15.2)INH only 8 (8.7)RMP only 1 (1.1)EMB only -PZA only -
MDR 11 (12)
Classical DST, Sanger sequencing, IS6110 RFLP DNA fingerprinting,spoligotyping and 24-loci MIRU-VNTR typing available.
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 11 / 14
Feuerriegel et. al., BMC Microbiology, 2012
Sierra Leone dataset
No (%)
Total 92 (100)Fully sensitive 44 (47.8)
Any resistance 48 (52.2)Any SM resistance 22 (23.9)Any INH resistance 30 (32.6)Any RMP resistance 15 (16.3)Any EMB resistance 14 (15.2)Any PZA resistance 9 (9.8)
Any Mono-resistance 23 (25)SM only 14 (15.2)INH only 8 (8.7)RMP only 1 (1.1)EMB only -PZA only -
MDR 11 (12)
Classical DST, Sanger sequencing, IS6110 RFLP DNA fingerprinting,spoligotyping and 24-loci MIRU-VNTR typing available.
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 11 / 14
Feuerriegel et. al., BMC Microbiology, 2012
Sierra Leone dataset
No (%)
Total 92 (100)Fully sensitive 44 (47.8)
Any resistance 48 (52.2)Any SM resistance 22 (23.9)Any INH resistance 30 (32.6)Any RMP resistance 15 (16.3)Any EMB resistance 14 (15.2)Any PZA resistance 9 (9.8)
Any Mono-resistance 23 (25)SM only 14 (15.2)INH only 8 (8.7)RMP only 1 (1.1)EMB only -PZA only -
MDR 11 (12)
Classical DST, Sanger sequencing, IS6110 RFLP DNA fingerprinting,spoligotyping and 24-loci MIRU-VNTR typing available.
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 11 / 14
Feuerriegel et. al., BMC Microbiology, 2012
Sierra Leone dataset
No (%)
Total 92 (100)Fully sensitive 44 (47.8)
Any resistance 48 (52.2)Any SM resistance 22 (23.9)Any INH resistance 30 (32.6)Any RMP resistance 15 (16.3)Any EMB resistance 14 (15.2)Any PZA resistance 9 (9.8)
Any Mono-resistance 23 (25)SM only 14 (15.2)INH only 8 (8.7)RMP only 1 (1.1)EMB only -PZA only -
MDR 11 (12)
Classical DST, Sanger sequencing, IS6110 RFLP DNA fingerprinting,spoligotyping and 24-loci MIRU-VNTR typing available.
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 11 / 14
Feuerriegel et. al., BMC Microbiology, 2012
Sierra Leone dataset
No (%)
Total 92 (100)Fully sensitive 44 (47.8)
Any resistance 48 (52.2)Any SM resistance 22 (23.9)Any INH resistance 30 (32.6)Any RMP resistance 15 (16.3)Any EMB resistance 14 (15.2)Any PZA resistance 9 (9.8)
Any Mono-resistance 23 (25)SM only 14 (15.2)INH only 8 (8.7)RMP only 1 (1.1)EMB only -PZA only -
MDR 11 (12)
Classical DST, Sanger sequencing, IS6110 RFLP DNA fingerprinting,spoligotyping and 24-loci MIRU-VNTR typing available.
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 11 / 14
Feuerriegel et. al., BMC Microbiology, 2012
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Rough digestion into the 7 main phylogenetic lineages.
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Highest resolutional depth by using SNPs from Coll et al. 2015
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
MykrobePredictor TB is unable to classify strains belonging tolin. 5/ WA 1
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
Performance-Phylogenetic lineage
Genotype #strains CASTB KvarQ Mykr.Pred. PhyResSE TBProfilerEAI 4 lin. 1 lin. 1 lin. 1 lin.1.1.1 lin.1.1.1Beijing 4 lin. 2 lin. 2 lin. 2 lin.2.2.1 lin.2.2.1Ghana 1 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1Sierra Leone-1 7 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.1
X-type1 lin. 4 lin. 4 lin. 4 lin.4.1.1.1 lin.4.1.1.11 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.3
Haarlem 12 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.1
LAM
9 lin. 4 lin. 4 lin. 4 lin.4.3.3 lin.4.3.31 M. bovis lin. 4 lin. 4 lin.4.3.3 lin.4.3.32 lin. 4 lin. 4 lin. 4 lin.4.3.4.1 lin.4.3.4.13 lin. 4 lin. 4 lin. 4 lin.4.3.4.2 lin.4.3.4.2
S-type 3 lin. 4 lin. 4 lin. 4 lin.4.4.1.1 lin.4.4.1.1Cameroon 4 lin. 4 lin. 4 lin. 4 lin.4.6.2.2 lin.4.6.2.2Sierra Leone-2 9 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8WA 1 6 lin. 5 lin. 5 Unknown lin.5 lin.5WA 2 14 lin. 6 lin. 6 lin. 6 lin.6 lin.6
None
3 lin. 4 lin. 4 lin. 4 lin.4.1 lin.4.13 lin. 4 lin. 4 lin. 4 lin.4.1.1.3 lin.4.1.1.31 lin. 4 lin. 4 lin. 4 lin.4.1.2.1 lin.4.1.2.11 lin. 4 lin. 4 lin. 4 lin.4.6 lin.4.6.13 lin. 4 lin. 4 lin. 4 lin.4.8 lin.4.8
lin. 1:East-African/Indian; lin 4: Euro-American Superlineage; lin 5: West African 1; lin 6: WestAfrican 2
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 12 / 14
CASTB classified one strain belonging to lineage 4.3.3/LAM asM. bovis
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Use phylogenetic marker kasA Gly269Ser as marker for INH resistance.
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Miss markers embB Trp332Arg, Asp354Ala, Gly406Asp, Gln497Lys andHis1002Arg for EMB resistance
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Skip gidB for SM resistance prediction.
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Indels in gidB promotor region are reported but not flagged asresistance-mediating.
Performance-Resistance prediction
Antibiotic Sanger CASTB KvarQ MykrobePredictor PhyResSE TBProfiler#R #R = - + #R = - + #R = - + #R = - + #R = - +
Isoniazid 27 37 25 27 29 37inhA 2 3 2 0 1 3 2 0 1 0 0 2 0 4 2 0 2 1 0 2 1katG 24 23 23 1 n.a. 22 22 2 0 23 22 2 1 24 24 0 0 23 23 1 0ahpC 1 1 0 1 1 - - - - 0 0 0 0 1 1 0 0 5 0 1 5fabG1 n.a. 4 - - 4 - - - - 4 - - 4 4 - - 4 4 - - 4kasA n.a. 7 - - 7 - - - - - - - - - - - - 7 - - 7
Rifampicin 19 17 18 27 20 20rpoB 19 17 17 2 0 18 18 1 0 27 19 0 8 20 19 0 1 20 19 0 1
Ethambutol 16 8 7 8 15 15embB 16 8 8 8 0 7 7 8 0 8 7 9 1 15 15 1 0 15 15 1 0
Streptomycin 39 11 22 22 33 22rpsL 20 11 11 9 0 20 20 0 0 20 20 0 0 20 20 0 0 20 20 0 0gidB 17 0 0 17 0 0 0 17 0 0 0 17 0 11 11 6 0 0 0 17 0rrs 2 0 0 2 0 2 2 0 0 2 2 0 0 2 2 0 0 2 2 0 0
Pyrazinamid 11 5 5 9 7pncA 11 5 5 6 0 5 5 6 0 n.a. n.a. n.a. n.a. 9 8 3 1 7 6 5 1
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 13 / 14
Skips the analysis of pncA.
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Summary
• 5 automated tools for resistance prediction available
• Making NGS-based resistance determination available to a largercommunity.
• Tools differ in:
• Handling• Pipeline• Output presentation• Resistance Profile
y Consistent, approved database for resistance-conferring mutationsneeded!
V. Schleusener Comparison of automated software tools RaMi-NGS 2016 14 / 14
Acknowledgements
Molecular and Experimental Mycobacteriology:Stefan Niemann Susanne HomolkaSilke Feuerriegel Matthias MerkerChristiane Gerlach Judith PetersenThomas Kohl Patrick BeckertAnja Lüdemann Julia ZalletSilvia Maaß Vanessa MohrSven Malm Tanja UbbenTanja Struwe-Sonnenschein Leila JeljeliGlennah Kerubi Doreen BeyerBarbara Tizzano Christian UtpatelRobin Koch Yassir Adam ShuaibEcaterina Noroc Anna Engström
Thank you for your attention!
Contact: vschleusener@fz-borstel.de
Acknowledgements
Molecular and Experimental Mycobacteriology:Stefan Niemann Susanne HomolkaSilke Feuerriegel Matthias MerkerChristiane Gerlach Judith PetersenThomas Kohl Patrick BeckertAnja Lüdemann Julia ZalletSilvia Maaß Vanessa MohrSven Malm Tanja UbbenTanja Struwe-Sonnenschein Leila JeljeliGlennah Kerubi Doreen BeyerBarbara Tizzano Christian UtpatelRobin Koch Yassir Adam ShuaibEcaterina Noroc Anna Engström
Thank you for your attention!
Contact: vschleusener@fz-borstel.de
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