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Mycobacterium tuberculosis transmission analysis using
genome sequencing
Molecular and Experimental Mycobacteriology
National Reference Center for Mycobacteria
Research Center Borstel
Acosta et al 2014
MDR/XDR TB Epidemiology
How did we get into this situation?
What needs to be done?
Transmission important for MDR Epidemic?
Number of resistance mutations limiting
transmission?
Impact of treatment strategy?
Treatment failure vs Transmission
Patients
Epi-data
Case notification
Contact tracing investigation
stone-in-the-pond"
Reporting quality
Molecular Epidemiology
Pathogens
Culture/DNA
Genotyping
Sample needed
actGggcccactGggcccactTggccc
NGS infrastructure@Borstel
MiniSeq high 2x151bp 47 mio reads
(15 isolates per run, 2 days)
MiSeq 2x301bp 47 mio reads
(30 isolates per run, 3 days)
NextSeq mid 2x150bp 260 mio reads
(60 isolates per run, 2 days)
(198 isolates per run, high output)
Oxford NanoPore MinION
(~2 isolates per run, 1 day)
Illumina
MinION
IT
Genomic epidemiology
Distance
Transmission
Timing
Phylogeny
Function
Networks
SNPs
AGCCTTGGGTTTCCCCCGGGCCCTTGGTGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCTCCGGGCCCTTCGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCGGCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCTCCGGGCCCTTCGGGG G
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
AGCCTTGGGTTTCCCCCGGGCCCTTGGGGGGG
NGS data analysis
Mapping on reference genome -
detect variant positions
position
ref.
isolate 1
Isolate 2
isolate 3
isolate 4
...
1849
C
A
A
A
1977
A
G
G
G
4013
T
C
C
C
7362
G
C
7585
G
C
C
C
9304
G
A
A
A
11820
C
G
G
G
NGS data analysis
Resistome
Relationship
8
6
5
335
6
2
6
2
12
1
3
1
4
9
6
3
4