TB-Profiler result

Run: ERR4799888
Summary

Run ID: ERR4799888

Sample name:

Date: 2024-04-15T09:18:52.135837

Number of reads: 2870171

Percentage reads mapped: 99.5

Median coverage: 68.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.57
lineage2 East-Asian RD105 0.46
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.43
lineage2.2 East-Asian (Beijing) RD105;RD207 0.41
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
linezolid rplC p.Cys154Arg Assoc w R
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
gyrA 7582 p.Asp94Gly missense_variant 0.39 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.57 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.24 clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.54 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.55 linezolid Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.45 ethambutol Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.56 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.26 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.41 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.94 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.32 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.46 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.62 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.46 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.47 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.47 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473609 n.-49G>C upstream_gene_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.52 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.5 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.52 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.57 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.52 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.41 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.45 clofazimine
pretomanid
delamanid
rpoA 3879096 c.-589C>T upstream_gene_variant 0.24 rifampicin
panD 4044872 c.-591C>T upstream_gene_variant 0.67 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.5 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240067 p.Ser69Val missense_variant 0.41 ethambutol
embC 4242056 p.Pro732Ala missense_variant 0.51 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.43 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.49 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.52 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.32 ethambutol Not assoc w R
whiB6 4338356 c.161_165dupGGGCT frameshift_variant 0.34 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.35 streptomycin Not assoc w R