TB-Profiler result

Run: SRR25827440
Summary

Run ID: SRR25827440

Sample name:

Date: 2024-10-04T14:01:17.215873

Number of reads: 10926967

Percentage reads mapped: 98.72

Median coverage: 366.0

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 0.53
lineage2 East-Asian RD105 0.47
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.46
lineage2.2 East-Asian (Beijing) RD105;RD207 0.49
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 pncA p.Tyr41* Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide
clofazimine mmpR5 c.386delC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.386delC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
atpE p.Ala63Pro Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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 7570 p.Ala90Val missense_variant 0.44 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin Assoc w R
mmpR5 779371 c.386delC frameshift_variant 0.44 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.44 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.49 linezolid Assoc w R
atpE 1461231 p.Ala63Pro missense_variant 0.49 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.45 isoniazid Assoc w R High-level resistance
pncA 2289119 p.Tyr41* stop_gained 0.47 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.57 streptomycin 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
gyrB 6737 p.Thr500Ala missense_variant 0.42 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8131 p.Gln277Arg missense_variant 0.51 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Ser missense_variant 0.17 isoniazid
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.49 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.51 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.49 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657114 c.357T>C synonymous_variant 0.57 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.46 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.59 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.5 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 0.52 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.47 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.5 bedaquiline
clofazimine
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 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.44 pyrazinamide Not assoc w R - Interim
tsnR 1853766 p.Ala54Val missense_variant 0.56 linezolid Uncertain significance
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
katG 2156344 c.-233C>G upstream_gene_variant 0.51 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.51 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.51 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.5 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.49 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087626 c.808delG frameshift_variant 0.49 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.18 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.47 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640211 c.-332T>G upstream_gene_variant 0.5 pretomanid
delamanid
clofazimine
clpC1 4040753 c.-49G>A upstream_gene_variant 0.58 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.5 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.47 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.47 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.37 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.56 streptomycin Not assoc w R