TB-Profiler result

Run: ERR9992908
Summary

Run ID: ERR9992908

Sample name:

Date: 2024-10-04T22:03:34.730559

Number of reads: 4095574

Percentage reads mapped: 99.82

Median coverage: 127.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.8
lineage2 East-Asian RD105 0.14
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.14
lineage4 Euro-American None 0.85
lineage4.3.3 Euro-American (LAM) RD115 0.82
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Gly Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1312_1314delAAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1312_1314delAAC Mutation from literature
p.Leu452Pro Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.456dupC Assoc w R
streptomycin
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-11A>G Uncertain significance Mutation from literature
clofazimine pepQ c.931_940delACATCCGCCG Assoc w R - Interim
c.544dupG Assoc w R - Interim
c.299dupA Assoc w R - Interim
para-aminosalicylic_acid
delamanid
bedaquiline pepQ c.931_940delACATCCGCCG Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.544dupG Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
c.299dupA Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
linezolid
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 0.97 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 761110 p.Asp435Gly missense_variant 0.81 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761114 c.1312_1314delAAC conservative_inframe_deletion 0.12 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rifampicin Mutation from literature
rpoB 761161 p.Leu452Pro missense_variant 0.82 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.88 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.13 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1673432 c.-770T>A upstream_gene_variant 0.86 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid Assoc w R High-level resistance
pncA 2288785 c.456dupC frameshift_variant 0.81 pyrazinamide Assoc w R
pepQ 2859478 c.931_940delACATCCGCCG frameshift_variant 0.1 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
pepQ 2859874 c.544dupG frameshift_variant 0.11 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
pepQ 2860119 c.299dupA frameshift_variant 0.56 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.8 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 0.82 ethionamide Uncertain significance Mutation from literature
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 6575 p.Arg446Gly missense_variant 0.78 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 8040 p.Gly247Ser missense_variant 0.82 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 0.12 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.13 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.19 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.14 rifampicin Not assoc w R
rpoB 763123 p.Ile1106Thr missense_variant 0.82 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.83 rifampicin Not assoc w R
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 0.12 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779237 p.Leu83Pro missense_variant 0.15 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13 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 0.1 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 0.11 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.81 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.17 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 2154023 p.Val697Phe missense_variant 0.13 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.17 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 0.76 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.79 isoniazid
Rv2752c 3065824 p.Pro123Leu missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.79 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087895 c.1081dupG frameshift_variant 0.8 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.19 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 0.17 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841147 p.Ala92Thr missense_variant 0.81 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.78 pyrazinamide 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 0.16 ethambutol Not assoc w R
embB 4249563 p.Asp1017Ala missense_variant 0.14 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.1 ethambutol Not assoc w R
ubiA 4269271 p.Val188Ala missense_variant 0.82 ethambutol Uncertain significance
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 0.16 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R