TB-Profiler result

Run: SRR25827850
Summary

Run ID: SRR25827850

Sample name:

Date: 2024-10-03T17:02:12.686576

Number of reads: 5109558

Percentage reads mapped: 98.47

Median coverage: 174.0

Strain: lineage2.2.1.1;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 0.82
lineage2 East-Asian RD105 0.19
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.19
lineage2.2 East-Asian (Beijing) RD105;RD207 0.2
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.21
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
p.Ala451Val Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid inhA 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 p.Val139Met Assoc w R
p.His71Arg Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.906A>G Uncertain significance Mutation from literature
gid c.331delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 gyrB p.Glu501Asp Assoc w R - Interim
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.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA p.Ala341Val Assoc w R - Interim
clofazimine mmpR5 c.321dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.321dupC 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
gyrB 6742 p.Glu501Asp missense_variant 0.17 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7570 p.Ala90Val missense_variant 0.18 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 761109 p.Asp435Tyr missense_variant 0.83 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.2 rifampicin Assoc w R
rpoB 761158 p.Ala451Val missense_variant 0.31 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
mmpR5 779309 c.321dupC frameshift_variant 0.17 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 0.16 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.17 linezolid Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.16 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 0.82 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 1.0 isoniazid Assoc w R High-level resistance
pncA 2288827 p.Val139Met missense_variant 0.77 pyrazinamide Assoc w R
pncA 2289030 p.His71Arg missense_variant 0.15 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4326452 p.Ala341Val missense_variant 0.21 ethionamide Assoc w R - Interim
gid 4407871 c.331delG frameshift_variant 0.8 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
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 0.16 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 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.17 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 761266 p.Asn487Ser missense_variant 0.24 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.83 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 0.17 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
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25 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
fbiC 1305366 p.Met812Ile missense_variant 0.87 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471926 n.81C>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.19 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
tlyA 1918172 p.Ala78Val missense_variant 0.75 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
katG 2156008 p.Asn35Thr missense_variant 0.81 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 0.84 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.77 pyrazinamide
kasA 2519092 p.Ile326Met missense_variant 0.86 isoniazid
eis 2714846 p.Val163Ile missense_variant 0.15 kanamycin Not assoc w R
amikacin Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.8 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.84 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
whiB7 3568857 c.-178C>T upstream_gene_variant 0.75 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.23 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 0.23 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044023 c.259C>T synonymous_variant 0.83 pyrazinamide Not assoc w R
panD 4044530 c.-249C>T upstream_gene_variant 0.8 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.77 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.77 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
glpK 4139048 c.708G>A synonymous_variant 0.86 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.84 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 0.17 ethambutol Not assoc w R
embB 4247880 p.Val456Ala missense_variant 0.26 ethambutol Uncertain significance
embB 4248103 c.1590G>A synonymous_variant 0.8 ethambutol Not assoc w R - Interim
embB 4248115 c.1602C>T synonymous_variant 0.18 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.19 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 0.19 streptomycin Not assoc w R