TB-Profiler result

Run: SRR25827325
Summary

Run ID: SRR25827325

Sample name:

Date: 2024-10-03T21:09:42.461140

Number of reads: 2210772

Percentage reads mapped: 99.18

Median coverage: 71.0

Strain: lineage2.2.1;lineage4.9

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.76
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.75
lineage4 Euro-American None 0.12
lineage4.9 Euro-American (H37Rv-like) None 0.05
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 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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ser66* Assoc w R
streptomycin rpsL p.Lys43Arg 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)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
gyrA p.Ala90Val Assoc w R
p.Asp94Gly 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
ethA c.1351_1360delTCGCGTACAC Assoc w R
clofazimine mmpR5 p.Arg156* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Arg156* 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 0.12 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)
gyrA 7582 p.Asp94Gly missense_variant 0.68 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.86 rifampicin Assoc w R
mmpR5 779455 p.Arg156* stop_gained 0.41 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 0.74 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.51 linezolid Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.65 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.16 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)
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2289045 p.Ser66* stop_gained 0.5 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.48 ethambutol Assoc w R
ethA 4326113 c.1351_1360delTCGCGTACAC frameshift_variant 0.49 ethionamide 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 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13680 c.-122G>T upstream_gene_variant 0.42 isoniazid Uncertain significance
fgd1 491290 p.Val170Met missense_variant 0.25 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.7 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.74 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.79 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.16 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.83 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.74 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.92 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 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 0.75 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673263 c.-939C>A upstream_gene_variant 0.45 isoniazid
ethionamide
rpsA 1834177 c.636A>C synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
tsnR 1854044 p.Tyr147Asp missense_variant 0.38 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.92 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.85 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.89 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.84 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.95 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.78 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626448 p.Ala56Ser missense_variant 0.4 rifampicin Uncertain significance
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 0.81 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840259 p.Tyr388Asp missense_variant 0.39 cycloserine
rpoA 3877956 p.Glu184Asp missense_variant 0.48 rifampicin Uncertain significance
ddn 3987079 p.Lys79Arg missense_variant 0.49 pretomanid
delamanid
embC 4241022 p.Ala387Val missense_variant 0.23 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.96 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.8 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.51 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.64 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 0.91 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.89 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.19 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.78 streptomycin Not assoc w R