TB-Profiler result

Run: SRR25827558
Summary

Run ID: SRR25827558

Sample name:

Date: 2024-04-15T15:44:32.073175

Number of reads: 9251991

Percentage reads mapped: 99.02

Median coverage: 309.0

Strain: lineage2.2.1.1;lineage2.2.1.2;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 0.11
lineage2 East-Asian RD105 0.83
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.82
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.2
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 0.07
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ile317Val Uncertain significance Mutation from literature
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg 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)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Trp240* Assoc w R
p.Met1? Assoc w R
clofazimine mmpR5 c.386dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.386dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 0.17 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 0.41 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Trp missense_variant 0.29 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.61 rifampicin Assoc w R
mmpR5 779371 c.386dupC frameshift_variant 0.17 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 0.74 streptomycin Assoc w R
katG 2155163 p.Ile317Val missense_variant 0.13 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.16 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol Assoc w R
ethA 4326755 p.Trp240* stop_gained 0.24 ethionamide Assoc w R
ethA 4327472 p.Met1? start_lost 0.16 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
dnaA 1332 c.1332A>C synonymous_variant 0.14 isoniazid Not assoc w R - Interim
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.6 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.83 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.97 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.79 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.96 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.79 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 0.94 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 0.82 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.91 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.84 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 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.95 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 2289027 p.Cys72Phe missense_variant 0.27 pyrazinamide Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.17 pyrazinamide Not assoc w R
eis 2714846 p.Val163Ile missense_variant 0.2 amikacin Not assoc w R
kanamycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.15 streptomycin
amikacin
kanamycin
whiB7 3569220 c.-541C>T upstream_gene_variant 0.18 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.84 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 0.86 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877960 p.Val183Gly missense_variant 0.18 rifampicin Uncertain significance
embC 4241022 p.Ala387Val missense_variant 0.37 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.15 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.84 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.19 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.8 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.23 ethionamide Uncertain significance
whiB6 4338233 p.Ser97Pro missense_variant 0.17 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338365 p.Cys53Gly missense_variant 0.31 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 0.97 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.28 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.8 streptomycin Not assoc w R