TB-Profiler result

Run: SRR25827669
Summary

Run ID: SRR25827669

Sample name:

Date: 2024-10-04T01:14:54.388184

Number of reads: 3646624

Percentage reads mapped: 50.07

Median coverage: 103.0

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 0.28
lineage2 East-Asian RD105 0.73
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.67
lineage2.2 East-Asian (Beijing) RD105;RD207 0.72
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 embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.412delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Arg446His Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Arg446His Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Tyr115* Assoc w R
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.144dupC 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 6576 p.Arg446His missense_variant 0.29 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Gly missense_variant 0.73 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.71 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.15 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 0.71 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.17 linezolid Assoc w R
tlyA 1918284 p.Tyr115* stop_gained 0.14 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.68 isoniazid Assoc w R High-level resistance
embA 4243221 c.-12C>T upstream_gene_variant 0.32 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.66 ethambutol Assoc w R
gid 4407790 c.412delG frameshift_variant 0.34 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 6771 p.Thr511Asn missense_variant 0.18 levofloxacin
moxifloxacin
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 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.74 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.71 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 0.74 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.29 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.37 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.76 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72 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 0.67 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416814 c.534G>A synonymous_variant 0.25 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.7 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 1.0 isoniazid Not assoc w R
katG 2155796 p.Ala106Pro missense_variant 0.31 isoniazid
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 0.25 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.34 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31 isoniazid Not assoc w R
ahpC 2726117 c.-76T>G upstream_gene_variant 0.3 isoniazid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.33 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
ribD 2987100 p.Val88Met missense_variant 0.42 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448851 p.Trp116* stop_gained 0.68 ethionamide Uncertain significance
whiB7 3568857 c.-178C>T upstream_gene_variant 0.33 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.68 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 0.63 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640525 c.-18G>A upstream_gene_variant 0.29 pretomanid
delamanid
clofazimine Uncertain significance
panD 4044023 c.259C>T synonymous_variant 0.26 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.3 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.22 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 4241022 p.Ala387Val missense_variant 0.71 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.31 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 0.66 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.6 ethambutol Not assoc w R
ethA 4327064 p.Cys137Tyr missense_variant 0.75 ethionamide Uncertain significance
whiB6 4338365 p.Cys53Arg missense_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.71 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R