TB-Profiler result

Run: ERR8665695
Summary

Run ID: ERR8665695

Sample name:

Date: 2024-04-15T16:43:47.780780

Number of reads: 1832869

Percentage reads mapped: 99.61

Median coverage: 42.0

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 0.36
lineage2 East-Asian RD105 0.67
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.6
lineage2.2 East-Asian (Beijing) RD105;RD207 0.66
lineage4 Euro-American None 0.36
lineage4.3.3 Euro-American (LAM) RD115 0.37
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
p.Ser450Leu Assoc w R
rpoC p.Ile491Thr Uncertain significance Mutation from literature
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>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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 embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
p.Gln497Arg Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Val139Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine ald c.464delG Mutation from literature
alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
ethA c.1386delA Assoc w R
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
delamanid
bedaquiline mmpR5 c.198dupG 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 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 0.45 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.55 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.69 rifampicin Uncertain significance Mutation from literature
mmpR5 779181 c.198dupG frameshift_variant 0.34 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 0.62 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.32 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.47 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1673432 c.-770T>C upstream_gene_variant 0.53 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Ala missense_variant 0.7 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.34 kanamycin Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.73 para-aminosalicylic_acid Mutation from literature
ald 3087278 c.464delG frameshift_variant 0.59 cycloserine Mutation from literature
alr 3841083 p.Leu113Arg missense_variant 0.36 cycloserine Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.37 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.58 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.33 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.48 ethambutol Uncertain significance Mutation from literature
ethA 4326087 c.1386delA frameshift_variant 0.6 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 698 p.Arg233Gln missense_variant 0.25 isoniazid 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 0.36 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 0.62 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.54 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.6 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656122 p.Leu450Pro missense_variant 0.66 ethionamide
Rv0565c 657081 c.390G>A synonymous_variant 0.67 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.76 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.42 rifampicin Not assoc w R
rpoC 766834 p.Glu1155Asp missense_variant 0.41 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.61 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.64 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpR5 779255 p.Arg89Gln missense_variant 0.45 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 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 0.59 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.28 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.42 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.45 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.38 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 0.74 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.34 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.46 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
kasA 2518919 p.Gly269Ser missense_variant 0.32 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.47 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 0.47 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.43 para-aminosalicylic_acid
thyA 3073887 c.584delC frameshift_variant 0.64 para-aminosalicylic_acid
ald 3086731 c.-89A>G upstream_gene_variant 0.71 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568892 c.-214_-213insA upstream_gene_variant 0.56 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69 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 0.67 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.38 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.58 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.69 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.54 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.76 capreomycin Not assoc w R
amikacin Not assoc w R
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 0.6 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.68 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.22 streptomycin Not assoc w R