TB-Profiler result

Run: ERR13290960
Summary

Run ID: ERR13290960

Sample name:

Date: 2024-10-04T04:55:47.011715

Number of reads: 6121351

Percentage reads mapped: 99.67

Median coverage: 182.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.98
lineage4 Euro-American None 1.0
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG c.18dupA Assoc w R High-level resistance
ethambutol
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
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
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.98 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2156093 c.18dupA frameshift_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.98 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.97 kanamycin 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 1048 p.Arg350Trp missense_variant 0.99 isoniazid Uncertain significance
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 7892 c.591G>A synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9788 p.Asp829Glu missense_variant 0.96 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
ccsA 620029 c.139C>T synonymous_variant 0.98 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
rpoC 766485 p.Val1039Ala missense_variant 0.97 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 2156484 c.-373A>C upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.99 pyrazinamide Not assoc w R
Rv1979c 2221722 c.1443C>T synonymous_variant 0.96 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518928 p.Ser272Ala missense_variant 0.94 isoniazid
Rv2752c 3065932 c.259dupA frameshift_variant 0.96 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641555 c.21C>T synonymous_variant 0.94 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoA 3878575 c.-68C>T upstream_gene_variant 0.97 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 1.0 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.95 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244214 p.Ala328Thr missense_variant 0.97 ethambutol
embB 4247595 p.Cys361Tyr missense_variant 0.98 ethambutol Uncertain significance
ubiA 4269742 p.Leu31Pro missense_variant 0.96 ethambutol 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