TB-Profiler result

Run: ERR459445
Summary

Run ID: ERR459445

Sample name:

Date: 2024-10-04T19:05:58.939025

Number of reads: 1781713

Percentage reads mapped: 99.59

Median coverage: 57.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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 katG c.18dupA Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Ser447Phe Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Thr500Asn Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Ser447Phe Assoc w R - Interim
p.Thr500Asn Uncertain significance Mutation from literature
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
gyrB 6579 p.Ser447Phe missense_variant 0.39 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrB 6738 p.Thr500Asn missense_variant 0.87 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2156093 c.18dupA frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576057 c.712dupG frameshift_variant 0.71 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576372 p.Ala342Glu missense_variant 0.31 isoniazid
ethionamide
mmaA3 737761 p.Ala130Val missense_variant 1.0 isoniazid
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
Rv1129c 1253554 c.981G>C synonymous_variant 0.98 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1253865 p.Thr224Ala missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170530 p.Ala28Glu missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726568 p.Asn126Asp missense_variant 1.0 isoniazid
thyA 3074422 p.Pro17Leu missense_variant 1.0 para-aminosalicylic_acid
glpK 4139183 c.572dupG frameshift_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239809 c.-54C>T upstream_gene_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 4338863 c.-342C>G upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin