TB-Profiler result

Run: ERR4800309
Summary

Run ID: ERR4800309

Sample name:

Date: 2024-10-03T22:04:26.517618

Number of reads: 3768550

Percentage reads mapped: 99.48

Median coverage: 106.0

Strain: lineage4.2.2.2

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.98
lineage4.2 Euro-American None 0.98
lineage4 Euro-American None 1.0
lineage4.2.2.2 Euro-American (Ural) None 0.98
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 embB p.Gly406Cys Assoc w R
pyrazinamide pncA p.Val139Gly Assoc w R
streptomycin rpsL p.Lys88Met 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.666_671delCGAGAA Mutation from literature
clofazimine mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198delG 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
gyrA 7570 p.Ala90Val missense_variant 0.97 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)
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin Assoc w R
mmpR5 779181 c.198delG frameshift_variant 0.46 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 781822 p.Lys88Met missense_variant 0.99 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.97 linezolid Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Gly missense_variant 0.99 pyrazinamide Assoc w R
embB 4247729 p.Gly406Cys missense_variant 0.98 ethambutol Assoc w R
ethA 4326802 c.666_671delCGAGAA disruptive_inframe_deletion 0.98 ethionamide Mutation from literature
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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser 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
mshA 575212 c.-136G>C upstream_gene_variant 0.96 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 576077 c.730C>T synonymous_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.97 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.96 rifampicin Not assoc w R
rpoB 762340 p.Arg845Gln missense_variant 0.99 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.99 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776402 c.2079C>G synonymous_variant 0.95 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpR5 779199 p.Asn70Lys missense_variant 0.44 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.97 linezolid
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
bacA 2063685 c.1044G>A synonymous_variant 0.98 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.98 para-aminosalicylic_acid
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.98 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087556 p.Ala246Glu missense_variant 0.59 cycloserine
Rv3083 3449486 p.Gly328Asp missense_variant 0.27 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841433 c.-13G>C upstream_gene_variant 0.5 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.98 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