TB-Profiler result

Run: ERR9992901
Summary

Run ID: ERR9992901

Sample name:

Date: 2024-04-16T07:45:51.051402

Number of reads: 4388535

Percentage reads mapped: 99.83

Median coverage: 136.0

Strain: lineage4.3.3;lineage4.4.1.1

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 0.74
lineage4.4.1 Euro-American (S-type) None 0.21
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.19
lineage4.3.3 Euro-American (LAM) RD115 0.75
lineage4.4 Euro-American None 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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 embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA c.389delT Assoc w R
streptomycin
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)
p.Ser91Pro 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
p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-11A>G Uncertain significance Mutation from literature
clofazimine mmpR5 c.11delA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.11delA Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.144dupC 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 7570 p.Ala90Val missense_variant 0.88 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7572 p.Ser91Pro missense_variant 0.1 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.18 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin Assoc w R
mmpR5 778998 c.11delA frameshift_variant 0.11 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
mmpR5 779130 c.144dupC frameshift_variant 0.87 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
inhA 1673432 c.-770T>A upstream_gene_variant 0.75 isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. 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>A
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2288852 c.389delT frameshift_variant 0.74 pyrazinamide Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.79 cycloserine Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 0.75 ethambutol Uncertain significance Mutation from literature
ethA 4327484 c.-11A>G upstream_gene_variant 0.72 ethionamide Uncertain significance 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 8040 p.Gly247Ser missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.24 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
rpoC 764840 p.Ile491Val missense_variant 0.82 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.74 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.18 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.73 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.72 capreomycin Not assoc w R
linezolid Uncertain significance
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
ndh 2102990 p.Val18Ala missense_variant 0.21 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.15 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.25 pyrazinamide Not assoc w R
Rv1979c 2223051 p.Glu38Asp missense_variant 0.76 clofazimine Uncertain significance
bedaquiline Uncertain significance
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 0.81 isoniazid
Rv2752c 3065824 p.Pro123Leu missense_variant 0.73 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv2752c 3066485 c.-294A>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.71 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.15 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.18 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.2 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.83 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.2 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.31 ethambutol
ubiA 4269124 p.Ala237Val missense_variant 0.21 ethambutol Uncertain significance
ethA 4327367 p.Glu36Val missense_variant 0.19 ethionamide
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 4407927 p.Glu92Asp missense_variant 0.17 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R