TB-Profiler result

Run: ERR8975687
Summary

Run ID: ERR8975687

Sample name:

Date: 2024-04-16T07:41:33.986940

Number of reads: 3152544

Percentage reads mapped: 99.73

Median coverage: 101.0

Strain: lineage2.2.2;lineage4.3.2.1

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 0.39
lineage2 East-Asian RD105 0.59
lineage4.3.2 Euro-American (LAM) None 0.39
lineage4.3.2.1 Euro-American (LAM) RD761 0.37
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.57
lineage2.2 East-Asian (Beijing) RD105;RD207 0.57
lineage4 Euro-American None 0.42
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.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. 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
pyrazinamide pncA c.517dupG Assoc w R
p.His57Tyr Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA p.Ala381Pro Uncertain significance Mutation from literature
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 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
gyrB 6742 p.Glu501Asp missense_variant 0.73 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Ala missense_variant 0.37 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 761110 p.Asp435Val missense_variant 0.62 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.42 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.17 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.62 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.57 capreomycin Assoc w R
kanamycin Assoc w R
amikacin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.57 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.65 pyrazinamide Assoc w R
pncA 2289073 p.His57Tyr missense_variant 0.41 pyrazinamide Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.55 cycloserine Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.32 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.56 ethambutol Assoc w R
ethA 4326333 p.Ala381Pro missense_variant 0.6 ethionamide Uncertain significance Mutation from literature
gid 4407967 p.Leu79Ser missense_variant 0.56 streptomycin 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
gyrB 5520 p.Pro94Leu missense_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656131 c.1338_1339dupGC frameshift_variant 0.59 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.53 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.59 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.54 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.38 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 776100 p.Thr794Ile missense_variant 0.51 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.53 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 0.58 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.35 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.48 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 0.65 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.59 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 0.61 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
thyA 3073868 p.Thr202Ala missense_variant 0.44 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.58 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.46 pyrazinamide Not assoc w R
clpC1 4040976 c.-272T>G upstream_gene_variant 0.58 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 0.66 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.6 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.67 ethambutol Not assoc w R
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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.59 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.62 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.59 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.42 streptomycin Not assoc w R