TB-Profiler result

Run: SRR28045691
Summary

Run ID: SRR28045691

Sample name:

Date: 2024-05-22T11:27:52.397482

Number of reads: 12072240

Percentage reads mapped: 99.53

Median coverage: 355.0

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 1.0
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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.Ile491Phe Assoc w R
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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.His1002Arg Uncertain significance Mutation from literature
pyrazinamide pncA p.Met1? Assoc w R
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
clofazimine mmpR5 p.Met146Thr Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
delamanid
bedaquiline mmpR5 p.Met146Thr Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. 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 7581 p.Asp94His missense_variant 1.0 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin Assoc w R
mmpR5 779426 p.Met146Thr missense_variant 1.0 clofazimine Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5
inhA 1673432 c.-770T>C upstream_gene_variant 1.0 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. 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 2289239 p.Met1? start_lost 1.0 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4249518 p.His1002Arg missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin 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
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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 759940 p.Pro45Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
ndh 2102672 p.Ser124Phe missense_variant 1.0 ethionamide
delamanid
isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747363 p.Ala79Val missense_variant 0.99 para-aminosalicylic_acid
Rv2477c 2783716 p.Leu109Phe missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612188 p.Met310Thr missense_variant 1.0 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239654 c.-209C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4239763 c.-100C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.25 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.18 ethambutol
embB 4249408 c.2895G>A synonymous_variant 1.0 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 4338599 c.-78A>C upstream_gene_variant 1.0 capreomycin
amikacin Uncertain significance
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin