TB-Profiler result

Run: SAMEA5569694
Summary

Run ID: SAMEA5569694

Sample name:

Date: 2024-04-16T11:55:32.787187

Number of reads: 9171838

Percentage reads mapped: 99.81

Median coverage: 280.0

Strain: lineage4.1.1.1;lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-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 0.89
lineage4.1 Euro-American None 0.1
lineage4.1.1.1 Euro-American (X-type) RD183 0.09
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.11
lineage4.3.4 Euro-American (LAM) RD174 0.89
lineage4.3.4.2 Euro-American (LAM) RD174 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Phe Assoc w R
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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
p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide pncA p.Val139Ala Assoc w R
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.382_383delGC Assoc w R
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
rpoB 761155 p.Ser450Phe missense_variant 1.0 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.12 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Asn missense_variant 0.15 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Ala missense_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.14 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.88 ethambutol Assoc w R
ethA 4327090 c.382_383delGC frameshift_variant 1.0 ethionamide Assoc w R
gid 4407851 c.351delG frameshift_variant 0.11 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
dnaA 1465 p.Glu489Gln missense_variant 0.13 isoniazid Uncertain significance
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 657303 c.168C>T synonymous_variant 0.1 ethionamide Not assoc w R - Interim
rpoB 761147 c.1341C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.15 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 765719 p.Glu784Gln missense_variant 0.13 rifampicin Not assoc w R
rpoC 766070 c.2701C>T synonymous_variant 0.11 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 0.12 linezolid
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.89 moxifloxacin
levofloxacin
rifampicin
isoniazid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2747453 p.Arg49Gln missense_variant 0.91 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.89 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86 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 0.91 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.14 ethambutol Not assoc w R
embA 4243222 c.-11C>T upstream_gene_variant 0.9 ethambutol Uncertain significance
embB 4248736 c.2223G>T synonymous_variant 0.88 ethambutol Not assoc w R - Interim
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 4338600 c.-79T>C upstream_gene_variant 0.89 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408054 p.Leu50Arg missense_variant 0.9 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.88 streptomycin Not assoc w R