TB-Profiler result

Run: ERR4799796
Summary

Run ID: ERR4799796

Sample name:

Date: 2024-10-05T07:14:47.187076

Number of reads: 5418534

Percentage reads mapped: 99.62

Median coverage: 134.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.96
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.Gln497Lys Assoc w R
pyrazinamide pncA p.Val155Met Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA 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.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198dupG 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 7572 p.Ser91Pro missense_variant 0.96 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 0.98 rifampicin Assoc w R
mmpR5 779181 c.198dupG frameshift_variant 0.53 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 781687 p.Lys43Arg missense_variant 0.99 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2288779 p.Val155Met missense_variant 0.98 pyrazinamide Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.98 ethambutol 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
gyrB 5332 c.93C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.95 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.98 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766485 p.Val1039Ala missense_variant 0.98 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 778982 c.-77A>G upstream_gene_variant 0.19 bedaquiline Uncertain significance
clofazimine
mmpR5 779216 p.Gln76Arg missense_variant 0.22 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.98 pyrazinamide 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
eis 2715340 c.-8C>T upstream_gene_variant 0.97 kanamycin Uncertain significance
amikacin Uncertain significance
folC 2747470 p.Ile43Ala missense_variant 0.97 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.96 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.98 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.98 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245417 p.Gly729Arg missense_variant 0.97 ethambutol Uncertain significance
ubiA 4269298 p.Ile179Thr missense_variant 0.97 ethambutol Uncertain significance
ethA 4327301 p.Asp58Gly missense_variant 0.97 ethionamide 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