TB-Profiler result

Run: SRR22175219
Summary

Run ID: SRR22175219

Sample name:

Date: 2024-10-04T02:34:01.037798

Number of reads: 1748753

Percentage reads mapped: 99.23

Median coverage: 53.0

Strain: lineage2.2.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.53
lineage2 East-Asian RD105 0.49
lineage4.2 Euro-American None 0.51
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.49
lineage2.2 East-Asian (Beijing) RD105;RD207 0.52
lineage4 Euro-American None 0.56
lineage4.2.2.2 Euro-American (Ural) None 0.45
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.Met306Val Assoc w R
p.Gly406Cys Assoc w R
pyrazinamide pncA p.Thr177Pro Assoc w R
p.Val139Gly Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Met Assoc w R
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.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.666_671delCGAGAA Mutation from literature
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
delamanid
bedaquiline mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
linezolid rplC p.Cys154Arg Assoc w R
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 0.6 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)
gyrA 7582 p.Asp94Gly missense_variant 0.42 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.17 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
mmpR5 779181 c.198delG frameshift_variant 0.6 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 0.41 streptomycin Assoc w R
rpsL 781822 p.Lys88Met missense_variant 0.37 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
pncA 2288713 p.Thr177Pro missense_variant 0.53 pyrazinamide Assoc w R
pncA 2288826 p.Val139Gly missense_variant 0.29 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.42 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.56 ethambutol Assoc w R
embB 4247729 p.Gly406Cys missense_variant 0.48 ethambutol Assoc w R
ethA 4326802 c.666_671delCGAGAA disruptive_inframe_deletion 0.5 ethionamide 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 8688 p.Ala463Ser missense_variant 0.58 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 0.42 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575212 c.-136G>C upstream_gene_variant 0.52 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.42 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.57 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.52 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.5 ethionamide Uncertain significance
Rv0565c 657425 p.Gly16Ser missense_variant 0.47 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.6 rifampicin Not assoc w R
rpoB 762340 p.Arg845Gln missense_variant 0.41 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.41 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.55 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.61 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.5 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776402 c.2079C>G synonymous_variant 0.46 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.45 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.5 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.6 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
bacA 2063685 c.1044G>A synonymous_variant 0.58 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.51 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.48 isoniazid Not assoc w R
katG 2155126 p.Asp329Gly missense_variant 0.33 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.32 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.51 para-aminosalicylic_acid
Rv2752c 3065935 c.255_256dupCC frameshift_variant 0.56 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065996 c.194_195dupGC frameshift_variant 0.26 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.41 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.53 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.52 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.51 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841433 c.-13G>C upstream_gene_variant 0.5 cycloserine
embC 4241022 p.Ala387Val missense_variant 0.42 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.47 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.54 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.5 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.4 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.42 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.46 streptomycin Not assoc w R