TB-Profiler result

Run: ERR11465987
Summary

Run ID: ERR11465987

Sample name:

Date: 2024-10-04T17:13:49.048217

Number of reads: 2215555

Percentage reads mapped: 99.35

Median coverage: 37.0

Strain: lineage1.2.2.2;lineage4.8.1

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.74
lineage1.2.2.2 Indo-Oceanic RD239 0.73
lineage4 Euro-American None 0.28
lineage4.8 Euro-American (mainly T) RD219 0.29
lineage1 Indo-Oceanic RD239 0.68
lineage4.8.1 Euro-American (mainly T) RD219 0.23
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-29_-28delCT Uncertain significance Mutation from literature
embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.375_389delCGATGAGGTCGATGT Assoc w R - Interim
c.375_389delCGATGAGGTCGATGT Mutation from literature
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Gly88Ala Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.138_139delTG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.138_139delTG 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 7564 p.Gly88Ala missense_variant 0.43 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761140 p.His445Leu missense_variant 0.68 rifampicin Assoc w R
mmpR5 779121 c.138_139delTG frameshift_variant 0.5 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.78 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid Assoc w R High-level resistance
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 0.56 pyrazinamide Assoc w R - Interim
pyrazinamide Mutation from literature
embA 4243203 c.-29_-28delCT upstream_gene_variant 0.52 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.73 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 5075 c.-165C>T upstream_gene_variant 0.85 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.64 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.64 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.7 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.68 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.57 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.75 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.51 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.87 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.76 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.55 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.7 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.67 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.64 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpR5 779130 p.Asp47Glu missense_variant 0.53 bedaquiline Uncertain significance
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.62 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.57 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.89 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.81 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853974 c.369C>T synonymous_variant 0.9 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.44 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.97 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.8 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.45 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.67 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.18 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.7 pyrazinamide Uncertain significance
PPE35 2170892 c.-280G>A upstream_gene_variant 0.22 pyrazinamide
Rv1979c 2222098 p.Thr356Lys missense_variant 0.69 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.72 bedaquiline Not assoc w R - Interim
clofazimine 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.76 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.76 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74 isoniazid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.33 capreomycin
thyX 3068062 c.-117A>C upstream_gene_variant 0.6 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.73 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.62 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.68 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.62 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
fbiB 3642874 p.Leu447Arg missense_variant 0.24 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.68 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.77 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.74 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.68 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.96 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.64 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.9 ethambutol Not assoc w R
embB 4246567 c.54_55insT frameshift_variant 0.35 ethambutol
embB 4246979 p.Gly156Cys missense_variant 0.71 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.76 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.58 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.67 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.65 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.73 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.72 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.86 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin 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 4338603 c.-82C>T upstream_gene_variant 0.77 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.76 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.71 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.69 streptomycin Not assoc w R