TB-Profiler

TB-Profiler result

Run: ERR4796359

Summary

Run ID: ERR4796359

Sample name:

Date: 2024-04-14T23:16:08.504409

Number of reads: 3369551

Percentage reads mapped: 99.75

Median coverage: 82.0

Strain: lineage3

Spoligotype:

Drug-resistance: XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs

Lineage	Family	RDs	Frequency
lineage3	East-African-Indian	RD750	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.Ser450Leu	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)
isoniazid	katG	p.Ser315Thr	Assoc w R	High-level resistance
ethambutol	embB	p.Met306Ile	Assoc w R
pyrazinamide	pncA	p.Phe94Cys	Assoc w R
streptomycin
fluoroquinolones
moxifloxacin	gyrB	p.Thr500Ile	Uncertain significance	Mutation from literature
moxifloxacin	gyrA	p.Ala90Val	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin	gyrB	p.Thr500Ile	Uncertain significance	Mutation from literature
levofloxacin	gyrA	p.Ala90Val	Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide	inhA	c.-770T>C	Assoc w R - Interim	Alias fabG1_c.-8T>C
ethionamide	ethA	c.1152dupT	Assoc w R
clofazimine	mmpR5	c.326_329delGGGC	Assoc w R	Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid	folC	p.Ile43Thr		Mutation from literature
delamanid
bedaquiline	mmpR5	c.326_329delGGGC	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
gyrB	6738	p.Thr500Ile	missense_variant	1.0	moxifloxacin	Uncertain significance	Mutation from literature
gyrB	6738	p.Thr500Ile	missense_variant	1.0	levofloxacin	Uncertain significance	Mutation from literature
gyrA	7570	p.Ala90Val	missense_variant	1.0	moxifloxacin	Assoc w R	Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA	7570	p.Ala90Val	missense_variant	1.0	levofloxacin	Assoc w R
rpoB	761155	p.Ser450Leu	missense_variant	1.0	rifampicin	Assoc w R
mmpR5	779313	c.326_329delGGGC	frameshift_variant	1.0	bedaquiline	Assoc w R	Can only confer resistance if genetically linked to a functional MmpL5
mmpR5	779313	c.326_329delGGGC	frameshift_variant	1.0	clofazimine	Assoc w R	Can only confer resistance if genetically linked to a functional MmpL5
rplC	801268	p.Cys154Arg	missense_variant	1.0	linezolid	Assoc w R
inhA	1673432	c.-770T>C	upstream_gene_variant	1.0	ethionamide	Assoc w R - Interim	Alias fabG1_c.-8T>C
inhA	1673432	c.-770T>C	upstream_gene_variant	1.0	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	2288961	p.Phe94Cys	missense_variant	1.0	pyrazinamide	Assoc w R
folC	2747471	p.Ile43Thr	missense_variant	1.0	para-aminosalicylic_acid		Mutation from literature
embB	4247431	p.Met306Ile	missense_variant	1.0	ethambutol	Assoc w R
ethA	4326321	c.1152dupT	frameshift_variant	1.0	ethionamide	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
gyrA	7362	p.Glu21Gln	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	7585	p.Ser95Thr	missense_variant	1.0	moxifloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	levofloxacin	Not assoc w R
gyrA	9304	p.Gly668Asp	missense_variant	1.0	moxifloxacin	Not assoc w R
fgd1	491742	c.960T>C	synonymous_variant	1.0	clofazimine	Not assoc w R
					pretomanid
					delamanid	Not assoc w R - Interim
Rv0565c	657081	c.390G>A	synonymous_variant	1.0	ethionamide	Not assoc w R - Interim
rpoB	759746	c.-61C>T	upstream_gene_variant	1.0	rifampicin	Not assoc w R
rpoB	762434	c.2628T>G	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoB	763031	c.3225T>C	synonymous_variant	1.0	rifampicin	Not assoc w R
rpoC	764817	p.Val483Gly	missense_variant	1.0	rifampicin	Uncertain significance
mmpL5	775639	p.Ile948Val	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	775639	p.Ile948Val	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	clofazimine	Not assoc w R
mmpL5	776100	p.Thr794Ile	missense_variant	1.0	bedaquiline	Not assoc w R - Interim
rpsL	781395	c.-165T>C	upstream_gene_variant	1.0	streptomycin	Not assoc w R
Rv1129c	1253437	p.Trp366Cys	missense_variant	1.0	moxifloxacin	Uncertain significance
					levofloxacin	Uncertain significance
					rifampicin	Uncertain significance
					isoniazid	Uncertain significance
Rv1129c	1254562	c.-28T>C	upstream_gene_variant	1.0	moxifloxacin	Not assoc w R
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
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
katG	2154724	p.Arg463Leu	missense_variant	1.0	isoniazid	Not assoc w R
PPE35	2167926	p.Leu896Ser	missense_variant	1.0	pyrazinamide	Not assoc w R
Rv1979c	2222700	c.465C>T	synonymous_variant	1.0	clofazimine	Not assoc w R - Interim
Rv1979c	2222700	c.465C>T	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	clofazimine	Not assoc w R
Rv1979c	2223293	c.-129A>G	upstream_gene_variant	1.0	bedaquiline	Not assoc w R - Interim
pncA	2289047	c.195C>T	synonymous_variant	1.0	pyrazinamide	Not assoc w R
pncA	2289365	c.-125delC	upstream_gene_variant	1.0	pyrazinamide
ahpC	2726105	c.-88G>A	upstream_gene_variant	1.0	isoniazid	Not assoc w R
Rv2477c	2782498	c.1545C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R
					kanamycin	Not assoc w R
					rifampicin	Not assoc w R
					amikacin	Not assoc w R
ald	3086788	c.-32T>C	upstream_gene_variant	1.0	cycloserine
lpqB	3623174	c.1737G>C	synonymous_variant	1.0	bedaquiline	Not assoc w R - Interim
lpqB	3623174	c.1737G>C	synonymous_variant	1.0	rifampicin	Not assoc w R - Interim
mtrB	3625065	p.Met517Leu	missense_variant	1.0	bedaquiline	Uncertain significance
mtrB	3625065	p.Met517Leu	missense_variant	1.0	rifampicin	Not assoc w R
alr	3841473	c.-53G>A	upstream_gene_variant	1.0	cycloserine
panD	4044872	c.-591C>T	upstream_gene_variant	1.0	pyrazinamide
glpK	4138622	c.1134C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
					moxifloxacin	Not assoc w R
					streptomycin	Not assoc w R - Interim
					levofloxacin	Not assoc w R
					rifampicin	Not assoc w R
					isoniazid	Not assoc w R
embC	4242075	p.Arg738Gln	missense_variant	1.0	ethambutol	Not assoc w R
embC	4242643	c.2781C>T	synonymous_variant	1.0	ethambutol	Not assoc w R
aftB	4267492	p.Ala449Thr	missense_variant	1.0	ethambutol	Uncertain significance
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	4338732	c.-211C>T	upstream_gene_variant	1.0	capreomycin
					amikacin
					kanamycin
gid	4407588	c.615A>G	synonymous_variant	1.0	streptomycin	Not assoc w R
gid	4407967	p.Leu79Trp	missense_variant	1.0	streptomycin	Uncertain significance