PathogenSeq: TBDR

This tool processes raw sequence data to infer strain type and identify known drug resistance markers.

A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.

This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.

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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).

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Summary

ID: 5d3b13bcede6c

Date: Fri Jul 26 15:53:56 2019

Strain: lineage4.3.1

Drug-resistance: Sensitive

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid

Rifampicin

Ethambutol

Pyrazinamide

Streptomycin

Ethionamide

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

lineage4 Euro-American LAM;T;S;X;H None

lineage4.3 Euro-American (LAM) mainly-LAM None

lineage4.3.1 Euro-American (LAM) LAM9 None

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrB	6082	c.843G>A	0.304
gyrA	7362	p.Glu21Gln	1.000
gyrA	7585	p.Ser95Thr	0.533
rpoC	764995	c.1626C>G	0.714
rpsL	781395	c.-165T>C	1.000
embR	1416222	p.Phe376Leu	0.231
embR	1416234	p.Cys372Gly	0.231
rrs	1472193	r.348a>c	0.235
rrs	1472215	r.370a>g	0.263
rrs	1472223	r.378c>g	0.263
rrs	1472225	r.380c>a	0.368
rrs	1472228	r.383g>c	0.263
rrs	1472234	r.389t>c	0.263
rrs	1472240	r.395g>a	0.250
rrs	1472251	r.406g>c	0.278
rrs	1472279	r.434t>g	0.267
rrs	1472286	r.441c>g	0.214
rrs	1472289	r.444t>g	0.214
rrs	1472290	r.445c>g	0.214
rrs	1472293	r.448c>a	0.214
rrs	1472297	r.452g>c	0.214
rrs	1472298	r.453g>c	0.214
rrs	1472324	r.479g>c	0.214
rrs	1472325	r.480g>c	0.214
rrs	1472328	r.483g>c	0.150
rrs	1472333	r.488g>a	0.214
rrs	1472339	r.494c>t	0.465
rrs	1472344	r.499c>t	0.744
rrs	1472349	r.504a>c	0.284
rrs	1472374	r.529t>g	0.276
rrs	1472378	r.533g>t	0.527
rrs	1472379	r.534t>g	0.485
rrs	1472382	r.537g>a	0.408
rrs	1472389	r.544g>a	0.667
rrs	1472396	r.551a>t	0.603
rrs	1472400	r.555c>t	0.627
rrs	1472517	r.672t>c	0.368
rrs	1472518	r.673g>a	0.208
rrs	1472530	r.685g>a	0.317
rrs	1472537	r.692c>t	0.780
rrs	1472544	r.699c>a	0.636
rrs	1472545	r.700a>t	0.708
rrs	1472549	r.704g>a	0.667
rrs	1472557	r.712g>a	0.759
rrs	1472571	r.726g>c	0.763
rrs	1472573	r.728c>t	0.306
rrs	1472579	r.734g>t	0.660
rrs	1472581	r.736a>t	0.700
rrs	1472583	r.738t>c	0.446
rrs	1472598	r.753a>c	0.899
rrs	1472599	r.754g>a	0.667
rrs	1472607	r.762g>a	0.345
rrs	1472612	r.767g>t	0.551
rrs	1472614	r.769g>t	0.258
rrs	1472616	r.771g>a	0.245
rrs	1472634	r.789t>c	0.468
rrs	1472635	r.790g>a	0.405
rrl	1474001	r.344c>t	0.364
thyA	3073868	p.Thr202Ala	0.900
alr	3841652	c.-232A>T	0.263
alr	3841654	c.-234A>C	0.333
alr	3841662	c.-242A>G	0.556
alr	3841663	c.-243G>A	0.556
embC	4242643	c.2781C>T	1.000
embA	4246161	p.Val977Leu	0.364
gid	4408156	p.Leu16Arg	0.750

Analysis pipeline specifications

TBProfiler Version: 2.1.1

Analysis	Program
Mapping	bwa
Variant Calling	BCFtools

Log

Drug Details

The estimated accuracy of drug resistance predictions is:

Drug¹	Sensitivity (%)	Specificity (%)
Isoniazid	92.8 (89.9-95.7)	100 (100-100)
Rifampicin	96.2 (93.9-98.5)	98.1 (96.8-99.4)
Ethambutal	88.7 (83.6-93.8)	81.7 (77.6-85.8)
Pyrazinamide	70.9 (62.4-79.4)	93.9 (90.6-97.2)
Streptomycin	87.1 (82.7-91.5)	89.7 (86.0-93.4)
Ethionamide	73.6 (66.7-80.5)	93.3 (89.6-97.0)
Moxifloxacin	60.0 (29.6-90.4)	68.7 (52.6-84.8)
Ofloxacin	85.5 (79.1-91.9)	94.9 (91.8-98.0)
Amikacin	82.9 (74.4-91.4)	98.3 (96.0-100)
Capreomycin	60.7 (50.6-70.8)	90.7 (87.2-94.2)
Kanamycin	87.3 (81.3-93.3)	93.4 (89.9-96.9)
Para-aminosalisylic acid	Not determined	Not determined
Linezolid	Not determined	Not determined
Clofazimine	Not determined	Not determined
Bedaquiline	Not determined	Not determined
Multi drug resistance	91.2 (87.8-94.6)	98.4 (97.2-99.6)
Extremely drug resistance	75.9 (64.5-87.3)	98.4 (97.3-99.5)

Lineages

Lineage²	Location	Strain	RD type
lineage1	Indo-Oceanic	EAI	RD239
lineage1.1	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
lineage1.1.1	Indo-Oceanic	EAI4;EAI5	RD239
lineage1.1.1.1	Indo-Oceanic	EAI4;ZERO	RD239
lineage1.1.2	Indo-Oceanic	EAI3;EAI5	RD239
lineage1.1.3	Indo-Oceanic	EAI6	RD239
lineage1.2	Indo-Oceanic	EAI1;EAI2	RD239
lineage1.2.1	Indo-Oceanic	EAI2	RD239
lineage1.2.2	Indo-Oceanic	EAI1	RD239
lineage2	East-Asian	Beijing	RD105
lineage2.1	East-Asian (non-Beijing)	None	None
lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
lineage2.2.1	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
lineage2.2.1.2	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
lineage2.2.1.1	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
lineage3	East-African-Indian	CAS	RD750
lineage3.1	East-African-Indian	Non-CAS1-Delhi	RD750
lineage3.1.1	East-African-Indian	CAS1-Kili	RD750
lineage3.1.2	East-African-Indian	CAS;CAS2	RD750
lineage3.1.2.1	East-African-Indian	CAS2	RD750
lineage3.1.2.2	East-African-Indian	CAS	RD750
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.1	Euro-American	T;X;H	None
lineage4.1.2	Euro-American (X-type)	T;H	None
lineage4.1.2.1	Euro-American (X-type)	T1;H1	RD182
lineage4.1.1	Euro-American (X-type)	X1;X2;X3	None
lineage4.1.1.2	Euro-American (X-type)	X1	None
lineage4.1.1.1	Euro-American (X-type)	X2	RD183
lineage4.1.1.3	Euro-American (Haarlem)	X1;X3	RD193
lineage4.2	Euro-American	H;T;LAM	None
lineage4.2.2	Euro-American (Ural)	T;LAM7-TUR	None
lineage4.2.2.1	Euro-American	LAM7-TUR	None
lineage4.2.1	Euro-American (TUR)	H3;H4	None
lineage4.3	Euro-American (LAM)	mainly-LAM	None
lineage4.3.1	Euro-American (LAM)	LAM9	None
lineage4.3.3	Euro-American (LAM)	LAM;T	RD115
lineage4.3.4	Euro-American (LAM)	LAM	RD174
lineage4.3.4.1	Euro-American (LAM)	LAM1;LAM2	RD174
lineage4.3.4.2	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
lineage4.3.4.2.1	Euro-American (LAM)	LAM11	RD174
lineage4.3.2	Euro-American (LAM)	LAM3	None
lineage4.3.2.1	Euro-American (LAM)	LAM3	RD761
lineage4.4	Euro-American	S;T	None
lineage4.4.2	Euro-American	T1;T2	None
lineage4.4.1	Euro-American (S-type)	S;T	None
lineage4.4.1.2	Euro-American	T1	None
lineage4.4.1.1	Euro-American	S;Orphans	None
lineage4.5	Euro-American	H;T	RD122
lineage4.6	Euro-American	T;LAM	None
lineage4.6.1	Euro-American (Uganda)	T2	RD724
lineage4.6.1.1	Euro-American	T2-Uganda	RD724
lineage4.6.1.2	Euro-American	T2	RD724
lineage4.6.2	Euro-American	T;LAM	RD726
lineage4.6.2.1	Euro-American	T3	RD726
lineage4.6.2.2	Euro-American (Cameroon)	LAM10-CAM	RD726
lineage4.7	Euro-American (mainly T)	T1;T5	None
lineage4.8	Euro-American (mainly T)	T1;T2;T3;T5	RD219
lineage4.9	Euro-American (H37Rv-like)	T1	None
lineage5	West-Africa 1	AFRI_2;AFRI_3	RD711
lineage6	West-Africa 2	AFRI_1	RD702
lineage7	Lineage 7	None	None
lineageBOV	M. bovis	BOV_1;BOV_2	None

Citations

1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer

This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.

Drug¹	Resistance	Supporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage²	Family	Main Spoligotype	RDS
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.3	Euro-American (LAM)	mainly-LAM	None
lineage4.3.1	Euro-American (LAM)	LAM9	None