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: 5d7b84e199c86

Date: Fri Sep 13 13:02:11 2019

Strain: lineage4.3

Drug-resistance: Drug-resistant

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid

Rifampicin

Ethambutol

Pyrazinamide

Streptomycin R rrs r.462c>t (0.75)

Ethionamide

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

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

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrA	7853	c.552C>G	0.600
gyrA	9182	c.1881T>C	1.000
gyrA	9191	c.1890G>C	1.000
gyrA	9200	c.1899A>G	1.000
gyrA	9204	p.Ser635Thr	1.000
rpoB	760046	c.240G>C	1.000
rpoB	760060	p.Tyr85Leu	1.000
rpoB	760067	c.261G>C	1.000
rpoB	760070	c.264T>G	1.000
rpoB	760091	c.285G>C	1.000
rpoB	760101	c.295T>C	1.000
rpoB	760112	c.306T>C	1.000
rpoB	760118	c.312T>G	1.000
rpoB	760121	c.315T>C	1.000
rpoB	760130	p.Asp108Glu	1.000
rpoB	760139	c.333A>G	1.000
rpoB	760142	c.336C>G	1.000
rpoB	760181	c.375T>C	1.000
rpoB	760184	c.378A>G	1.000
rpoB	760196	c.390C>G	1.000
rpoB	760591	p.Val262Ala	1.000
rpoB	760611	c.805T>C	1.000
rpoB	760646	c.840C>G	1.000
rpoB	760655	c.849A>G	1.000
rpoB	761570	c.1764T>C	1.000
rpoB	761573	c.1767C>G	1.000
rpoB	761579	c.1773G>C	1.000
rpoB	761588	c.1782C>T	1.000
rpoC	764968	c.1599T>C	1.000
rpoC	765553	c.2184C>T	0.455
rpoC	765556	c.2187G>C	0.455
rpoC	765559	c.2190G>C	0.455
rpoC	765613	p.His748Gln	1.000
rpoC	765625	c.2256C>G	1.000
rpoC	765628	c.2259G>C	1.000
rpoC	765631	p.Asp754Glu	1.000
rpoC	766447	c.3078T>C	1.000
rpoC	766462	c.3093G>C	1.000
rpoC	766795	c.3426C>T	1.000
rpoC	766801	c.3432C>G	1.000
rpoC	766804	c.3435A>G	1.000
rpoC	766900	c.3531T>C	1.000
rpoC	766933	c.3564A>G	1.000
rpoC	767033	c.3664T>A	1.000
rplC	800814	c.6A>G	1.000
rplC	800817	c.9A>T	1.000
rplC	800844	c.36T>C	1.000
rplC	801367	p.Ala187Thr	1.000
rplC	801402	c.594T>C	1.000
rplC	801405	c.597T>C	1.000
rplC	801423	c.615G>C	1.000
rplC	801426	c.618C>G	1.000
rplC	801427	p.Met207Val	1.000
rplC	801438	c.630T>C	1.000
rplC	801442	p.Ile212Val	1.000
rrs	1472193	r.348a>t	0.390
rrs	1472197	r.352a>t	0.261
rrs	1472225	r.380c>g	0.154
rrs	1472240	r.395g>c	0.568
rrs	1472242	r.397c>t	0.525
rrs	1472251	r.406g>t	0.581
rrs	1472252	r.407g>a	0.425
rrs	1472253	r.408g>t	0.500
rrs	1472256	r.411t>a	0.475
rrs	1472259	r.414c>a	0.525
rrs	1472278	r.433c>t	0.400
rrs	1472279	r.434t>c	0.524
rrs	1472285	r.440a>g	0.609
rrs	1472286	r.441c>g	0.190
rrs	1472287	r.442c>t	0.400
rrs	1472289	r.444t>g	0.800
rrs	1472290	r.445c>g	0.650
rrs	1472298	r.453g>c	0.200
rrs	1472311	r.466c>t	0.400
rrs	1472313	r.468g>a	0.333
rrs	1472315	r.470t>g	0.765
rrs	1472324	r.479g>c	0.684
rrs	1472325	r.480g>c	0.700
rrs	1472327	r.482g>a	0.136
rrs	1472328	r.483g>c	0.174
rrs	1472344	r.499c>t	0.935
rrs	1472349	r.504a>c	0.510
rrs	1472374	r.529t>g	0.514
rrs	1472382	r.537g>a	0.683
rrs	1472389	r.544g>a	0.755
rrs	1472390	r.545t>a	0.627
rrs	1472391	r.546c>t	0.711
rrs	1472412	r.567a>c	0.720
rrs	1472415	r.570t>g	0.456
rrs	1472418	r.573t>c	0.326
rrs	1472422	r.577t>c	0.471
rrs	1472435	r.590t>c	0.789
rrs	1472438	r.593t>c	0.368
rrs	1472439	r.594c>t	0.789
rrs	1472443	r.598a>t	0.353
rrs	1472446	r.601t>g	0.235
rrs	1472447	r.602c>t	0.250
rrs	1472448	r.603t>c	0.714
rrs	1472450	r.605a>g	0.643
rrs	1472451	r.606c>g	0.286
rrs	1472452	r.607g>a	0.429
rrs	1472461	r.616g>c	0.250
rrs	1472462	r.617t>c	0.692
rrs	1472464	r.619a>g	0.769
rrs	1472466	r.621c>a	0.333
rrs	1472467	r.622g>c	0.333
rrs	1472471	r.626g>a	0.786
rrs	1472485	r.640g>a	0.643
rrs	1472489	r.644a>t	0.786
rrs	1472494	r.649a>g	0.500
rrs	1472498	r.653c>t	0.600
rrs	1472507	r.662c>g	0.261
rrs	1472517	r.672t>a	0.689
rrs	1472518	r.673g>t	0.189
rrs	1472530	r.685g>a	0.736
rrs	1472537	r.692c>t	0.637
rrs	1472541	r.696t>g	0.478
rrs	1472544	r.699c>a	0.282
rrs	1472545	r.700a>t	0.699
rrs	1472553	r.708c>t	0.389
rrs	1472557	r.712g>a	0.270
rrs	1472558	r.713g>a	0.333
rrs	1472569	r.724g>a	0.227
rrs	1472571	r.726g>c	0.583
rrs	1472573	r.728c>t	0.250
rrs	1472579	r.734g>t	0.440
rrs	1472581	r.736a>t	0.511
rrs	1472584	r.739a>t	0.245
rrs	1472596	r.751g>t	0.161
rrs	1472598	r.753a>c	0.410
rrs	1472599	r.754g>t	0.241
rrs	1472607	r.762g>a	0.424
rrs	1472612	r.767g>t	0.339
rrs	1472614	r.769g>t	0.130
rrs	1472616	r.771g>a	0.262
rrs	1472634	r.789t>g	0.234
rrs	1472635	r.790g>a	0.237
rpsA	1833554	p.Thr5Ala	1.000
rpsA	1834021	c.480C>T	1.000
rpsA	1834030	c.489C>G	1.000
kasA	2518459	c.345T>C	1.000
kasA	2518462	c.348A>C	1.000
kasA	2518468	c.354A>C	1.000
kasA	2518474	c.360G>A	1.000
kasA	2518480	c.366T>C	1.000
kasA	2518483	c.369C>G	1.000
kasA	2518504	c.390T>C	1.000
embC	4240780	c.918T>C	1.000
embC	4240783	c.921G>C	1.000
embC	4240789	c.927T>C	1.000
embC	4240819	c.957A>G	1.000
embC	4240828	c.966G>A	1.000
embC	4240831	c.969T>G	1.000
embC	4241038	c.1176G>C	1.000
embC	4241089	c.1227C>G	1.000
embC	4241770	c.1908T>C	1.000
embC	4241791	c.1929G>C	1.000
embC	4241794	c.1932C>G	1.000
embC	4241797	c.1935C>T	1.000
embC	4241809	c.1947A>C	1.000
embC	4242859	c.2997C>T	1.000
embC	4242862	c.3000A>G	1.000
embC	4242863	p.Tyr1001Asn	1.000
embC	4242883	c.3021C>G	1.000
embC	4242892	c.3030G>C	1.000
embC	4242901	c.3039G>C	1.000
embC	4242919	c.3057A>G	1.000
embA	4244585	c.1353A>G	1.000
embA	4244670	p.Ala480Leu	1.000
embA	4244675	c.1443A>G	1.000
embA	4244678	c.1446G>C	1.000
embA	4244681	c.1449A>C	1.000
embA	4244690	c.1458G>A	1.000
embA	4244702	c.1470C>G	1.000
embA	4244708	c.1476C>G	1.000
embA	4245137	c.1905T>C	1.000
embA	4245146	c.1914G>A	1.000
embA	4245149	c.1917C>G	1.000
embA	4245153	p.Ile641Val	1.000
embA	4245182	c.1950T>C	1.000
embA	4245198	p.Leu656Ile	1.000
embA	4245207	c.1975T>C	1.000
embA	4245215	c.1983A>C	1.000
embA	4245222	p.Tyr664Gln	1.000
embA	4245248	c.2016G>C	1.000
embA	4245257	c.2025A>G	1.000
embB	4247866	c.1353G>C	0.400
embB	4247875	c.1362G>C	0.273
embB	4247876	c.1363C>T	0.273
embB	4248304	c.1791G>C	1.000
embB	4248316	c.1803C>G	1.000

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	R	rrs r.462c>t (0.75)
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage²	Family	Main Spoligotype	RDS
lineage4.3	Euro-American (LAM)	mainly-LAM	None