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: 5cc80fac484a1

Date: Tue Apr 30 10:08:01 2019

Strain: root

Drug-resistance: Sensitive

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid

Rifampicin

Ethambutol

Pyrazinamide

Streptomycin

Ethionamide

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrB	5452	c.213G>A	1.000
gyrB	6454	c.1215C>T	1.000
gyrA	7362	p.Glu21Gln	1.000
gyrA	7585	p.Ser95Thr	1.000
gyrA	7835	c.534A>G	0.987
gyrA	8714	c.1413A>G	1.000
gyrA	9143	c.1842T>C	1.000
gyrA	9304	p.Gly668Asp	1.000
rpoB	762689	c.2883G>A	1.000
rpoB	763031	c.3225T>C	1.000
rpoC	763375	c.6C>A	1.000
rpoC	763660	c.291T>C	1.000
rpoC	764134	c.765C>G	1.000
rpoC	764152	c.783C>T	1.000
rpoC	764159	c.790C>T	1.000
rpoC	764278	c.909A>G	1.000
rpoC	764287	c.918C>T	1.000
rpoC	764293	c.924G>A	1.000
rpoC	764365	c.996C>T	1.000
rpoC	764405	c.1036A>C	1.000
rpoC	764497	c.1128A>G	1.000
rpoC	764506	c.1137C>T	1.000
rpoC	764510	c.1141C>T	1.000
rpoC	764521	c.1152T>C	1.000
rpoC	764533	c.1164C>T	1.000
rpoC	764536	c.1167G>C	1.000
rpoC	764539	c.1170C>G	0.992
rpoC	764554	c.1185C>T	1.000
rpoC	764575	c.1206T>G	1.000
rpoC	764578	c.1209C>G	1.000
rpoC	764626	c.1257C>T	1.000
rpoC	764632	c.1263T>G	0.993
rpoC	764650	c.1281G>C	1.000
rpoC	764651	c.1282T>A	1.000
rpoC	764752	c.1383G>C	1.000
rpoC	764761	c.1392C>T	1.000
rpoC	765082	c.1713G>A	1.000
rpoC	765220	c.1851A>G	1.000
rpoC	765409	c.2040T>C	1.000
rpoC	765478	c.2109T>C	1.000
rpoC	765637	c.2268C>G	1.000
rpoC	766010	c.2641T>A	1.000
rpoC	766900	c.3531T>C	1.000
rpoC	766945	c.3576A>G	1.000
rpoC	767030	c.3661C>T	1.000
rpoC	767062	c.3693C>A	1.000
Rv0678	779283	c.294C>T	1.000
Rv0678	779295	c.306T>C	1.000
Rv0678	779431	p.Asn148Gln	1.000
Rv0678	779452	p.Gly155Arg	1.000
Rv0678	779472	c.483C>T	1.000
rpsL	781395	c.-165T>C	1.000
rpsL	781875	p.Gly106Ser	1.000
rplC	800946	c.138T>C	1.000
rplC	801109	p.Leu101Val	1.000
embR	1416222	p.Phe376Leu	0.223
embR	1416234	p.Cys372Gly	0.253
embR	1417294	c.54T>C	1.000
embR	1417454	c.-107C>A	1.000
embR	1417474	c.-127C>T	1.000
embR	1417554	c.-207C>G	1.000
rrs	1471845	c.-1G>GT	0.976
rrl	1473403	c.-255C>T	1.000
rrl	1473749	r.92a>g	1.000
rrl	1474777	r.1120t>c	1.000
inhA	1674816	c.615T>C	1.000
rpsA	1833381	c.-161T>C	1.000
rpsA	1834912	c.1371A>G	1.000
tlyA	1917972	c.33A>G	1.000
katG	2154724	p.Arg463Leu	1.000
katG	2156055	c.57G>A	1.000
pncA	2289104	c.138T>C	1.000
kasA	2518132	c.18C>T	1.000
kasA	2519287	c.1173T>C	1.000
eis	2714628	c.705T>G	1.000
folC	2746174	c.1425T>G	1.000
folC	2746425	p.Ala392Thr	1.000
folC	2746451	p.Gly383Ala	1.000
folC	2747374	c.225C>T	1.000
folC	2747549	p.Val17Ala	1.000
folC	2747572	c.27A>G	1.000
folC	2747575	c.24C>G	1.000
ribD	2986929	p.Leu31Phe	1.000
thyX	3067239	p.Ala236Asp	1.000
thyA	3073782	c.690T>C	1.000
thyA	3074160	c.312T>C	1.000
thyA	3074238	c.234G>A	1.000
thyA	3074247	c.225G>A	1.000
ald	3086788	c.-32T>C	1.000
fbiA	3640935	c.393C>G	1.000
alr	3840527	c.894T>G	1.000
alr	3841199	c.222A>G	1.000
alr	3841419	p.Val1Ala	1.000
alr	3841524	c.-104G>A	1.000
alr	3841531	c.-111A>G	1.000
alr	3841532	c.-112A>G	1.000
alr	3841539	c.-119C>T	1.000
alr	3841546	c.-126C>G	1.000
alr	3841568	c.-148G>A	1.000
alr	3841662	c.-242A>G	0.201
alr	3841663	c.-243G>A	0.193
embC	4240671	p.Thr270Ile	1.000
embC	4242643	c.2781C>T	1.000
embA	4243377	p.Ser49Arg	1.000
embA	4243690	p.Met153Thr	1.000
embA	4243919	c.687G>A	1.000
embA	4244154	p.Thr308Pro	1.000
embA	4244312	c.1080T>G	1.000
embA	4245023	c.1791A>G	1.000
embA	4245701	c.2469G>T	0.990
embB	4246584	p.Arg24Pro	0.300
embB	4247646	p.Glu378Ala	1.000
embB	4248206	p.Ser565Gly	1.000
ethA	4327546	c.-73T>CT	0.929
ethR	4327830	c.282C>T	1.000
gid	4407588	c.615T>C	1.000
gid	4408185	c.18G>A	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
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin