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: 5d760e16ab83a

Date: Mon Sep 9 09:34:28 2019

Strain: lineage4.2.2

Drug-resistance: MDR

Drug¹ Resistance Supporting Mutations (frequency)

Isoniazid R katG p.Ser315Thr (1.00)

Rifampicin R rpoB p.Ser450Leu (0.99)

Ethambutol R embB p.Gly406Ala (1.00), embB p.Asp1024Asn (1.00)

Pyrazinamide R pncA p.Val130Gly (1.00)

Streptomycin R rpsL p.Lys88Thr (0.99)

Ethionamide R ethA p.Met1Arg (1.00)

Fluoroquinolones

Amikacin

Capreomycin

Kanamycin

Lineage² Family Main Spoligotype RDS

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

lineage4.2 Euro-American H;T;LAM None

lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None

Mutations in candidate genes:

Gene	Chromosome Position	Mutation	Estimated fraction
gyrA	7362	p.Glu21Gln	1.000
gyrA	7585	p.Ser95Thr	1.000
gyrA	8688	p.Ala463Ser	1.000
gyrA	9304	p.Gly668Asp	1.000
rpoB	761489	c.1683G>A	1.000
rpsL	781395	c.-165T>C	1.000
embR	1416222	p.Phe376Leu	0.183
embR	1416234	p.Cys372Gly	0.220
rrs	1472137	r.292g>a	0.143
rrs	1472150	r.305t>a	0.162
rrs	1472151	r.306c>t	0.162
rrs	1472172	r.327t>c	0.183
rrs	1472203	r.358g>a	0.154
rrs	1472259	r.414c>a	0.120
rrs	1472379	r.534t>c	0.145
rrs	1472400	r.555c>t	0.155
rrs	1472530	r.685g>a	0.116
rrs	1472537	r.692c>t	0.123
rrs	1472566	r.721g>a	0.120
rrs	1472571	r.726g>c	0.127
rrs	1472655	r.810g>a	0.125
rrs	1472660	r.815t>c	0.119
rrs	1472714	r.869a>g	0.169
rrs	1472790	r.945t>c	0.140
rrs	1472895	r.1050c>t	0.237
rrs	1472956	r.1111t>c	0.134
rrs	1472990	r.1145a>g	0.208
rrs	1473035	r.1190g>a	0.290
rrs	1473055	r.1210c>t	0.190
rrs	1473056	r.1211a>t	0.306
rrs	1473066	r.1221a>g	0.194
rrs	1473081	r.1236c>t	0.125
rrs	1473177	r.1332g>a	0.143
rrs	1473192	r.1347a>g	0.185
rrs	1473205	r.1360t>c	0.186
rrs	1473252	r.1407t>c	0.155
rrs	1473259	r.1414c>t	0.158
rrs	1473352	r.1507c>t	0.117
rrl	1474249	r.592g>t	0.228
rrl	1474310	r.653t>g	0.145
rrl	1474348	r.691c>t	0.137
rrl	1474351	r.694g>t	0.143
rrl	1474362	r.705a>g	0.130
rrl	1474387	r.730c>t	0.122
rrl	1474626	r.969t>c	0.123
rrl	1474634	r.977t>c	0.170
rrl	1474636	r.979a>c	0.184
rrl	1474637	r.980c>t	0.200
rrl	1474638	r.981c>g	0.204
rrl	1474640	r.983c>t	0.192
rrl	1474675	r.1018c>g	0.148
rrl	1474677	r.1020a>g	0.150
rrl	1474709	r.1052g>a	0.138
rrl	1474734	r.1077g>t	0.140
rrl	1474779	r.1122g>a	0.123
rrl	1474780	r.1123c>t	0.123
rrl	1474782	r.1125g>a	0.123
rrl	1474794	r.1137c>t	0.164
rrl	1474802	r.1145t>c	0.154
rrl	1474823	r.1166c>g	0.176
rrl	1474830	r.1173a>g	0.161
rrl	1474831	r.1174a>g	0.167
rrl	1474832	r.1175a>t	0.164
rrl	1474864	r.1207c>t	0.237
rrl	1474901	r.1244a>g	0.194
rrl	1474904	r.1247g>c	0.274
rrl	1474913	r.1256t>c	0.203
rrl	1474933	r.1276a>g	0.175
rrl	1474934	r.1277c>t	0.161
rrl	1475129	r.1472g>t	0.149
rrl	1475499	r.1842c>t	0.135
rrl	1475526	r.1869c>t	0.157
rrl	1475539	r.1882a>t	0.163
rrl	1475545	r.1888t>g	0.163
rrl	1475548	r.1891c>t	0.125
rrl	1475573	r.1916g>t	0.167
rrl	1475777	r.2120a>t	0.133
rrl	1475803	r.2146t>c	0.162
rrl	1475804	r.2147g>c	0.149
rrl	1475816	r.2159c>g	0.153
rrl	1475817	r.2160a>g	0.172
rrl	1475858	r.2201t>c	0.149
rrl	1475866	r.2209t>a	0.141
rrl	1475883	r.2226a>c	0.157
rrl	1475884	r.2227a>g	0.138
rrl	1475896	r.2239a>g	0.119
rrl	1475898	r.2241a>g	0.200
rrl	1475899	r.2242g>a	0.203
rrl	1475916	r.2259c>g	0.170
rrl	1475937	r.2280a>t	0.184
rrl	1475943	r.2286g>a	0.243
rrl	1475945	r.2288c>a	0.216
rrl	1475952	r.2295a>g	0.200
rrl	1475970	r.2313c>t	0.148
rrl	1475975	r.2318c>t	0.148
rrl	1476131	r.2474c>t	0.174
rrl	1476179	r.2522c>t	0.222
rrl	1476194	r.2537a>g	0.257
rrl	1476200	r.2543a>t	0.289
rrl	1476201	r.2544c>t	0.211
rrl	1476204	r.2547c>t	0.222
rrl	1476221	r.2564t>c	0.167
rrl	1476224	r.2567a>g	0.250
rrl	1476227	r.2570c>t	0.211
rrl	1476245	r.2588c>t	0.175
rrl	1476260	r.2603a>g	0.175
rrl	1476359	r.2702c>g	0.262
rrl	1476372	r.2715t>c	0.123
rrl	1476381	r.2724g>c	0.302
rrl	1476425	r.2768g>t	0.151
rrl	1476428	r.2771c>t	0.306
rrl	1476429	r.2772a>t	0.200
rrl	1476466	r.2809c>t	0.234
rrl	1476481	r.2824t>c	0.464
rrl	1476506	r.2849t>c	0.500
rrl	1476567	r.2910c>t	0.132
tlyA	1917972	c.33A>G	1.000
ahpC	2726146	c.-47G>GT	0.949
ald	3086788	c.-32T>C	1.000
alr	3841652	c.-232A>T	0.294
alr	3841654	c.-234A>C	0.333
alr	3841662	c.-242A>G	0.406
alr	3841663	c.-243G>A	0.377
embC	4242643	c.2781C>T	1.000
gid	4407997	p.Gly69Asp	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	R	katG p.Ser315Thr (1.00)
Rifampicin	R	rpoB p.Ser450Leu (0.99)
Ethambutol	R	embB p.Gly406Ala (1.00), embB p.Asp1024Asn (1.00)
Pyrazinamide	R	pncA p.Val130Gly (1.00)
Streptomycin	R	rpsL p.Lys88Thr (0.99)
Ethionamide	R	ethA p.Met1Arg (1.00)
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage²	Family	Main Spoligotype	RDS
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.2	Euro-American	H;T;LAM	None
lineage4.2.2	Euro-American (Ural)	T;LAM7-TUR	None