Curated Database of Drug Resistance Mutations in TB

Following review of available data, a library of mutations predictive of drug resistance was compiled. First, mutations from two publically available web-based tools TBDreaMDB [18 (link)] and MUBII-TB-DB [19 (link)] were extracted. Second, phylogenetic SNPs at drug resistance loci were removed (see Additional file 1: Table S2 for the full list), as they have been historically misclassified as drug resistance markers [20 (link),21 (link)]. And third, recent literature was consulted to include mutations and loci not described in TBDreaMDB and MUBII-TB-DB. (See Additional file 1: Table S1 for a list of source materials). Drugs included were amikacin (AMK), capreomycin (CAP), ethambutol (EMB), ethionamide (ETH), isoniazid (INH), kanamycin (KAN), moxifloxacin (MOX), ofloxacin (OFX), pyrazinamide (PZA), rifampicin (RMP), streptomycin (STR), para-aminosalicylic acid (PAS), linezolid (LZD), clofazimine (CFZ) and bedaquiline (BDQ). As presented in Table 1, the library comprised 1,325 polymorphisms (SNPs and indels) at 992 nucleotide positions from 31 loci, six promoters and 25 coding regions (see [22 ] for full list). In addition to examining individual drugs we considered the cumulative loci for MDR- and XDR-TB. Circos software [23 (link)] was used to construct circular genomic region variation maps. Polymorphisms associated with MDR- and XDR-TB are shown in Figure 1 (See Additional file 1: Figure S1 for full details).Table 1

Summary of mutations included in the curated whole genome drug resistance library

Drug	Loci	No. variable sites	SNPs	Indels
INH	katG	241	286	25
	katG promoter	3	3	0
	inhA	12	15	0
	inhA promoter	9	11	0
	ahpC	8	8	0
	ahpC promoter	13	14	0
	kasA	8	11	0
RMP	rpoB	89	135	19
	rpoC	8	8	0
EMB	embB	123	153	1
	embA	5	5	0
	embA promoter	3	3	0
	embC	25	26	0
	embR	22	24	0
STR	rrs	21	25	0
	rpsL	14	19	0
PZA	pncA	215	269	64
	pncA promoter	4	6	0
	rpsA	3	4	0
	panD	9	11	1
ETH	ethA	33	29	5
	ethR	3	4	0
	inhA promoter	3	3	0
	inhA	3	3	0
FLQs	gyrA	15	22	0
	gyrB	22	29	0
AMK	rrs	8	9	0
CAP	rrs	3	4	0
	tlyA	26	18	10
KAN	rrs	3	4	0
	eis promoter	9	10	0
PAS	thyA	23	17	5
	folC	16	19	0
	ribB	1	1	0
LZD	rrl	2	2	0
	rplC	1	1	0
BDQ CFZ	Rv0678	7	5	2

AMK, amikacin; BDQ, bedaquiline; CAP, capreomycin; CFZ, clofazimine; EMB, ethabutol; ETH, ethionamide; FLQs, fluoroquinolones; INH, isoniazid; KAN, kanamycin; LZD, linezolid; PAS, para-aminosalycylic acid; PZ, pyrazinamide; RMP, rifampicin; STR, streptomycin.

Figure 1

Polymorphism in the curated library used for predicting multi-drug resistant TB (MDR-TB) and extensive-drug resistant TB (XDR-TB). (A) Polymorphisms associated with MDR-TB. (B) Polymorphisms associated with XDR-TB. Colour-coded bars in the Circos plot represent genes described to be involved in drug resistance (from Table 1). On top of each of these bars a grey histogram shows the mutation density (calculated as the number of polymorphic sites within windows of 20 bp) derived from the curated list of DR-associated mutations. These grey areas highlight the presence of DR-associated regions in candidate genes, which in some cases span the whole gene (for example, katG) or are confined to a certain region of the gene (for example, rpoB). Vertical black lines indicate the frequency of mutations (that is, the number of times the mutation has been observed) in phenotypically resistance isolates. Internal black lines show co-occurring mutations both within and between genes. The thickness of these lines is proportional to the frequency of the mutations appearing together.