Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

Katale, Bugwesa Z.; Mbelele, Peter M.; Lema, Nsiande A.; Campino, Susana; Mshana, Stephen E.; Rweyemamu, Mark M.; Phelan, Jody E.; Keyyu, Julius D.; Majigo, Mtebe; Mbugi, Erasto V.; Dockrell, Hazel M.; Clark, Taane G.; Matee, Mecky I.; Mpagama, Stellah

doi:10.1186/s12864-020-6577-1

Table 5 Description of lineages, spoligotype, cluster of drug resistance M. tuberculosis and genotype at important drug loci

From: Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

Isolate ID	Lineages	Spoligotype	WGS cluster	Genotype at drug loci
				RIF	ZN	AMK	PZ	FLR	AMG	EMB		ST
				rpoB	katG	rrs	pncA	gyrB	rrs	embB	embC-embA	rpsL_	rrs
1	lineage3	CAS	MDR	S450L	S315T		Large deletion pncA Rv2044c
7	lineage3	CAS	MDR	S450L	S315T
11	lineage4	LAM	DR				D8N
20	lineage4	LAM	DR	D435Y
38	lineage3	CAS	MDR	S450L	N138S					M306V, Q497R, G406A
42	lineage3	CAS	DR		S315T
51	lineage4	LAM	DR		S315T
52	lineage1	EAI	DR		S315T					Y319C
63	lineage3	CAS	MDR	S450L	S315T					M306I
71	lineage3	CAS	DR		S315T		G17D			Q497R
75	lineage3	CAS	DR		S315T					G406D
81	lineage4	LAM	DR		S315T		L85P			G406S, M306I
82	lineage3	CAS	MDR	S450L	S315T		V128G			M306L
85	lineage3	CAS	MDR	S450L	S315T	C517T			C517T	G406A			C517T
92	lineage4	LAM	DR		S315T					Q497R, G406S
98	lineage4	LAM	DR		S315T
104	lineage4	LAM	DR		S315T
106	lineage4	LAM	MDR	S450L	S315T		Q10R
110	lineage4	LAM	DR		S315T
111	lineage4	LAM	DR		S315T
115	lineage4	LAM	DR		S315T, S302R
130	lineage 4	LAM	MDR	S450L	S315T
143	lineage 4	LAM	DR		S315T						C16T
144	lineage 4	CAS	MDR	S450L	S315T
146	lineage 3	CAS	MDR	S450L	S315T		V128G
151	lineage 3	CAS	MDR	S450L	S315T		V128G			Q497R
100-S17	lineage 3	CAS	MDR	S450L	S315T		V128G			Q497R
101-S16	lineage 4	LAM	MDR	S450L	S315T, S302R		D49G			Q497R
113-S15	lineage 4	LAM	DR		S315T
114-S19	lineage 4	LAM	MDR	S450L	S315T		D63A
132_S10	lineage 4	LAM	DR		S315T
134_S8	lineage 3	CAS	MDR	S450L	S315T					G406S
137-S22	lineage2	Beijing	MDR	S450L	S315T			R446C
139-S17	lineage 1	EAI	DR
140-S21	lineage1	EAI	DR		OxyR-ahpC, C52T, large deletion, S315T		A193AT
141-S1	lineage 4	LAM	DR		S315T		Large, deletion, pncA-Rv2044c
145-S11	lineage 2	Beijing	MDR	S450L	S315T		P69L			M306T, G406A		K43R
17-S14	lineage 4	LAM	DR		S315T
301-S24	lineage 3	CAS	MDR	S450L	S315T	C517T	A46V		C517T	M306G, G406S
342-S10	lineage 3	CAS	DR		S315T					G406S
43-S19	lineage4	LAM	DR		S315T
44-S20	lineage 3	CAS	DR		S315T
50-S18	lineage 3	CAS	MDR	S450L	S315T		V128G			Y334H,	C16T
56-S6	lineage 4	LAM	DR		S315T
60-S3	lineage 4	LAM	DR	S450L
73-S5	lineage3	CAS	DR	S450L
78-S15	lineage4	LAM	DR		S315T
79-S12	lineage4	LAM	DR		S315T						C16T
80-S3	lineage3	CAS	DR							M306I	C16T
89-S18	lineage4	LAM	MDR	S450L	S315T
90-S23	lineage 3	CAS	MDR	S450L	S315T		V128G			Q497R, M306V
91-S8	lineage 3	CAS	MDR	S450L	S315T		V128G,			Q497R
94-S14	lineage 3	CAS	MDR	S450L	S315T
96-S11	lineage1	EAI	MDR	S450L	S315T
99-S4	lineage 4	LAM	DR		S315T
S23	lineage		DR		S315T						C16T	K43R
S9	lineage 3	CAS	DR		S315T

RIF Rifampicin, INH Isoniazid, AMK Amikacin, PZ Pyrazinamide, FLR Fluoroquinolones, AMG Aminoglycosides, EMB Ethambutol, ST Streptomycin

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