Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains

Freidlin, Paul Jeffrey; Nissan, Israel; Luria, Anna; Goldblatt, Drora; Schaffer, Lana; Kaidar-Shwartz, Hasia; Chemtob, Daniel; Dveyrin, Zeev; Head, Steven Robert; Rorman, Efrat

doi:10.1186/s12864-017-3560-6

Table 1 Characteristics of NGS sequenced deleted-DR sample strains A, B, C and intact-DR T3_Eth, and whole genome sequences obtained on-line or assembled from on-line read sets#

From: Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains

MTBC Strain, ID	Spoligotype Octal	SIT or RD Family	Drug Res	CRISPR IS6110	mutation in			regions of difference (RD)
MTBC Strain, ID	Spoligotype Octal	SIT or RD Family	Drug Res	CRISPR IS6110	mutT4	T2	ogt	105	207	181	150	142	182	239	750
Beijing
BT1, CP002883	000000000003771	1,Beijing	TDR^a	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
BT2, CP002882	000000000003771	1,Beijing	TDR^a	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
CCDC5079, CP001641	000000000003771	1,Beijing	DS^b	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
CCDC5180, NC_017522.1	000000000003771	1,Beijing	MDR^b	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
HKBS1, CP002871.1	000000000003771	1,Beijing	DS^a	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
Beijing [−like], CP010873.1	000000000003731	190,Beijing	MDR^c	inv	48	58	12	del	del	del	wt	wt	wt	wt	wt
SRR671761	000000000003771	1,Beijing	?^d	unk	48	58	12	del	del	del	del	wt	wt	wt	wt
SRR671726	000000000003770	1,Beijing	XDR^d	unk	48	58	12	del	del	del	wt	wt	wt	wt	wt
B_1042-11	000000000000000	nS,Beijing	DS^e	wt	48	58	12	del	ext	del	wt	wt	wt	wt	wt
B_1114-11	000000000000000	nS,Beijing	DS^e	wt	48	58	12	del	ext	del	wt	wt	wt	wt	wt
Proto-Beijing
SRR1710057	777777777777731	246, U	panS^d	unk	wt	wt	wt	ext	wt	wt	wt	wt	wt	wt	wt
SRR1710058	777777777775331	nS	panS^d	unk	wt	wt	wt	ext	wt	wt	wt	wt	wt	wt	wt
SRR1710061	777777777777771	523, U	panS^d	unk	wt	wt	wt	ext	wt	wt	wt	wt	wt	wt	wt
Non-Beijing
ERR176616	777777607060771	nS	MDR^d	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
ERR190365	000037777403471	nS,EAI	DR^d	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	del	wt
ERR212132	776337777760771	71, S	panS^d	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
SRR671740	777777777760771	53, T1	XDR^d	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
SRR1188186	000000000000000	nS,CAS	panS^d	unk	wt	wt	wt	wt	new	wt	wt	wt	wt	wt	del
A_0389-12	000000000000000	nS,Haarlem	DS^e	wt	wt	wt	15	wt	new	wt	wt	wt	del	wt	wt
A_1124-11	000000000000000	nS,Haarlem	DS^e	wt	wt	wt	15	wt	new	wt	wt	wt	del	wt	wt
C_0253-12	000000000000000	nS,EAI	DS^e	inv	wt	wt	wt	wt	new	wt	wt	wt	wt	del	wt
C_0309-12	000000000000000	nS,EAI	DS^e	inv	wt	wt	wt	wt	new	wt	wt	wt	wt	del	wt
T3_Eth_0140-11	777000377760771	149,T3_Eth	DS^e	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
T3_Eth_0192-11	777000377760771	149,T3_Eth	MDR^e	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
T3_Eth_0525-11	777000377760771	149,T3_Eth	DS^e	unk	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
BCG1173P2, NC_008769.1	676773777777600	482,BCG	DR^f	wt	wt	wt	wt	wt	wt	wt	wt	del	wt	wt	wt
CDC1551, AE000516.2	700076757760771	549,X3	DS^g	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
CTRI-2, CP002992	777777607760771	42,LAM9	DS^g	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
F11, CP000717.1	776177607760771	33,LAM3	DS^g	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt	wt
Haarlem, CP001664	775777774020751	H1-like	DR^g	wt	wt	wt	15	wt	wt	wt	wt	wt	del	wt	wt

^#ID, sample, read set or NCBI accession number; octal, from spoligosome17, SIT, spoligotype international type and associated family; nS, no SIT; Drug Res, resistant to drug, I-isoniazide, R-rifampicin, E- ethanbutol, S-streptomycin, P-pyrazinamide, DS (drug sensitive): none, DR (drug resistant): at least one but not I&R together: MDR (multiple drug resistant): at least I&R, XDR (extensively drug resistant): at least MDR plus defined 2^nd line drugs consisting of at least 1 quinolone and at least one of the injectable drugs kanamycin, capreomycin or amikacin, TDR (totally drug resistant): resistant to all 1^st and 2^nd line drugs. a-g: Additional file 2: List S1 – sources of drug sensitivity data; wt, identical to reference genome H37Rv NC_000962.3; CRISPR IS6110, orientation of the IS6110 mobile element found in the direct repeat region, wt: same orientation as in H37Rv, inv: inverted, unk: unknown; mutation in mutT4 (Rv3908), codon 48: Arg CGG GGG Gly; mutation in mutT2 (Rv1160), codon 58: Gly GGA CGA Arg; mutation in ogt (Rv1316c), silent codon 12: Gly CCC TCC Gly, missense codon 15: Thr GGT GCT Ser (note: ogt gene is in inverse orientation); regions of difference RD, 105: proto and all modern Beijing, 207: LSP in CRISPR region defining modern Beijing – includes cas gene deletions, 181-150-142: polymorphic LSPs for Beijing, 182: marker for Haarlem, 239: marker for EAI, 750: marker for CAS

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ISSN: 1471-2164

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