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Genetic characteristics of Mycobacterium bovis BCG Thai Red Cross Society strain

Wichit Thaveekarn
Wichit Thaveekarn
, 
Sunchai Payungporn
Sunchai Payungporn
, 
Narumol Pakmanee
Narumol Pakmanee
, 
Sunutcha Suntrarachun
Sunutcha Suntrarachun
, 
Suchitra Khunsap
Suchitra Khunsap
 e 
Suthidee Petsong
Suthidee Petsong
   | 31 ago 2017
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Article Category: Brief communication (Original)
Pubblicato online: 31 ago 2017
Pagine: 245 - 254
DOI: https://doi.org/10.5372/1905-7415.1103.555
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© 2017 Wichit Thaveekarn, Sunchai Payungporn, Narumol Pakmanee, Sunutcha Suntrarachun, Suchitra Khunsap, Suthidee Petsong
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Electrophoresis of PCR products of the RD16 region in a 12.5% polyacrylamide gel. Lane 1: BCG TRCS strain working seed lot. BCG TRCS had 2 types of band, the upper is type II (with the 22-bp deletion) and the lower is type I (BCG TRCS is composed of type I and II subpopulations). Lane 2: TB H37Rv was used as a positive control.The far-left lane shows a marker ladder (VC 100bp DNA Ladder, Vivantis) in units of bp.
Electrophoresis of PCR products of the RD16 region in a 12.5% polyacrylamide gel. Lane 1: BCG TRCS strain working seed lot. BCG TRCS had 2 types of band, the upper is type II (with the 22-bp deletion) and the lower is type I (BCG TRCS is composed of type I and II subpopulations). Lane 2: TB H37Rv was used as a positive control.The far-left lane shows a marker ladder (VC 100bp DNA Ladder, Vivantis) in units of bp.

Figure 2

Sequencing and alignment of the RD16 region in the 2 different types of BCG using CLC Genomics Workbench 9 (CLC bio software, Qiagen).
Sequencing and alignment of the RD16 region in the 2 different types of BCG using CLC Genomics Workbench 9 (CLC bio software, Qiagen).

Figure 3

RD16 region alignment of BCG Tokyo172 (type I), TB H37Rv, and BCG TRCS (type I) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).
RD16 region alignment of BCG Tokyo172 (type I), TB H37Rv, and BCG TRCS (type I) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).

Figure 4

16S rRNA sequence alignment analysis of the BCG TRCS strain (CP014566) and BCG Tokyo 172 (AP010918) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).
16S rRNA sequence alignment analysis of the BCG TRCS strain (CP014566) and BCG Tokyo 172 (AP010918) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).

Figure 5

Analysis of ppsA gene alignment between the BCG TRCS strain (CP014566) and BCG Tokyo type II (AB665170) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).
Analysis of ppsA gene alignment between the BCG TRCS strain (CP014566) and BCG Tokyo type II (AB665170) using CLC Genomics Workbench 9 (CLC bio software, Qiagen).

Different points of amino acids between the BCG TRCS strain (CP014566) and BCG Tokyo 172 (AP010918) found by next-generation sequencing.

No.GeneGene positionDifference of amino acid positionNo.GeneGene positionDifference of amino acid positionNo.GeneGene positionDifference of amino acid position
1PE_PGRS3a331866–56710PE_PGRS20.21193553–1,4,11–14,18,17PE_PGRS2761378–49–51,53,
334616119475820–22,25,30,33,43a276280557–59,61,
36,39–41,43–17,79,82,85–
49–50,52,56,59,87,90,92–
65,68–71,74–75,93,97
80,83–84,86,90,
94–96
2PE_PGRS4337829–2531116S rRNA1471256–Nonprotein coding18Lhr3621834–796
34033314727923626375
3JTY_0628707570–18512PE_PGRS301840495–455–156,458–19sdliB3693240–88
7081751843551459,463,465,3694031
467–168,473
4PE_PGRS10840318–25513wag22b1973263–50020JTY 33963700080–Protein
84299925819756743700778pattern
changes
5JTY_09771066242–4–514PE_PGRS412650648–21821PE_PGRS3908313–515,520,
10670992651730543914465537,561, 564,570
6PE_PGRS161092510–441–442,457,15rpfE2709525–Protein pattern22PE_PGRS3923290–654,656–
1094003482,485–486,2710121changes573925359659,661–
491–497683
7PEPGRS161093960–Protein pattern16PE_PGRS43b2757960–Protein pattern23JTY_37534105089–178,214
1095282changes2761286changes4106411
8PE_PGRS191190568–256,265,268,
1192583277,302
9PE_PGRS20.11192916–197,201,203–
1193530205

Comparison of single nucleotide polymorphisms between BCG TRCS strain (CP014566) and BCG Tokyo 172 (AP010918).

GenePositionBCG 172 Tokyio
ThaiJapanese
GenBank: CP014566GenBank: AP010918
pckA253,186AA
JTY_0567644,562TT
rpoC765,342CC
Intergenic2,717,585CC
JTY_32783,606,131GG
JTY_37354,087,391GG

Seven regions of difference (RDs) in the variable-number tandem repeat (VNTR) locus of the BCG TRCS strain.

RD in VNTR locusSequence from 5’→3’Number of repeats
0557/intergenic (Rv0487–Rv0488) (ETR-C)GTCGAGCCCGACGACGATGCAGAGCGCGCAGCGCGATGAGAAGGAGTTGGGCGGTTAG (58 bp) 3
0580/intergenic (Rv0490–Rv0491) (senX3–regX3)TGCGCCGACGACGATGCAGAGCGTAGCGATGAGGTGGGGGCACCACCCGCTTGCGGGGGAGAGTGGCGCTGATGACC (77 bp) 3
3155/intergenic (Rv2847c–Rv2848c)CGACCCGCGGCGCCCGGTCCCCGCGCTTGCGATCGCCACTGGCCCTGATGGTGG (54 bp) 4
3336/intergenic(Rv2980-Rv2981c)TGCGCCGGGCGCGGCGGGTCGGCACCATCGGGCTAAGTGCCGATCGCAAGCGCGGCGCT (177 bp = 59 bpx3) 6
3820/intergenic (Rv3401–Rv3402c)CGATGCGGGCCGCGTAGCGGCCCGAGGAGGAGCCGGGCAATCCAGCCTGAGCCCGGTGA (59 bp) 3
4052 (Rv3611)CCATCAGCCCCGTGGCGATCGCAAACCCCGCGCCTGGCGACAATGCGGCCCGCAAAACGGGCCGAGGAGGAGCCAGGCAATCACCCCAGAGCCGGGTGCAGCGGGTCGCCA (111 bp) 4
4155(Rv3710:leuA)TCGCGAGCCCGGCGCAGCCGGGCGAAGCGGGTCGGCACGCATCGGACCCCGTGACGA (57 bp) 11
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