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Asadian M, Hassanzadeh SM, Safarchi A, Douraghi M. Genomic characteristics of two most widely used BCG vaccine strains: Danish 1331 and Pasteur 1173P2. BMC Genomics 2022; 23:609. [PMID: 35987561 PMCID: PMC9392950 DOI: 10.1186/s12864-022-08826-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022] Open
Abstract
Background Bacillus Calmette–Guérin (BCG) refers to a group of vaccine strains with unique genetic characteristics. BCG is the only available vaccine for preventing tuberculosis (TB). Genetic and biochemical variations among the BCG vaccine strains have been considered as one of the significant parameters affecting the variable protective efficacy of the vaccine against pulmonary tuberculosis. To track genetic variations, here two vaccine strains (Danish 1331 and Pasteur 1173P2) popularly used according to the BCG World Atlas were subjected to a comparative analysis against the Mycobacterium tuberculosis H37Rv, Mycobacterium bovis AF2122/97, and Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 reference genomes. Besides, the presence or absence of the experimentally verified human T cell epitopes was examined. Results Only two variants were identified in BCG Danish 1331 that have not been reported previously in any BCG strains with the complete submitted genome yet. Furthermore, we identified a DU1-like 14,577 bp region in BCG Danish 1331; The duplication which was previously seemed to be exclusive to the BCG Pasteur. We also found that 35% of the T cell epitopes are absent from both strains, and epitope sequences are more conserved than the rest of the genome. Conclusions We provided a comprehensive catalog of single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) in BCG Danish 1331 and BCG Pasteur 1173P2. These findings may help determine the effect of genetic variations on the variable protective efficacy of BCG vaccine strains. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08826-9.
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Asadian M, Safarchi A, Hassanzadeh SM, Yaseri M, Douraghi M. Genomic evidence for stability of the Bacillus Calmette-Guérin (BCG) vaccine strain (Pasteur 1173P2) from different batches in Iran. J Appl Microbiol 2021; 132:2379-2388. [PMID: 34787956 DOI: 10.1111/jam.15365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/30/2022]
Abstract
AIMS Investigate the genetic stability of the BCG vaccine produced in Iran from different batches compared to the reference strain. METHODS AND RESULTS We comparatively analyzed the whole genome sequences of the vaccine batches from different years. Eleven vials of different batches from 2010, 2018, and 2019 were included. Complete genome analyses revealed no difference between the old (2010) and new (2018 and 2019) vaccine batches. Additionally, minor genetic changes include five single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were observed compared to the BCG Pasteur 1173P2 reference strain, which were shared among all batches. Besides, the batches were identical to the reference strain in terms of antibiotic resistance genes, prophage sequences, and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems. CONCLUSIONS High genetic stability of the BCG vaccine used in the national immunization program was confirmed, which indicates the optimal conditions in the vaccine production process. SIGNIFICANCE AND IMPACT OF THE STUDY Genetic differences within and between vaccine strains have been declared as one of the main parameters related to the BCG vaccine variable protective efficacy. No study has been done to investigate the genetic variations of the vaccine batches at the single-base level.
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Affiliation(s)
- Mahla Asadian
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Mehdi Yaseri
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC. Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. BMC Genomics 2019; 20:561. [PMID: 31286858 PMCID: PMC6615170 DOI: 10.1186/s12864-019-5909-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.
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Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Petra Tiels
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Annelies Van Hecke
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Evelyn Plets
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Gitte Michielsen
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
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Voronina OL, Kunda MS, Aksenova EI, Semenov AN, Ryzhova NN, Lunin VG, Gintsburg AL. Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequences' mobility. BMC Genomics 2016; 17:1009. [PMID: 28105923 PMCID: PMC5249017 DOI: 10.1186/s12864-016-3355-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The control of genome stability is relevant for the worldwide BCG vaccine preventing the acute forms of childhood tuberculosis. BCG sub-strains whole genome comparative analysis and revealing the triggers of sub-strains transition were the purpose of our investigation. RESULTS Whole genome sequencing of three BCG Russia seed lots (1963, 1982, 2006 years) confirmed the stability of vaccine sub-strain genome. Comparative analysis of three Mycobacteruim bovis and nine M. bovis BCG genomes shown that differences between "early" and "late" sub-strains BCG genomes were associated with specific prophage profiles. Several prophages common to all BCG genomes included ORFs which were homologues to Caudovirales. Surprisingly very different prophage profiles characterized BCG Tice and BCG Montreal genomes. These prophages contained ORFs which were homologues to Herpesviruses. Phylogeny of strains cohort based on genome maps restriction analysis and whole genomes sequence data were in agreement with prophage profiles. Pair-wise alignment of unique BCG Tice and BCG Montreal prophage sequences and BCG Russia 368 genome demonstrated only similarity of fragmetary sequences that suggested the contribution of prophages in genome mosaic structure formation. CONCLUSIONS Control of the extended sequences is important for genome with mosaic structure. Prophage search tools are effective instruments in this analysis.
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Affiliation(s)
- Olga L. Voronina
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Marina S. Kunda
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Ekaterina I. Aksenova
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Andrey N. Semenov
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Natalia N. Ryzhova
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Vladimir G. Lunin
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
| | - Alexandr L. Gintsburg
- N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia
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Correction: Genomic analysis of a Mycobacterium bovis bacillus Calmette-Guérin strain isolated from an adult patient with pulmonary tuberculosis. PLoS One 2015; 10:e0129753. [PMID: 26024365 PMCID: PMC4449214 DOI: 10.1371/journal.pone.0129753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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