Newly sequenced genomes of four Bacillus Calmette Guerin vaccines  

Mycobacterium bovis Bacillus Calmette Guerin, commonly known as BCG, is the only vaccine against tuberculosis. The original BCG strain was obtained by serial passages of a M. bovis strain in potato-bile media.⁽¹⁾ Deletion of the region of difference (RD) 1 was later confirmed as one of the reasons for the attenuation of its virulence.^{(2, 3)} After its first use in humans, the vaccine was sent to different laboratories worldwide where different culturing conditions originated strains with different genetic compositions.⁽⁴⁾

At present, there are more than 10 different vaccine strains being administered worldwide.⁽⁵⁾ In two countries in Latin-America, namely Venezuela and Argentina, the strains BCG Danish 1331 (Statens serum Institut, Denmark), BCG Pasteur 1173P2 (Instituto Nacional de Producción de Biológicos ― ANLIS Carlos G Malbrán, Argentina) and BCG Sofia SL222 (BB NCIPD Ltd, Bulgaria) are licensed for use. The vaccine BCG Pasteur produced in Argentina is a secondary seed lot of the French BCG Pasteur strain 1173P2 and is administered in the Province of Buenos Aires, while the rest of the country is vaccinated either with the Sofia or the Danish strain. In Brazil, BCG Moreau RDJ (Fundação Ataulpho de Paiva, Brazil) was used as a vaccine until 2017, when it was replaced by the Russian strain.

Whole genome sequencing data of the strains Moreau, Pasteur and Danish are already available^{(6, 7, 8)}and obtained either by using shotgun sequencing and specific primers designed to close the gaps in the assembly (for Moreau and Pasteur strains) or a combination of Illumina and PacBio technology (for the Danish strain). BCG Sofia has so far only been subjected to whole genome analysis using microarrays.⁽⁹⁾ We sequenced the genome of these four vaccine strains with Illumina technology in an effort to update the sequencing data available and for BCG Sofia, we report the first sequence data obtained with newer technology.

Genome sequencing of the four vaccine strains was performed using the Nextera XT DNA Library preparation kit on an Illumina HiSeq 2500 platform. De novo assembly was done using Unicycler⁽¹⁰⁾ and annotated with RAST.⁽¹¹⁾ To determine intra-strain genomic variability of each vaccine, we compared the genomes with previous assemblies obtained from the NCBI^{(6, 7, 8)} using the software Artemis Comparison tool⁽¹²⁾ and Snippy.⁽¹³⁾ The strain BCG Sofia SL222 originated from the Russian vaccine BCG-1 and was chosen as a master seed at the BCG Bulgarian laboratory.⁽⁹⁾ Because there is no whole genome assembly available for BCG Sofia SL222, we decided to use the assembly of its parental strain BCG-1 Russia for the comparative studies.⁽¹⁴⁾

Among the four genomes, we obtained between 82 and 108 contigs, an average guanine-cytosine content (GC) of 65%, a size ranging between 4.2 and 4.3 Mb and the number of coding sequences (CDS) between 4205 and 4245 (Table I). The differences in the size of BCG strains genomes we noticed when compared to those available in public databases is probably due to variation in sequencing technologies and of assemblers used.

The genome of BCG Moreau RDJ strain revealed 55 single nucleotide polymorphisms (SNPs) compared to that of the shotgun sequencing based genome of the same strain obtained in 2011, 28 of these SNPs are non-synonymous (ns) (Table II). We also detected five insertions and four deletions of 3-4 nucleotides (data not shown) and an inverted IS1608 transposase gene (position 3717335-3717826 bp).

Upon sequencing BCG Sofia SL222 and after comparison with the BCG-1 Russian strain, we observed one synonymous (s) SNP in the gene coding for an uridylyltransferase, in addition to three inverted regions of 42,965 bp, 17,778 bp and 6,765 bp in length. Furthermore, by mapping the reads obtained from the Sofia strain to the genome of the Danish vaccine strain, we confirmed the presence of the 1.6 kb deletion described by Stefanova et al.⁽⁹⁾ This deletion affects part of the gene coding for type II toxin-antitoxin system VapC family toxin, the gene for the antitoxin VapB48 and part of the glutamate - cysteine ligase gene.

The genome of BCG Danish 1331 was the last to be assembled by using a combination of Illumina and PacBio reads.⁽⁷⁾ One advantage of performing PacBio sequencing is that it generates longer reads that improves detection of repeated regions and duplications. Upon sequencing, we observed five SNPs including four nsSNP and a stop codon (Table III). We also observed a deletion of five nucleotides in a SRPBCC family protein gene and two inversions of 26,170 bp and 7,565 bp.

Genome assembly of BCG Pasteur presented a nsSNP in the GTP-binding protein Obg gen (Asn599Asp) and two inframe insertions of three nucleotides each in the genes coding for NADPH epimerase/NADPH dehydratase and a probable cutinase. We also found one inverted region of 31,516 pb.

De novo sequencing of genomes deposited in public databases becomes imperative as new sequencing technologies arise. Recently, Abdallah et al.⁽¹⁵⁾ reviewed the genomes and transcriptomes of fourteen BCG vaccine strains and together with the work of Borgers on the Danish vaccine comprise the most recent studies in BCG strains genealogy. We announce the initial draft genome of four of the most common BCG vaccines licensed worldwide in an effort to contribute to the update of publicly available data. The comparative analysis of BCG strains remains of crucial importance to trace their divergence in terms of genetic sequence, transcription and proteomic profile and, subsequently, to describe possible variation in the protective efficacy.

Accession numbers - The reads of each genome have been deposited under SRA accession PRJNA575846, BioProject ID: PRJNA575846.

ACKNOWLEDGEMENTS

To the sequencing platform of Fiocruz (RPT01J) and Ricardo Junqueira for assistance in the preparation of libraries. We also acknowledge Kamila Chagas Peronni from the Laboratory of Molecular Genetics and Bioinformatics from the Regional Centre of Haemotherapy and Professor Valdes Bollela from the School of Medicine, São Paulo University in Ribeirão Preto.

AUTHORS' CONTRIBUTION

PNS and RSD conceived the study design and analyses; MCS performed the DNA extraction, conceived and performed the Bioinformatic analyses; MGS assisted in the culture and DNA extraction; BL, CA, LM and JDW provided the vaccines ampoule or DNA and revised the manuscript. The manuscript was elaborated by MCS, PNS and RSD.