Genomic evidence for stability of the Bacillus Calmette-Guérin (BCG) vaccine strain (Pasteur 1173P2) from different batches in Iran

Asadian, Mahla; Safarchi, Azadeh; Hassanzadeh, Seyed Mehdi; Yaseri, Mehdi; Douraghi, Masoumeh

doi:10.1111/jam.15365

Cited by 3 publications

(1 citation statement)

References 70 publications

(100 reference statements)

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“…Hackflex has been widely validated and used in the context of whole-genome sequencing for bacterial isolates [4][5][6][7][8][9][10][11] and amplicon sequencing [12]. Although Hackflex has been used in metagenomic analyses, its accuracy has only been tested in the context of simple mock communities containing seven species of known relative abundances [13,14].…”

Section: Introductionmentioning

confidence: 99%

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

Preprint

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Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

show abstract

Section: Introductionmentioning

confidence: 99%

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

ISME Communications

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Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

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The whole genome sequence of Polish vaccine strain Mycobacterium bovis BCG Moreau

Krysztopa-Grzybowska,

Lach,

Polak

et al. 2024

Microbiol Spectr

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Currently, tuberculosis immunoprophylaxis is based solely on Bacillus Calmette-Guérin (BCG) vaccination, and some of the new potential tuberculosis vaccines are based on the BCG genome. Therefore, it is reasonable to analyze the genomes of individual BCG substrains. The aim of this study was the genetic characterization of the BCG-Moreau Polish (PL) strain used for the production of the BCG vaccine in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. As a result of comparison, BCG-Moreau PL with BCG-Moreau Rio de Janeiro (RDJ) 143 single nucleotide polymorphisms (SNPs) and 32 insertion/deletion mutations (INDELs) were identified. However, the verification of these mutations showed that the most significant were accumulated in the BCG-Moreau RDJ genome. The mutations unique to the Polish strain genome are 1 SNP and 2 INDEL. The strategy of combining short-read sequencing with long-read sequencing is currently the most optimal approach for sequencing bacterial genomes. With this approach, the only available genomic sequence of BCG-Moreau PL was obtained. This sequence will primarily be a reference point in the genetic control of the stability of the vaccine strain in the future. The results enrich knowledge about the microevolution and attenuation of the BCG vaccine substrains. IMPORTANCE The whole genome sequence obtained is the only genomic sequence of the strain that has been used for vaccine production in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. The comprehensive genomic analysis performed not only enriches knowledge about the microevolution and attenuation of the BCG vaccine substrains but also enables the utilization of identified markers as a reference point in the genetic control and identity tests of the stability of the vaccine strain in the future.

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Genomic evidence for stability of the Bacillus Calmette-Guérin (BCG) vaccine strain (Pasteur 1173P2) from different batches in Iran

Cited by 3 publications

References 70 publications

Hackflex library preparation enables low-cost metagenomic profiling

Hackflex library preparation enables low-cost metagenomic profiling

Hackflex library preparation enables low-cost metagenomic profiling

The whole genome sequence of Polish vaccine strain Mycobacterium bovis BCG Moreau

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