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Sci Rep. 2017 Mar 31;7:45771. doi: 10.1038/srep45771.

Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus.

Author information

1
Research Programs Unit, Immunobiology, University of Helsinki, and Helsinki University Central Hospital, Helsinki, Finland.
2
Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
3
Bacterial Infections Unit, National Institute for Health and Welfare, Turku, Finland.
4
Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland.
5
Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Biomedicum Helsinki, Helsinki, Finland.
6
Department of Genetics and Molecular Medicine, King's College London, London, UK.

Abstract

Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation.

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