Abstract
We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
Highlights
We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases
Streptococcus pyogenes, within the β-haemolytic, Lancefield group A Streptococcus (GAS)[1], is an important clinically-relevant and strictly-human pathogen causing a wide range of diseases, including local and invasive infections, severe toxin-mediated diseases and immune-mediated diseases[2]
Inaugural high error rates (> 30%; currently ~ 7%)[10,11,12] caused some degree of doubt within the scientific community, more recent developments and studies have allayed much of the initial scepticism
Summary
We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. Illumina has led the field in high-throughput DNA sequencing, by providing highly accurate and relatively inexpensive sequence reads Their short lengths (few hundred base-pairs) have restricted efficacy to resolve problematic genomic regions (e.g., repeats, ribosomal operons, long sequence motifs), sometimes yielding fragmented and incomplete assemblies[7]. Inaugural high error rates (> 30%; currently ~ 7%)[10,11,12] caused some degree of doubt within the scientific community, more recent developments and studies have allayed much of the initial scepticism Resulting from these technological developments, in 2019-06-29, 1,883 genome sequences of S. pyogenes were publicly available in GenBank, of which 195 were complete. Of those 195, only the complete genome sequences presented in this study represented the type and an important reference strain of the species
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