Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies

Francisco Salvà-Serra; Daniel Jaén-Luchoro; Hedvig E. Jakobsson; Lucia Gonzales-Siles; Roger Karlsson; Antonio Busquets; Margarita Gomila; Antoni Bennasar-Figueras; Julie E. Russell; Mohammed Abbas Fazal; Sarah Alexander; Edward R.B. Moore

doi:10.1038/s41598-020-68249-y

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies

Francisco Salvà-Serra^*
, Daniel Jaén-Luchoro
, Hedvig E. Jakobsson
, Lucia Gonzales-Siles
, Roger Karlsson
, Antonio Busquets
, Margarita Gomila
, Antoni Bennasar-Figueras
, Julie E. Russell
, Mohammed Abbas Fazal
, Sarah Alexander
, Edward R.B. Moore

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

14 Citations (Scopus)

Abstract

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198^T and CCUG 4207^T, 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 8198^T and CCUG 4207^T are derived from deposit of the same strain at two different culture collections. NCTC 8198^T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207^T 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.

Original language	English
Article number	11656
Journal	Scientific Reports
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41598-020-68249-y
Publication status	Published - 1 Dec 2020

Bibliographical note

Funding Information:
Open access funding provided by University of Gothenburg. This work was supported by the European Commission 7th Framework Programme: TAILORED-Treatment (Project No. 602860), by the Swedish Västra Götaland regional funding (Projects No. ALFGBG-437221 and ALFGBG-720761), the Swedish Västra Götaland FoU Grant No. VGFOUREG-665141, Laboratoriemedicin FoU (Project No. 51060-6268) and by the Wellcome Trust (Project No. 101503/Z/13/Z). DJL, RK and ERBM acknowledge the support of the Joint Programme Initiative—AntiMicrobial Resistance (JPIAMR) (Vetenskapsrådet Project No. 2016-06504). The Culture Collection University of Gothenburg (CCUG) was supported by the Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden. FS-S was supported by a stipend for Basic and Advanced Research from the CCUG, through the Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg. FS-S, DJ-L, HEJ, LG-S, RK, NK and ERBM acknowledge the support from the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg. Antonio Busquets was supported by a postdoctoral contract from the University of the Balearic Islands. The authors acknowledge Gemma Langridge, Julian Parkhill and Nick Grayson, at the Wellcome Trust Sanger Institute (Hinxton, United Kingdom), for the PacBio assembly and thank them and Timur Tunovic for valuable comments and suggestions.

Publisher Copyright:
© 2020, The Author(s).

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10.1038/s41598-020-68249-y

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Salvà-Serra, F., Jaén-Luchoro, D., Jakobsson, H. E., Gonzales-Siles, L., Karlsson, R., Busquets, A., Gomila, M., Bennasar-Figueras, A., Russell, J. E., Fazal, M. A., Alexander, S., & Moore, E. R. B. (2020). Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies. Scientific Reports, 10(1), Article 11656. https://doi.org/10.1038/s41598-020-68249-y

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title = "Complete genome sequences of Streptococcus pyogenes type strain reveal 100\%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies",

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.",

author = "Francisco Salv{\`a}-Serra and Daniel Ja{\'e}n-Luchoro and Jakobsson, \{Hedvig E.\} and Lucia Gonzales-Siles and Roger Karlsson and Antonio Busquets and Margarita Gomila and Antoni Bennasar-Figueras and Russell, \{Julie E.\} and Fazal, \{Mohammed Abbas\} and Sarah Alexander and Moore, \{Edward R.B.\}",

note = "Funding Information: Open access funding provided by University of Gothenburg. This work was supported by the European Commission 7th Framework Programme: TAILORED-Treatment (Project No. 602860), by the Swedish V{\"a}stra G{\"o}taland regional funding (Projects No. ALFGBG-437221 and ALFGBG-720761), the Swedish V{\"a}stra G{\"o}taland FoU Grant No. VGFOUREG-665141, Laboratoriemedicin FoU (Project No. 51060-6268) and by the Wellcome Trust (Project No. 101503/Z/13/Z). DJL, RK and ERBM acknowledge the support of the Joint Programme Initiative{\textemdash}AntiMicrobial Resistance (JPIAMR) (Vetenskapsr{\aa}det Project No. 2016-06504). The Culture Collection University of Gothenburg (CCUG) was supported by the Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden. FS-S was supported by a stipend for Basic and Advanced Research from the CCUG, through the Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg. FS-S, DJ-L, HEJ, LG-S, RK, NK and ERBM acknowledge the support from the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg. Antonio Busquets was supported by a postdoctoral contract from the University of the Balearic Islands. The authors acknowledge Gemma Langridge, Julian Parkhill and Nick Grayson, at the Wellcome Trust Sanger Institute (Hinxton, United Kingdom), for the PacBio assembly and thank them and Timur Tunovic for valuable comments and suggestions. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = dec,

day = "1",

doi = "10.1038/s41598-020-68249-y",

language = "English",

volume = "10",

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Salvà-Serra, F, Jaén-Luchoro, D, Jakobsson, HE, Gonzales-Siles, L, Karlsson, R, Busquets, A, Gomila, M, Bennasar-Figueras, A, Russell, JE, Fazal, MA, Alexander, S & Moore, ERB 2020, 'Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies', Scientific Reports, vol. 10, no. 1, 11656. https://doi.org/10.1038/s41598-020-68249-y

TY - JOUR

T1 - Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies

AU - Salvà-Serra, Francisco

AU - Jaén-Luchoro, Daniel

AU - Jakobsson, Hedvig E.

AU - Gonzales-Siles, Lucia

AU - Karlsson, Roger

AU - Busquets, Antonio

AU - Gomila, Margarita

AU - Bennasar-Figueras, Antoni

AU - Russell, Julie E.

AU - Fazal, Mohammed Abbas

AU - Alexander, Sarah

AU - Moore, Edward R.B.

N1 - Funding Information: Open access funding provided by University of Gothenburg. This work was supported by the European Commission 7th Framework Programme: TAILORED-Treatment (Project No. 602860), by the Swedish Västra Götaland regional funding (Projects No. ALFGBG-437221 and ALFGBG-720761), the Swedish Västra Götaland FoU Grant No. VGFOUREG-665141, Laboratoriemedicin FoU (Project No. 51060-6268) and by the Wellcome Trust (Project No. 101503/Z/13/Z). DJL, RK and ERBM acknowledge the support of the Joint Programme Initiative—AntiMicrobial Resistance (JPIAMR) (Vetenskapsrådet Project No. 2016-06504). The Culture Collection University of Gothenburg (CCUG) was supported by the Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden. FS-S was supported by a stipend for Basic and Advanced Research from the CCUG, through the Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg. FS-S, DJ-L, HEJ, LG-S, RK, NK and ERBM acknowledge the support from the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg. Antonio Busquets was supported by a postdoctoral contract from the University of the Balearic Islands. The authors acknowledge Gemma Langridge, Julian Parkhill and Nick Grayson, at the Wellcome Trust Sanger Institute (Hinxton, United Kingdom), for the PacBio assembly and thank them and Timur Tunovic for valuable comments and suggestions. Publisher Copyright: © 2020, The Author(s).

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85088017886

U2 - 10.1038/s41598-020-68249-y

DO - 10.1038/s41598-020-68249-y

M3 - Article

C2 - 32669560

AN - SCOPUS:85088017886

SN - 2045-2322

VL - 10

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 11656

ER -

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies

Abstract

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