Open access
Announcement
17 December 2015

Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate

ABSTRACT

Streptococcus anginosus is an opportunistic human pathogen that causes abscesses of the brain, liver, and other organs. Here, we announce the complete genome sequence of a clinically isolated strain of S. anginosus J4211. The genome sequence contains two prophages and multiple mobile genetic elements.

GENOME ANNOUNCEMENT

Streptococcus anginosus belongs to the S. anginosus group (SAG), a subgroup of viridans streptococci. This group includes two other species, Streptococcus intermedius and Streptococcus constellatus (1, 2). These streptococci are typically commensal human flora of the oral cavity and gastrointestinal and genital tracts (3). However, they can occasionally cause opportunistic infections, particularly brain and liver abscesses, and are emerging pathogens in cystic fibrosis patients (4, 5). S. anginosus strain J4211 was originally a clinical isolate from the University of Texas Health Sciences Center at San Antonio, San Antonio, TX.
The strain was grown in Todd-Hewitt broth with 2% yeast extract (THY) broth supplemented with 5% heat-inactivated horse serum (THY-HS) overnight at 37°C. Chromosomal DNA was isolated as previously described (6, 7). The DNA library was prepared using the Nextera DNA library preparation kit (Illumina, Inc., San Diego, CA), and library quality was checked with an Agilent high-sensitivity DNA chip. Genome sequencing was performed by the Illumina MiSeq using paired-end 250-bp sequencing with high coverage (600-fold) at the University of Oklahoma Health Sciences Center, Laboratory for Genomics and Bioinformatics, Oklahoma City, OK. DNA assembly was done using the software package Geneious. Sequence gaps were closed by PCR amplification. Gene annotation was performed by the Rapid Annotations using Subsystems Technology (RAST) pipeline (8, 9). Genome annotation was completed using Artemis software (10) and a BLAST search.
The complete genome sequence of S. anginosus J4211 contains 1,924,513 bp, with a G+C content of 38.99%. The number of predicted coding regions is 1,926, with 13 rRNA genes and 60 tRNA genes. Analysis using the Web-based tool IslandViewer (11) revealed seven genomic islands, including mobile genetic elements and incomplete prophages. The PHAge Search Tool (PHAST), another Web-based program, confirmed the presence of two incomplete prophages (positions 120772 to 153677 and 1362153 to 1402752) (12). There are three clustered regularly interspaced short palindromic repeat (CRISPR) regions (positions 384703 to 385609, 910080 to 911303, and 1299282 to 1299517) in the genome identified by CRISPRFinder (13). The complete capsular polysaccharide (CPS) locus, as mentioned by Tsunashima et al. (14), is present in the genome sequence (positions 1789505 to 1820948). The genome sequence of this S. anginosus strain will help us in the future to understand the pathogenic mechanisms of this organism.

Nucleotide sequence accession number.

The complete genome sequence of S. anginosus J4211 has been deposited at GenBank under the accession number no. CP012805. This paper describes the first version of the genome.

ACKNOWLEDGMENTS

This work was made possible by an Oklahoma Center for the Advancement of Science and Technology (OCAST) grant HR11-133 and by NIH grant no. R15A1072718 to W.M.M.

REFERENCES

1.
Jensen A, Hoshino T, Kilian M. 2013. Taxonomy of the anginosus group of the genus Streptococcus and description of Streptococcus anginosus subsp. whileyi subsp. nov. and Streptococcus constellatus subsp. viborgensis subsp. nov. Int J Syst Evol Microbiol 63:2506–2519.
2.
Asam D, Spellerberg B. 2014. Molecular pathogenicity of Streptococcus anginosus. Mol Oral Microbiol 29:145–155.
3.
Whiley RA, Beighton D, Winstanley TG, Fraser HY, Hardie JM. 1992. Streptococcus intermedius, Streptococcus constellatus, and Streptococcus anginosus (the Streptococcus milleri group): association with different body sites and clinical infections. J Clin Microbiol 30:243–244.
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Whiley RA, Fraser H, Hardie JM, Beighton D. 1990. Phenotypic differentiation of Streptococcus intermedius, Streptococcus constellatus, and Streptococcus anginosus strains within the “Streptococcus milleri group.” J Clin Microbiol 28:1497–1501.
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Parkins MD, Sibley CD, Surette MG, Rabin HR. 2008. The Streptococcus milleri group—an unrecognized cause of disease in cystic fibrosis: a case series and literature review. Pediatr Pulmonol 43:490–497.
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Pitcher DG, Saunders NA, Owen RJ. 1989. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156.
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McShan WM, McLaughlin RE, Nordstrand A, Ferretti JJ. 1998. Vectors containing streptococcal bacteriophage integrases for site-specific gene insertion. Methods Cell Sci 20:51–57.
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Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214.
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Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945.
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Langille MGI, Brinkman FSL. 2009. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25:664–665.
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Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352.
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Ibtissem G, Gilles V, Christine P. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57.
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Tsunashima H, Miyake K, Motono M, Iijima S. 2012. Organization of the capsule biosynthesis gene locus of the oral streptococcus Streptococcus anginosus. J Biosci Bioeng 113:271–278.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 631 December 2015
eLocator: 10.1128/genomea.01440-15

History

Received: 18 October 2015
Accepted: 27 October 2015
Published online: 17 December 2015

Contributors

Authors

Maliha Rahman
Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, Oklahoma, USA
Scott V. Nguyen
Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, Oklahoma, USA
Kimberly A. McCullor
Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, Oklahoma, USA
Catherine J. King
Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, Oklahoma, USA
James H. Jorgensen
Departments of Pathology and Medicine, University of Texas Health Sciences Center at San Antonio, San Antonio, Texas, USA
W. Michael McShan
Department of Pharmaceutical Sciences, The University of Oklahoma College of Pharmacy, Oklahoma City, Oklahoma, USA

Notes

Address correspondence to W. Michael McShan, [email protected].

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