ABSTRACT
Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory tract of humans and is a common cause of pneumonia and bacterial meningitis. Here, we report the draft genome sequences of six S. pneumoniae strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272.
GENOME ANNOUNCEMENT
Streptococcus pneumoniae (pneumococcus) is an alpha-hemolytic clinically relevant bacterium that causes infections in humans worldwide (1, 2). Although S. pneumoniae is observed among the normal nasopharyngeal microbiota in children and resides asymptomatically in most healthy carriers, it is also the most common cause of bacterial meningitis in adults and a common cause of pneumonia and mortality in the elderly (1, 2). There are 97 different serotypes of capsulated pneumococci (3), identified by variations in the polysaccharide capsule. Current 23-valent and 13-valent pneumococcal vaccines target different capsular serotypes (1, 2). In this project, the genome sequences of six S. pneumoniae strains, CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272, isolated from different clinical samples in blood, cerebrospinal fluid, and the nasopharynx, have been determined and analyzed. The strains were cultivated and DNA extracted as previously described (4). DNA was sequenced with an Illumina MiSeq instrument (SciLifeLab, Stockholm, Sweden), generating paired-end reads of 300 bp. The data are presented in Table 1. Sequence reads were trimmed and assembled de novo with CLC Genomics Workbench version 8 (CLC bio, Aarhus, Denmark). Assembly quality was assessed using Quast version 3.1 (5). Following trimming, the average length of reads was 245 bp. The genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (6). The statistics for each draft genome sequence are summarized in Table 1. Comparative analyses of the genome sequences, by average nucleotide identity based on BLAST (ANIb) (7), using JSpecies version 1.2.1 (8), with the genome sequences of the S. pneumoniae NCTC 7465 type strain resulted in ANIb values higher than 98%. Comparisons to the type strains of the other species of the Mitis group resulted in ANIb values ranging from 73% to 94%. The analysis of the genome sequences for the presence of clustered regularly interspaced short palindromic repeat (CRISPR)–CRISPR-associated (Cas) systems (9) with CRISPRFinder (10) confirmed the presence of a CRISPR-Cas region in strain CCUG 7206 and one region in strain CCUG 35272 formed by one array of spacer repeats that contained five spacers in CCUG 7206 and three spacers in CCUG 35272. For strains CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, and CCUG 35180, no antibiotic resistance genes were found when the genomes were analyzed using ResFinder 2.1 (selected % identification [ID] threshold, 90%). Antibiotic resistance genes were found in strain CCUG 35272: cat for chloramphenicol resistance and tet(M) for tetracycline resistance, as predicted by phenotype.
TABLE 1 .
Assembly statistics for the six Streptococcus pneumoniae draft genome sequences
| Strain | Serotype | Accession no. | Coverage (×) | No. of contigs | G+C content (%) | N50 (kbp) | Genome size (bp) | No. of CDSsa |
|---|---|---|---|---|---|---|---|---|
| CCUG 7206 | 18C | LWCD00000000 | 239 | 172 | 39.7 | 110.5 | 2,087,379 | 2,207 |
| CCUG 1350 | 6B | LQQG00000000 | 75 | 91 | 39.6 | 83.4 | 2,147,337 | 2,138 |
| CCUG 11780 | 6A | LQQH00000000 | 82 | 78 | 39.5 | 85.9 | 2,171,058 | 2,178 |
| CCUG 33774 | 5 | LQQJ00000000 | 68 | 55 | 39.6 | 98.2 | 2,031,618 | 1,972 |
| CCUG 35180 | 19A | LQQK00000000 | 69 | 75 | 39.6 | 84.7 | 2,087624 | 2,032 |
| CCUG 35272 | 23F | LQQI00000000 | 72 | 72 | 39.4 | 87.6 | 2,141,195 | 2,108 |
CDSs, coding sequences.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession numbers listed in Table 1. The versions described in this paper are the first versions, LQQJ01000000, LQQG01000000, LQQH01000000, LQQI01000000, LWCD01000000, and LQQK01000000, for strains CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272, respectively.
ACKNOWLEDGMENTS
The CCUG is supported by the Sahlgrenska University Hospital. This work, including the efforts of Hedvig E. Jakobsson, Francisco Salvà-Serra, Roger Karlsson, Lucia Gonzales-Silès, Fredrik Boulund, Erik Kristiansson, and Edward R. B. Moore, was funded by European Commission: Tailored-Treatment, project no. 602860, and by the Swedish Västra Götaland regional funding, project no. ALFGBG-437221.
Footnotes
Citation Jakobsson HE, Salvà-Serra F, Thorell K, Karlsson R, Gonzales-Silès L, Boulund F, Engstrand L, Kristiansson E, Moore ERB. 2017. Draft genome sequences of six strains of Streptococcus pneumoniae from serotypes 5, 6A, 6B, 18C, 19A, and 23F. Genome Announc 5:e00125-17. https://doi.org/10.1128/genomeA.00125-17.
REFERENCES
- 1.Berical AC, Harris D, Dela Cruz CS, Possick JD. 2016. Pneumococcal vaccination strategies: an update and perspective. Ann Am Thorac Soc 13:933–944. doi: 10.1513/AnnalsATS.201511-778FR. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Keller LE, Robinson DA, McDaniel LS. 2016. Nonencapsulated Streptococcus pneumoniae: emergence and pathogenesis. mBio 7:e01792-15. doi: 10.1128/mBio.01792-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH. 2015. Pneumococcal capsules and their types: past, present, and future. Clin Microbiol Rev 28:871–899. doi: 10.1128/CMR.00024-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Salvà-Serra F, Jakobsson HE, Thorell K, Gonzales-Siles L, Hallbäck ET, Jaén-Luchoro D, Boulund F, Sikora P, Karlsson R, Svensson L, Bennasar A, Engstrand L, Kristiansson E, Moore ER. 2016. Draft genome sequence of Streptococcus gordonii type strain CCUG 33482T. Genome Announc 4(2):e00175-16. doi: 10.1128/genomeA.00175-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi: 10.1099/ijs.0.64483-0. [DOI] [PubMed] [Google Scholar]
- 8.Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. doi: 10.1073/pnas.0906412106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. doi: 10.1126/science.1138140. [DOI] [PubMed] [Google Scholar]
- 10.Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. doi: 10.1093/nar/gkm360. [DOI] [PMC free article] [PubMed] [Google Scholar]