Abstract
Streptococcus pneumoniae is a major pathogen causing bacterial infection in the middle ear of humans. We previously used S. pneumoniae strain ST556, a low-passage 19F isolate from an otitis media patient, to perform a whole-genome screen for ear infection-associated genes in a chinchilla model. This report presents the complete genome sequence of ST556. The genome sequence will provide information complementary to the experimental data from our genetic study of this strain.
GENOME ANNOUNCEMENT
Streptococcus pneumoniae is a nasopharyngeal commensal and also causes infections, including ear infection (or otitis media), pneumonia, and meningitis (10). In the context of high genome plasticity (3), this bacterium is classified into at least 92 serotypes based on the antigenic diversity in the capsular polysaccharide (6, 10, 12). S. pneumoniae strains of serotypes 14, 19, and 24 are among the most commonly encountered in otitis media patients (1, 7). We previously conducted the first whole-genome mutagenesis study to identify S. pneumoniae genes that are associated with bacterial infectivity (survival and growth) in the middle ear by using strain ST556 (2). ST556 is a low-passage multidrug-resistant serotype 19F isolate from an otitis media patient (7). That study led to the identification of 169 putative otitis media-associated S. pneumoniae genes (2). Due to the lack of genomic sequence information for this strain at the time, we reported our genetic data in the context of the gene number system of TIGR4, a capsular type 4 strain with a completely sequenced genome (13). To complement the in vivo screening data for ST556 (2), we have recently obtained the full genome sequence of this strain.
The genome was sequenced to 24.2-fold coverage using the 454 GS 20 sequencer as described previously (9). Lander-Waterman statistics predict that this level of coverage provided greater than 99.9% coverage of the genome. The Newbler de novo assembler used 200,678 reads with an average length of 250 bases to assemble the genome into 181 contigs as described previously (11). The 454-assembled contigs were ordered and oriented into scaffolds by alignment with complete S. pneumoniae genome sequences using Nucmer software (4) to identify the closest reference. The alignment included the genome sequences of strains R6 (accession no. NC_003098), D39 (accession no. NC_003098/NC_008533), TIGR4 (accession no. NC_003028), 670-6B (accession no. NC_014498), ATCC 700669 (accession no. NC_011900), Hungary19A-6 (accession no. NC_010380), TCH8431/19A (accession no. NC_014251), CGSP14 (accession no. NC_010582), Taiwan19F-14 (accession no. NC_012469), JJA (accession no. NC_012466), P1031 (accession no. NC_012467), 70585 (accession no. NC_012468), G54 (accession no. NC_011072), and AP200 (accession no. NC_014494). The sequence gaps were filled by PCR amplification and primer walking. Prediction of putative coding sequences and gene annotation were done by NCBI using the Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).
The ST556 genome consists of 2,145,902 nucleotides, with 2,162 predicted protein-encoding sequences and 4 rRNA loci. Among the strains with publicly available genome sequences, S. pneumoniae Taiwan19F-14 (accession no. NC_012469), a type 19F strain, is the closest to ST556 based on their similarities in genomic sequence and gene order, although the disease and isolation source associated with strain Taiwan19F-14 is unclear in the current genome annotation. A major difference between the genomes of ST556 and Taiwan19F-14 is the presence of an MM1-like phage (38,165 nucleotides) in the ST556 genome (5). The MM1 phage was previously reported to affect the colony opacity and adherence phenotypes of S. pneumoniae (8).
Nucleotide sequence accession number.
The sequence of the S. pneumoniae ST556 genome has been deposited in GenBank under the accession number CP003357.
ACKNOWLEDGMENTS
We are grateful to M. R. Jacobs for providing the ST556 strain and H. Tettelin for valuable advice on genome annotation.
This work was supported by a grant (to J.-R.Z.) from the NIH/NIDCD (no. DC006917) and a grant (to J.-R.Z. and G.F.G.) from the China Natural Sciences Foundation (NSFC; no. 30728014).
REFERENCES
- 1. Arguedas A, et al. 1998. Microbiology of acute otitis media in Costa Rican children. Pediatr. Infect. Dis. J. 17:680–689 [DOI] [PubMed] [Google Scholar]
- 2. Chen H, et al. 2008. Genetic requirement for pneumococcal ear infection. PLoS One 3:e2950 doi:10.1371/journal.pone.0002950. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Claverys JP, Prudhomme M, Mortier-Barriere I, Martin B. 2000. Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol. Microbiol. 35:251–259 [DOI] [PubMed] [Google Scholar]
- 4. Delcher AL, et al. 1999. Alignment of whole genomes. Nucleic Acids Res. 27:2369–2376 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Gindreau E, Lopez R, Garcia P. 2000. MM1, a temperate bacteriophage of the type 23F Spanish/USA multiresistant epidemic clone of Streptococcus pneumoniae: structural analysis of the site-specific integration system. J. Virol. 74:7803–7813 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Jin P, et al. 2009. First report of putative Streptococcus pneumoniae serotype 6D among nasopharyngeal isolates from Fijian children. J. Infect. Dis. 200:1375–1380 [DOI] [PubMed] [Google Scholar]
- 7. Joloba ML, et al. 2001. Pneumococcal conjugate vaccine serotypes of Streptococcus pneumoniae isolates and the antimicrobial susceptibility of such isolates in children with otitis media. Clin. Infect. Dis. 33:1489–1494 [DOI] [PubMed] [Google Scholar]
- 8. Loeffler JM, Fischetti VA. 2006. Lysogeny of Streptococcus pneumoniae with MM1 phage: improved adherence and other phenotypic changes. Infect. Immun. 74:4486–4495 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Margulies M, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Musher DM. 2010. Streptococcus pneumoniae, p 2623–2642. In Mandell GL, Bennett JE, Dolin RD. (ed), Principles and practice of infectious diseases, 7th ed, vol 2 Elsevier Churchill Livingstone, New York, NY [Google Scholar]
- 11. Mussmann M, et al. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol. 5:e230 doi:10.1371/journal.pbio.0050230. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Park IH, et al. 2007. Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. J. Clin. Microbiol. 45:1225–1233 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Tettelin H, et al. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498–506 [DOI] [PubMed] [Google Scholar]