• Streptococcus pneumoniae
• Genotyping and SNP detection of Streptococcus pneumoniae
• S. pneumoniae Sequence Download Tool
• Francisella tularensis
• Genotyping and SNP detection of Francisella tularensis
• F. tularensis Comparative Analysis Tool
• Haemophilus influenzae
• Genome Sequencing and Species Microarray for H. influenzae
• High Throughput Genotyping using Human DNA Isolated from Stored Serum Specimens
• Bioinformatic SNP Filter Scripts
• Poster Presentations

Genotyping and SNP Detection of Streptococcus pneumoniae Isolates by Resequencing Arrays

Project Abstract

The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447), in collaboration with Dr. M. Catherine McEllistrem's laboratory at The University of Pittsburg, has undertaken an evaluation of resequencing oligonucleotide array technology to detect genotypic variations in microorganisms. The primary goal was to establish expertise in the technology and methodologies while simultaneously addressing its value in the scientific community to identify and discover genotypic variations in microorganisms. Non-contiguous regions of Streptococcus pneumoniae isolates were resequenced in this collaborative project. The CustomSeq Resequencing Array consists of 231,688 probes covering 28,961 bases of non-contiguous sequences of the reference Streptococcus pneumoniae TIGR4 strain as shown below. The TIGR4 sequence details can be accessed through the Comprehensive Microbial Resource (CMR) database of JCVI.

Name/Locus	Gene/Sequence	Length(bp)
16S_rRNA	16SrRNA	1413
SP0117	Pneumococcal surface protein A	2232
SP0368	Cell wall surface anchor family protein	5301
SP0377_SP0378	Choline binding proteins C, J & intergenic region	2262
SP0390_SP0391	Choline binding proteins G, F & intergenic region	2078
SP0463_SP0466	Surface anchor, sortase & hypothetical proteins with intergenic region	4788
SP0667	Pneumococcal surface protein - putative	996
SP0834	Hemolysin-related protein	510
SP1204	Hemolysin A - putative	594
SP1466	Hemoylsin	645
SP1833	Cell wall surface anchor family protein	2124
SP1961	DNA-directed RNA polymerase, beta subunit	3609
SP1992	Cell wall surface anchor family protein	663
SP2145	Antigen, cell wall surface anchor family	2082

In order to maximize the scientific value of the data obtained, we have used ABI Sanger sequencing to supplement the sequence data obtained from the resequencing arrays for 11 of the 14 regions (excluding the 3 intergenic regions). The following pages provide access to the combined sequence data that were obtained from the two methods. You may choose to download data for all 72 strains, or choose a subset of the strains by sequence type, serotype or penicillin susceptibility. The download tool will deliver a compressed archive file containing a set of multi-FASTA files, one for each strain selected. A list of the experimental strains is available in this table.

Data and Resources