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Pipeline publication

[…] ntified by variations in the polysaccharide capsule. Current 23-valent and 13-valent pneumococcal vaccines target different capsular serotypes (, ). 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 (). DNA was sequenced with an Illumina MiSeq instrument (SciLifeLab, Stockholm, Sweden), generating paired-end reads of 300 bp. The data are presented in . 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 (). Following trimming, the average length of reads was 245 bp. The genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (). The statistics for each draft genome sequence are summarized in . Comparative analyses of the genome sequences, by average nucleotide identity based on BLAST (ANIb) (), using JSpecies version 1.2.1 (), 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 () with CRISPRFinder () 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., CDSs, coding sequences., This whole-genome shotgun project has been deposited in DDBJ/ENA/ […]

Pipeline specifications

Software tools CLC Genomics Workbench, QUAST, PGAP, CRISPRFinder
Databases ResFinder
Diseases Pneumonia, Meningitis, Central Nervous System Infections, Central Nervous System Bacterial Infections