Gentra puregene yeast bacteria dna extraction kit

Molecular characterization of the 2011–15 isolates was completed by whole genome sequencing. DNA was extracted using the Gentra Puregene yeast/bacteria DNA extraction kit (Qiagen) or with a chemagic Prepito instrument (PerkinElmer) using the Cyto Pure Kit. Genomic libraries were generated with NEBNext Ultra DNA Library preparation kits according to manufacturer specifications. Libraries were sequenced at CDC using 250 bp paired-end reads on a HiSeq 2500 or a MiSeq (Illumina). Raw sequencing reads were trimmed to remove adapters and low quality bases. De novo genomic assembly was completed with SPAdes, version 3.7.0.^{22 (link)} Sequences for the MLST genes and the fine typing genes (porA and fetA) were identified by a BLAST search of the genome assembly using the PubMLST allele collection (www.pubmlst.org/Neisseria) to identify the sequence type (ST), clonal complex (CC), and PorA and FetA types. Sequencing data is deposited to GenBank (BioProject: SRP144480).

All available isolates from the 2016 meningitis season (1 NmX, 101 NmC, and 22 NmW) and a subset of isolates from the 2017 season (8 NmX, 30 NmC, and 2 NmW) underwent molecular characterization. For 2017, all available NmX and NmW isolates and at least 2 NmC isolates per district were selected, when available. Isolates were sent to the US Centers for Disease Control and Prevention (CDC) Bacterial Meningitis Laboratory, a WHO Collaborating Centre for Meningitis, for whole-genome sequencing analysis.
Deoxyribonucleic acid (DNA) extractions were conducted using the Gentra Puregene yeast/bacteria DNA extraction kit (QIAGEN) or with a chemagic Prepito instrument (PerkinElmer) using the Cyto Pure Kit. The NEBNext Ultra DNA Library preparation kit was used according to manufacturer specifications to generate genomic libraries. Sequencing was completed at CDC using 250-base pair paired-end reads on a HiSeq 2500 or a MiSeq (Illumina). Raw reads were trimmed to remove adapters and low quality bases before de novo genomic assembly by SPAdes, version 3.7.0 [20 (link)]. To identify the sequence type (ST), clonal complex (CC), and PorA and FetA types, sequences for the MLST genes and the fine typing genes (porA and fetA) were identified by a BLAST search using the PubMLST allele collection (www.pubmlst.org/Neisseria) [21 (link)].