Whole-genome Sequencing of Neisseria meningitidis

All N. meningitidis carriage isolates were characterized with whole-genome sequencing (WGS). Genomic DNA was prepared for sequencing using the 5Prime ArchivePure DNA Purification kit (5Prime, Gaithersburg, MD) or Gentra Puregene yeast/bacteria DNA extraction kit (Qiagen, Germantown, MD) as previously described (34 (link)) for sequencing on Pacific Biosystems (PacBio, Menlo Park, CA, USA) and/or Illumina (HiSeq2500 or MiSeq; Illumina, San Diego, CA, USA) platforms; genomic DNA was further prepared for Illumina sequencing with the dual-index NEBNext Ultra DNA library preparation kits (New England BioLabs Inc., Ipswich, MA). Genomes generated using the PacBio platform were processed as previously described (35 (link)). The Illumina reads were trimmed with Cutadapt (36 (link)), and de novo short read assembly was carried out using SPAdes 3.7.0 (37 (link)) with the “careful” option. Assemblies were compared with BLAST (38 (link)) against the PubMLST Neisseria allele collection (39 (link)) to identify MLST alleles. The MLST genes were compared against the PubMLST MLST scheme collection to identify the N. meningitidis ST and CC.

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Joseph S.J., Topaz N., Chang H.Y., Whaley M.J., Vuong J.T., Chen A., Hu F., Schmink S.E., Jenkins L.T., Rodriguez-Rivera L.D., Thomas J.D., Acosta A.M., McNamara L., Soeters H.M., Mbaeyi S, & Wang X. (2020). Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities. mSphere, 5(2), e00197-20.

Publication 2020

Gentra Puregene yeast/bacteria DNA extraction kit HiSeq2500 NEBNext Ultra DNA library preparation kits

Alleles Bacteria dna Dna library Genes Genomes N meningitidis Neisseria Yeast

Corresponding Organization :

Other organizations : CDC Foundation, Centers for Disease Control and Prevention

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Variable analysis

independent variables

Whole-genome sequencing (WGS) of N. meningitidis carriage isolates

dependent variables

Identification of MLST alleles
Identification of N. meningitidis ST and CC

control variables

Genomic DNA preparation using the 5Prime ArchivePure DNA Purification kit or Gentra Puregene yeast/bacteria DNA extraction kit
Illumina library preparation using the dual-index NEBNext Ultra DNA library preparation kits
Genome assembly using SPAdes 3.7.0 with the "careful" option
BLAST comparison of MLST genes against the PubMLST Neisseria allele collection

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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