Genomic Surveillance of Invasive Meningococcal Disease

In Sweden, all clinical IMD isolates are routinely sent to the National Reference Laboratory for N. meningitidis at Örebro University Hospital, Örebro, Sweden, for susceptibility testing and subtyping using whole-genome sequencing on the Illumina platform, as previously described [9 (link)]. These genomes are continuously deposited in the Neisseria spp. pubMLST database[19 (link)]. The MenW genomes included in this study from the period 1995–2017 have previously been described by Eriksson et al. [9 (link)] and the isolates from 2018 to 2019 were sequenced using the same methods as part of the routine diagnostics. PubMLST IDs of all isolates are shown in Supplementary material S1.
Illumina reads from the MenW isolates were mapped onto a PacBio sequenced MenW genome deposited in the pubMLST database (pubMLST ID 82050) using CLC Genomics Workbench v. 20.0 (Qiagen, Venlo, The Netherlands). Single nucleotide polymorphism (SNP) trees were created using default parameters and the Neighbour Joining algorithm in CLC Genomics Workbench.