design: A total of 214 enriched and 20 unenriched CSF DNA samples as well as 109 isolate DNA samples were sequenced. DNA was quantified by Qubit; 1 g of enriched CSF DNA or isolate DNA and 1 to 100 ng of unenriched CSF DNA were used for library preparation. Each DNA sample was diluted in 55 l of 10 mM Trisbuffer (pH 7.5) and fragmented by Covaris ML230 focused ultrasonicator (Covaris, US) to obtain the average size of 550 bp. The libraries from CSF DNA were prepared by NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) and libraries from isolate DNA were prepared by NEBNext Ultra I DNA Library Prep Kit (New England Biolabs), using size-selection for 400-500 bp fragments and PCR amplification for 6 cycles. Isolate DNA were sequenced with Miseq 500-cycle V2 kits (Illumina, USA) with 32 isolates per run. Seventy-eight enriched and unenriched CSF DNA samples were sequenced with HiSeq 2500 rapid SBS 500-cycle V2 kits (Illumina, US) and remaining 156 enriched CSF DNA samples were sequenced on a Novaseq 6000 using SP flow cell and SP SBS cartridge for 500-cycle (Illumina, US).