Whole genome sequencing data of Candida krusei, the pathogen causing Candidaemia, from Department of Parasitology Culture Collection, Faculty of Medicine Universitas Indonesia

Sample collection and DNA extraction

The C. krusei clinical sample were retrieved from the Department of Parasitology Culture Collection, Faculty of Medicine, Universitas Indonesia. DNA was extracted using the QIAamp DNA Mini Kit (Qiagen, catalog number: 51304) with bead-beating methods.⁵ 100 μL culture of C. krusei were added into 1.5 ml microcentrifuge tube containing 200 μL ATL buffer (Qiagen). Three spoon full of sterilized sand were added into the mixture for bead-beating, which was performed for 10 minutes. 20 μL Proteinase K (Qiagen) were added and the mixture was incubated at 56°C until completely lysed (three hours), and agitated every 10 minutes during incubation time, until homogeneous. 200 μL Buffer AL (Qiagen) were added and the mixture was incubated at 70°C for 10 minutes. 200 μL pure ethanol were added and the mixture was transferred into the QIAamp Mini spin column (Qiagen). Column were centrifugated at 6000 × g for one minute and the flow-through were discarded. QIAamp Mini spin columns were placed innew 2 mL collection tubes and 500 μL Buffer AW1 were added into the column. Columns were centrifugated at 6000 × g for one minute and the flow-through was discarded. QIAamp Mini spin columns were placed into new 2 mL collection tubes and 500 μL Buffer AW2 (Qiagen) were added. Columns were centrifugated at 17000 × g for three minutes and the flow-through was discarded. QIAamp Mini spin columns were transferred into new 1.5 mL microcentrifuge tubes, and 200 μl distilled water were added. Columns were incubated at room temperature for one minute and centrifugated at 6000 × g for one minute to elute the DNA. The quality of extracted DNA (A260/280) was measured using a spectrophotometer (NanoDrop ND-1000). The quantity of extracted DNA was measured with Qubit 4.0 Fluorometer using the dsDNA HS Assay kit.

Library preparation

DNA libraries were prepared using the Illumina DNA Preparation Kit. The index used for the library preparation was Integrated DNA Technologies, Inc (IDT) for Illumina Nextera Indexes for ligation step. The library construction steps were as follows:

Tagmentation

100 ng DNA were added into a 96-well plate and mixed with tagmentation master mix from Illumina Nextera Kit (Illumina). The mix were then incubated at 55°C in a thermal cycler (The Applied Biosystems ProFlex PCR System) for 15 minutes.

Post tagmentation clean-up and amplification of tagmented DNA

Illumina Nextera Kit tagment stop buffer (Illumina) were added to the tagmentation reaction and incubated at 37°C for 15 minutes. The mixture was washed with Illumina Nextera Tagment wash buffer (Illumina) on the magnetic stand. The tagment Wash Buffer was discarded and Nextera PCR master mixes (Illumina) were added onto the beads. Index adapters were added as sample barcoding. The mixture was amplified in thermal cycler.

Libraries clean-up

The beads were added into the supernatant of the mixture and washed twice using 80% ethanol on a magnetic stand. Nextera resuspension buffer (Illumina) reagents were added onto beads and final libraries were retrieved from the supernatant. The libraries of each sample were pooled.⁶

Whole genome sequencing

The barcoded DNA libraries were sequenced using an Illumina Miseq Platform on the v3-Flow Cell. The DNA library was denatured according to the manufacturer’s protocol.⁷ For quality control, the library was spiked with 1% PhiX Control v3. The sequencing run produced 2 × 301 bp paired-end libraries. The data were deposited to the NCBI Sequence Read Archive (SRA) under BioProject. Total raw reads were obtained using FastQC software, and the total raw bases and percentage of Q30 were evaluated using q30 python scripts.⁸

Ethical approval

This research was approved by the Faculty of Medicine Universitas Indonesia Ethical Committee (approval number: 970/UN2.F1/ETIK/PPM.00.02/2021).

Underlying data

Raw data (FASTQ) files have been deposited into National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov).

BioProject: Raw sequence reads of Candida krusei from clinical samples, Accession Number: PRJNA819536; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA819536

BioSample: Pathogen: clinical or host-associated sample from Pichia kudriavzevii, Accession Number: SAMN26901813; https://identifiers.org/ncbiprotein:SAMN26901813

BioSample: Pathogen: clinical or host-associated sample from Pichia kudriavzevii, Accession Number: SAMN26901828; https://identifiers.org/ncbiprotein:SAMN26901828

Raw sequence reads of Candida krusei from clinical samples:

Sequence Read Archive: Raw sequence reads of Candida krusei from clinical samples, Accession Number: SRR18739949; https://identifiers.org/insdc.sra:SRR18739949

Sequence Read Archive: Raw sequence reads of Candida krusei from clinical samples, Accession Number: SRR18739964; https://identifiers.org/insdc.sra:SRR18739964