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

Candida krusei is a Candida non-albicans species with a high prevalence, which causes candidaemia. Current treatment guidelines include fluconazole as a primary therapeutic option for the treatment of these infections; however, it is only a fungistatic against Candida spp., and both inherent and acquired resistance to fluconazole have been reported. C. krusei species is also reported as the only Candida sp. which has an intrinsic resistance factor to fluconazole. Therefore, in dealing with antifungal resistance, it is necessary to develop new antifungal agents that are efficient in the treatment of fungal infections, especially those caused by C. krusei. The purpose of this study was to investigate the genome of clinical C. krusei isolates and correlate the resistant phenotypes with mutations in resistance genes. A total of 16 samples of C. krusei from clinical samples from hospitals in Jakarta were used in the experiment. All colonies were extracted using the QIAamp DNA Mini Kit. The library was prepared using the Illumina DNA Prep Kit. The sequencing process was carried out on the Illumina MiSeq Platform using a 2x301 paired-end configuration. FASTQ raw files are available under the BioProject Accession Number PRJNA819536 and Sequence Read Archive Accession Numbers SRR18739949 and SRR18739964.

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Introduction
Candida krusei (teleomorph Pichia kudriavzevii) is an opportunistic fungal pathogen. 1 It is the fourth most common non-albicans Candida species (NAC) causing high prevalence and invasive candidiasis and candidemia. 2,3 C. krusei is among unique species with natural resistance towards fluconazole, a commonly used antifungal for Candida infections. 4 Therefore, in dealing with antifungal resistance, it is necessary to develop new antifungal agents that are efficient in the treatment of fungal infections, especially those caused by C. krusei One approach in examining the drug resistance of C. krusei is by sequencing the genome with potential roles in resistance. Here we report the whole genome sequencing data of Candida krusei from Department of Parasitology Culture Collection, Faculty of Medicine Universitas Indonesia. The sequencing data obtained from this study will help to understand the correlation between phenotypes with mutations in resistance genes and the development of appropriate treatments and medication for the infection.

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 Â 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 Â g for one minute and the flowthrough 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 Â 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 Â 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

REVISED Amendments from Version 1
Revisions were made to the Introduction section within the manuscript.

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 Â 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

Results
The whole raw genome sequence data of 16 clinical isolates of C. krusei from the Department of Parasitology, Faculty of Medicine of Universitas Indonesia were deposited into NCBI data under BioProject accession number PRJNA819536 and SRA SRR18739949-SRR18739964. The DNA quality and quantity of the samples are shown in Table 1. Information regarding the raw data is described in Table 2. These raw data of C. krusei genome are useful for genome profiling and correlating the resistant phenotypes with mutations in resistance genes. Open Peer Review I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.