This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G1C content of 38.65%, and 5,467 genes. T his report is to present the draft genome sequence of a clinical isolate of Candida parapsilosis. C. parapsilosis is a yeast classified under cellular organisms, superkingdom of Eukaryota, kingdom of Fungi, subkingdom of Dikarya, phylum of Ascomycota, subfamily of Saccharomycotina, class of Saccharomycetes, order of Saccharomycetales, family of Debaryomycetaceae, and genus of Candida. This species is known as a causative agent for candidemia (1). The draft genome sequence of this species will enhance the current knowledge of the genetic variation among C. parapsilosis isolates. The organism was isolated from a patient with catheter-related bloodstream infection (CRBSI) in Hospital Universiti Sains Malaysia (USM), Kelantan, Malaysia. Ethical approvals were obtained from the Human Research Ethics of Universiti Sains Malaysia (JEPeM-USM-16040162). The isolate was cultivated overnight on a Sabouraud dextrose agar plate with yeast cultivation medium and incubated at 37°C. Pure colonies were collected during the stationary phase. DNA extraction was done using phenol-chloroform extraction followed by ethanol precipitation (2). Species identity was confirmed by the sequences of the internal transcribed spacer (ITS) region of ribosomal DNA (3). Sample quantity and quality were assessed prior to sequencing using the Illumina NovaSeq6000 system. Briefly, DNA fragmentation was performed by sonication to 350 bp. These fragments were end polished, A tailed, and ligated with the Illumina sequencing adapter prior to amplification by PCR. Library preparation was accomplished for the qualified DNA using the NEBNext Ultra DNA library prep kit (New England BioLabs [NEB], USA) according to the manufacturer's protocol. DNA libraries were purified using the AMPure XP system, analyzed for size distribution using an Agilent 2100 bioanalyzer, and quantified by real-time PCR. Then, the qualified libraries were sequenced to an average sequencing depth of 250Â using the Illumina NovaSeq 150PE protocol generating 2 Â 150-bp paired-end reads. The raw output was transformed into raw reads by CASAVA base calling and converted into FASTQ file format, which produced 22,252,138 raw paired-end reads. The quality of the FASTQ file was assessed using FastQC software. The adapter and low-quality sequences were discarded using Trimmomatic (v0.36) by performing sliding window trimming with a minimum average quality of 20 and a minimum sequence read length of 20 bases (4). De novo genome assembly for the C. parapsilosis USM039K strain and annotation analyses were conducted using the Galaxy platform with default parameters or those otherwise stated (5). The assembly was generated by SPAdes (v3.12.0) (6), and the quality was assessed using
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G+C content of 38.65%, and 5,467 genes.
Tropical Medicine and Infectious Disease, Aug 16, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Here, we report the draft genome sequence of a Candida parapsilosis clinical isolate (USM026) tha... more Here, we report the draft genome sequence of a Candida parapsilosis clinical isolate (USM026) that was recovered from a blood sample from a patient who was treated for a catheter-related bloodstream infection (CRBSI). The draft genome is 12,839,916 bp in length, with 22,076,712 reads, 249 scaffolds, and 5,537 genes. C andida parapsilosis, a yeast belonging to the cellular organisms (Eukaryota superkingdom, Fungi kingdom, Dikarya subkingdom, Ascomycota phylum, Saccharomycotina subfamily, Saccharomycetes class, Saccharomycetales order, Debaryomycetaceae family, and Candida genus), is a major cause of candidemia worldwide (1). In this announcement, we present the draft genome sequence of a clinical isolate of C. parapsilosis. This will contribute to our understanding of the genetic variability among C. parapsilosis isolates and provide clues to genomic evolution. This isolate was recovered from a patient who had been admitted to Hospital Universiti Sains Malaysia (USM) (Kota Bharu, Kelantan, Malaysia) and later developed a catheter-related bloodstream infection (CRBSI). This work was approved by the Human Research Ethics Committee of USM (approval number JEPeM-USM-16040162). The isolate was subcultured on a Sabouraud dextrose agar (SDA) plate and incubated at 37°C overnight. Pure colonies were harvested in the stationary phase. Genomic DNA (gDNA) was extracted using a conventional DNA extraction method, namely, the phenol-chloroform-isoamyl alcohol DNA extraction protocol (2). Molecular identification by sequencing of the internal transcribed spacer (ITS) region of ribosomal DNA was performed for species confirmation (3). The DNA sample was fragmented by sonication to a size of 350 bp. DNA fragments were end polished, A-tailed, and ligated with full-length adaptors for Illumina sequencing. Library preparation with further PCR amplification was performed using the NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs, USA) according to the manufacturer's protocol. PCR products were purified (AMPure XP system), and libraries were analyzed for size distribution with an Agilent 2100 Bioanalyzer and quantified using real-time PCR. The qualified libraries were used to carry out sequencing. The sequencing was performed using an Illumina NovaSeq 150-bp paired-end protocol. The original optic data obtained by high-throughput sequencing (Illumina platform) were transformed into raw sequence reads by CASAVA base calling and stored in FASTQ (fq) format. In total, the sequencing produced 22,076,712 raw paired-end reads. Quality control was performed using FastQC software, and the adapter and low-quality sequences were removed with Trimmomatic (v0.36) (4) by performing sliding window trimming with a minimum average quality score of 20 and a minimum sequence read length of 20 bases. Genome assembly and annotation were performed in the Galaxy platform using default parameters unless stated otherwise (5). The gDNA was sequenced to an average sequencing depth of 254Â using the Illumina NovaSeq 6000 platform, producing 2 Â 150-bp paired-end
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G+C content of 38.65%, and 5,467 genes.
A reliable estimate of Candida parapsilosis antifungal susceptibility in candidemia patients is i... more A reliable estimate of Candida parapsilosis antifungal susceptibility in candidemia patients is increasingly important to track the spread of C. parapsilosis bloodstream infections and define the true burden of the ongoing antifungal resistance. A systematic review and meta-analysis (SRMA) were conducted aiming to estimate the global prevalence and identify patterns of antifungal resistance. A systematic literature search of the PubMed, Scopus, ScienceDirect and Google Scholar electronic databases was conducted on published studies that employed antifungal susceptibility testing (AFST) on clinical C. parapsilosis isolates globally. Seventy-nine eligible studies were included. Using meta-analysis of proportions, the overall pooled prevalence of three most important antifungal drugs; Fluconazole, Amphotericin B and Voriconazole resistant C. parapsilosis were calculated as 15.2% (95% CI: 9.2–21.2), 1.3% (95% CI: 0.0–2.9) and 4.7% (95% CI: 2.2–7.3), respectively. Based on study enrolmen...
Catheter-related bloodstream infection (CRBSI) is an important healthcare-associated infection ca... more Catheter-related bloodstream infection (CRBSI) is an important healthcare-associated infection caused by various nosocomial pathogens. Candida parapsilosis has emerged as a crucial causative agent for the CRBSI in the last two decades. Many factors have been associated with the development of CRBSI including, demography, pre-maturity, comorbidities (diabetes mellitus, hypertension, heart diseases, neuropathy, respiratory diseases, renal dysfunction, hematological and solid organ malignancies, and intestinal dysfunction), intensive care unit (ICU) admission, mechanical ventilation (MV), total parenteral nutrition (TPN), prior antibiotic and/or antifungal therapy, neutropenia, prior surgery, immunosuppressant, and type, site, number, and duration of catheters. This study aims to determine C. parapsilosis CRBSI risk factors. A retrospective study has been performed in an 853-bedded tertiary-care hospital in north-eastern Malaysia. All inpatients with C. parapsilosis positive blood cult...
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G1C content of 38.65%, and 5,467 genes. T his report is to present the draft genome sequence of a clinical isolate of Candida parapsilosis. C. parapsilosis is a yeast classified under cellular organisms, superkingdom of Eukaryota, kingdom of Fungi, subkingdom of Dikarya, phylum of Ascomycota, subfamily of Saccharomycotina, class of Saccharomycetes, order of Saccharomycetales, family of Debaryomycetaceae, and genus of Candida. This species is known as a causative agent for candidemia (1). The draft genome sequence of this species will enhance the current knowledge of the genetic variation among C. parapsilosis isolates. The organism was isolated from a patient with catheter-related bloodstream infection (CRBSI) in Hospital Universiti Sains Malaysia (USM), Kelantan, Malaysia. Ethical approvals were obtained from the Human Research Ethics of Universiti Sains Malaysia (JEPeM-USM-16040162). The isolate was cultivated overnight on a Sabouraud dextrose agar plate with yeast cultivation medium and incubated at 37°C. Pure colonies were collected during the stationary phase. DNA extraction was done using phenol-chloroform extraction followed by ethanol precipitation (2). Species identity was confirmed by the sequences of the internal transcribed spacer (ITS) region of ribosomal DNA (3). Sample quantity and quality were assessed prior to sequencing using the Illumina NovaSeq6000 system. Briefly, DNA fragmentation was performed by sonication to 350 bp. These fragments were end polished, A tailed, and ligated with the Illumina sequencing adapter prior to amplification by PCR. Library preparation was accomplished for the qualified DNA using the NEBNext Ultra DNA library prep kit (New England BioLabs [NEB], USA) according to the manufacturer's protocol. DNA libraries were purified using the AMPure XP system, analyzed for size distribution using an Agilent 2100 bioanalyzer, and quantified by real-time PCR. Then, the qualified libraries were sequenced to an average sequencing depth of 250Â using the Illumina NovaSeq 150PE protocol generating 2 Â 150-bp paired-end reads. The raw output was transformed into raw reads by CASAVA base calling and converted into FASTQ file format, which produced 22,252,138 raw paired-end reads. The quality of the FASTQ file was assessed using FastQC software. The adapter and low-quality sequences were discarded using Trimmomatic (v0.36) by performing sliding window trimming with a minimum average quality of 20 and a minimum sequence read length of 20 bases (4). De novo genome assembly for the C. parapsilosis USM039K strain and annotation analyses were conducted using the Galaxy platform with default parameters or those otherwise stated (5). The assembly was generated by SPAdes (v3.12.0) (6), and the quality was assessed using
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G+C content of 38.65%, and 5,467 genes.
Tropical Medicine and Infectious Disease, Aug 16, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Here, we report the draft genome sequence of a Candida parapsilosis clinical isolate (USM026) tha... more Here, we report the draft genome sequence of a Candida parapsilosis clinical isolate (USM026) that was recovered from a blood sample from a patient who was treated for a catheter-related bloodstream infection (CRBSI). The draft genome is 12,839,916 bp in length, with 22,076,712 reads, 249 scaffolds, and 5,537 genes. C andida parapsilosis, a yeast belonging to the cellular organisms (Eukaryota superkingdom, Fungi kingdom, Dikarya subkingdom, Ascomycota phylum, Saccharomycotina subfamily, Saccharomycetes class, Saccharomycetales order, Debaryomycetaceae family, and Candida genus), is a major cause of candidemia worldwide (1). In this announcement, we present the draft genome sequence of a clinical isolate of C. parapsilosis. This will contribute to our understanding of the genetic variability among C. parapsilosis isolates and provide clues to genomic evolution. This isolate was recovered from a patient who had been admitted to Hospital Universiti Sains Malaysia (USM) (Kota Bharu, Kelantan, Malaysia) and later developed a catheter-related bloodstream infection (CRBSI). This work was approved by the Human Research Ethics Committee of USM (approval number JEPeM-USM-16040162). The isolate was subcultured on a Sabouraud dextrose agar (SDA) plate and incubated at 37°C overnight. Pure colonies were harvested in the stationary phase. Genomic DNA (gDNA) was extracted using a conventional DNA extraction method, namely, the phenol-chloroform-isoamyl alcohol DNA extraction protocol (2). Molecular identification by sequencing of the internal transcribed spacer (ITS) region of ribosomal DNA was performed for species confirmation (3). The DNA sample was fragmented by sonication to a size of 350 bp. DNA fragments were end polished, A-tailed, and ligated with full-length adaptors for Illumina sequencing. Library preparation with further PCR amplification was performed using the NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs, USA) according to the manufacturer's protocol. PCR products were purified (AMPure XP system), and libraries were analyzed for size distribution with an Agilent 2100 Bioanalyzer and quantified using real-time PCR. The qualified libraries were used to carry out sequencing. The sequencing was performed using an Illumina NovaSeq 150-bp paired-end protocol. The original optic data obtained by high-throughput sequencing (Illumina platform) were transformed into raw sequence reads by CASAVA base calling and stored in FASTQ (fq) format. In total, the sequencing produced 22,076,712 raw paired-end reads. Quality control was performed using FastQC software, and the adapter and low-quality sequences were removed with Trimmomatic (v0.36) (4) by performing sliding window trimming with a minimum average quality score of 20 and a minimum sequence read length of 20 bases. Genome assembly and annotation were performed in the Galaxy platform using default parameters unless stated otherwise (5). The gDNA was sequenced to an average sequencing depth of 254Â using the Illumina NovaSeq 6000 platform, producing 2 Â 150-bp paired-end
Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) ... more Here, we announce the draft genome sequence of a Candida parapsilosis clinical isolate (USM039K) recovered from a patient with catheter-related bloodstream infection (CRBSI). The genome size is 12,860,016 bp long, with 188 scaffolds, a G+C content of 38.65%, and 5,467 genes.
A reliable estimate of Candida parapsilosis antifungal susceptibility in candidemia patients is i... more A reliable estimate of Candida parapsilosis antifungal susceptibility in candidemia patients is increasingly important to track the spread of C. parapsilosis bloodstream infections and define the true burden of the ongoing antifungal resistance. A systematic review and meta-analysis (SRMA) were conducted aiming to estimate the global prevalence and identify patterns of antifungal resistance. A systematic literature search of the PubMed, Scopus, ScienceDirect and Google Scholar electronic databases was conducted on published studies that employed antifungal susceptibility testing (AFST) on clinical C. parapsilosis isolates globally. Seventy-nine eligible studies were included. Using meta-analysis of proportions, the overall pooled prevalence of three most important antifungal drugs; Fluconazole, Amphotericin B and Voriconazole resistant C. parapsilosis were calculated as 15.2% (95% CI: 9.2–21.2), 1.3% (95% CI: 0.0–2.9) and 4.7% (95% CI: 2.2–7.3), respectively. Based on study enrolmen...
Catheter-related bloodstream infection (CRBSI) is an important healthcare-associated infection ca... more Catheter-related bloodstream infection (CRBSI) is an important healthcare-associated infection caused by various nosocomial pathogens. Candida parapsilosis has emerged as a crucial causative agent for the CRBSI in the last two decades. Many factors have been associated with the development of CRBSI including, demography, pre-maturity, comorbidities (diabetes mellitus, hypertension, heart diseases, neuropathy, respiratory diseases, renal dysfunction, hematological and solid organ malignancies, and intestinal dysfunction), intensive care unit (ICU) admission, mechanical ventilation (MV), total parenteral nutrition (TPN), prior antibiotic and/or antifungal therapy, neutropenia, prior surgery, immunosuppressant, and type, site, number, and duration of catheters. This study aims to determine C. parapsilosis CRBSI risk factors. A retrospective study has been performed in an 853-bedded tertiary-care hospital in north-eastern Malaysia. All inpatients with C. parapsilosis positive blood cult...
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