scholarly journals 864. Whole Genome Sequencing is Unable to Track Candida auris Transmission

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S470-S471
Author(s):  
Scott C Roberts ◽  
Egon A Ozer ◽  
Teresa Zembower ◽  
Chao Qi
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Candida Auris ◽  
Healthcare Settings ◽  
Long Read ◽  
Outbreak Investigations ◽  
Phylogenetic Grouping

Abstract Background Candida auris (C. auris), an emerging yeast species, is often drug-resistant and has caused outbreaks in healthcare settings. Surging C. auris cases at our institution prompted whole genome sequencing (WGS) of patient and environmental specimens and comparison to local and international isolates. Methods WGS was performed on clinical and environmental isolates obtained from Northwestern Memorial Hospital (NMH) from June 2018 to December 2019. Genome sequences were compared against isolates from other institutions in the Chicagoland area obtained from a reference lab (ACL) and from the CDC. Two isolates underwent long-read sequencing on the Oxford Nanopore GridION platform to obtain closed genomes. WGS was performed on the remaining isolates with the Illumina MiSeq platform. Results Twenty isolates from NMH, five from ACL, and two from the CDC underwent WGS to yield 12.6 Mb genomes. Any two NMH isolates differed from each other by a maximum of 36 single nucleotide variants (SNV) (Figure 1). Two patients thought to be part of a transmission cluster (isolates CA06 and CA07), differed by 7 SNVs. No phylogenetic grouping between hospital systems across Chicagoland was observed. Isolates from room surfaces from a C. auris patient differed by 1-6 SNVs from each other and from 7-8 SNVs from the patient isolate. Samples taken from different body sites of another patient differed by 4-9 SNVs. Average SNV counts were lower among nosocomially acquired cases when compared to C. auris isolates present on admission (Figure 2). All NMH isolates were fluconazole sensitive, but a fluconazole resistant ACL isolate differed from a sensitive NMH isolate by only 4 SNVs. Figure 1: Phylogenetic tree of all NMH and ACL isolates with fluconazole sensitivities Figure 2: Observed pairwise SNP differences between nosocomial and POA strains Conclusion WGS of C. auris did not reveal identical isolates in any instance, even from the same patient or the patients and their environment. Generally, lower numbers of SNVs were observed for intra- versus inter-institutional isolates. More work is needed to determine the use, if any, of WGS in outbreak investigations. Disclosures All Authors: No reported disclosures

scholarly journals Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant

2021 ◽  
Author(s):  
Jeroen J. Smits ◽  
Suzanne E. de Bruijn ◽  
Cornelis P. Lanting ◽  
Jaap Oostrik ◽  
Luke O’Gorman ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Mapping ◽  
Whole Genome ◽  
Missing Heritability ◽  
Single Nucleotide Variants ◽  
Vestibular Aqueduct ◽  
Pathogenic Variants ◽  
Long Read

AbstractPathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.

scholarly journals Transmission of SARS-CoV-2 from asymptomatic and presymptomatic individuals in healthcare settings despite medical masks and eye protection

2021 ◽  
Author(s):  
Michael Klompas ◽  
Meghan A Baker ◽  
Diane Griesbach ◽  
Robert Tucker ◽  
Glen R Gallagher ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Eye Protection ◽  
Healthcare Settings

Abstract We describe 3 instances of SARS-CoV-2 transmission despite medical masks and eye protection, including transmission despite the source person being masked, transmission despite the exposed person being masked, and transmission despite both parties being masked. Whole genome sequencing confirmed perfect homology between source and exposed persons’ viruses in all cases.

scholarly journals Whole Genome Sequencing and Antimicrobial Resistance of Staphylococcus aureus from Surgical Site Infections in Ghana

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 196
Author(s):  
Beverly Egyir ◽  
Jeannette Bentum ◽  
Naiki Attram ◽  
Anne Fox ◽  
Noah Obeng-Nkrumah ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Meca Gene ◽  
Surgical Site Infections ◽  
Illumina Miseq ◽  
Multi Drug Resistance ◽  
Toxin Gene ◽  
Whole Genome ◽  
Flight Mass Spectrometry

Staphylococcus aureus (S. aureus) is a common cause of surgical site infections (SSIs) globally. Data on the occurrence of methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) among patients with surgical site infections (SSIs) in sub-Saharan African are scarce. We characterized S. aureus from SSIs in Ghana using molecular methods and antimicrobial susceptibility testing (AST). Wound swabs or aspirate samples were collected from subjects with SSIs. S. aureus was identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF-MS); AST was performed by Kirby-Bauer disk diffusion, and results were interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline. Detection of spa, mecA, and pvl genes was performed by polymerase chain reaction (PCR). Whole-genome sequencing (WGS) was done using the Illumina MiSeq platform. Samples were collected from 112 subjects, with 13 S. aureus isolates recovered. Of these, 92% were sensitive to co-trimoxazole, 77% to clindamycin, and 54% to erythromycin. Multi-drug resistance was detected in 5 (38%) isolates. The four mecA gene-positive MRSA isolates detected belonged to ST152 (n = 3) and ST5 (n = 1). In total, 62% of the isolates were positive for the Panton-Valentine leukocidin (pvl) toxin gene. This study reports, for the first time, a pvl-positive ST152-t355 MRSA clone from SSIs in Ghana. The occurrence of multi-drug-resistant S. aureus epidemic clones suggests that continuous surveillance is required to monitor the spread and resistance trends of S. aureus in hospital settings in the country.

Generating 1200bp tiled Amplicons for SARS-CoV2 Whole Genome Sequencing v2

2022 ◽  
Author(s):  
jason.nguyen not provided ◽  
Tracy Lee ◽  
Rebecca Hickman ◽  
Natalie Prystajecky ◽  
John Tyson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Oxford Nanopore ◽  
Sequencing Platforms

This procedure provides instructions for how to generate amplicons across the entire SARS-CoV-2 genome to be used for downstream whole genome sequencing applications, including Illumina MiSeq/NextSeq or Oxford Nanopore MinION sequencing platforms. The steps involved in this protocol were derived from version 3 of Freed et al protocol nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon)V.3 available at https://dx.doi.org/10.17504/protocols.io.bgggjttw

Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

2018 ◽  
Vol 64 (3) ◽  
pp. 191-197 ◽  
Author(s):  
Takeshi Mizuguchi ◽  
Tomoko Toyota ◽  
Hiroaki Adachi ◽  
Noriko Miyake ◽  
Naomichi Matsumoto ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Repeat Expansion ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Long Read

scholarly journals Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

2018 ◽  
Author(s):  
Maxime Garcia ◽  
Szilveszter Juhos ◽  
Malin Larsson ◽  
Pall I. Olason ◽  
Marcel Martin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Open Source ◽  
Genome Sequencing ◽  
Development Project ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Insertion And Deletion ◽  
Sample Heterogeneity

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

scholarly journals Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

2018 ◽  
Vol 12 (6) ◽  
pp. e0006566 ◽  
Author(s):  
Elizabeth M. Batty ◽  
Suwittra Chaemchuen ◽  
Stuart Blacksell ◽  
Allen L. Richards ◽  
Daniel Paris ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Orientia Tsutsugamushi ◽  
Human Pathogen ◽  
Long Read

Rapid, high throughput library preparation of SARS-CoV2 using Illumina’s DNA Prep Library Preparation Kit v2

2022 ◽  
Author(s):  
Jason Nguyen ◽  
Rebecca Hickman ◽  
Tracy Lee ◽  
Natalie Prystajecky ◽  
John Tyson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Library Preparation ◽  
Dna Libraries ◽  
Reaction Volumes ◽  
Single Size ◽  
Stop Buffer

This procedure provides instructions on how to prepare DNA libraries for whole genome sequencing on an Illumina MiSeq or NextSeq using Illumina’s DNA Prep Library Preparation Kit scaled to half reaction volumes with modifications to the post-PCR procedures; tagmentation stop buffer and associated washes are removed and libraries are pooled post PCR then a single size selection is performed. This protocol is used to sequence SARS-CoV-2 using the cDNA/PCR protocol: https://dx.doi.org/10.17504/protocols.io.b3viqn4e

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