A 10-year follow-up of a child with mild case of xeroderma pigmentosum complementation group D diagnosed by whole-genome sequencing

2016 ◽  
Vol 32 (4) ◽  
pp. 174-180 ◽  
Author(s):  
Ryusuke Ono ◽  
Taro Masaki ◽  
Franklin Mayca Pozo ◽  
Yuka Nakazawa ◽  
Sigrid M. A. Swagemakers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Xeroderma Pigmentosum ◽  
Complementation Group ◽  
Whole Genome ◽  
Mild Case ◽  
Group D

scholarly journals Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle

2017 ◽  
Vol 80 (4) ◽  
pp. 654-660 ◽  
Author(s):  
Samuel J. Crowe ◽  
Alice Green ◽  
Kimberly Hernandez ◽  
Vi Peralta ◽  
Lyndsay Bottichio ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Samples ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Salmonella Infections ◽  
Outbreak Investigations ◽  
Consumption Rates ◽  
Foodborne Outbreaks

ABSTRACT High consumption rates and a multitude of brands make multistate foodborne outbreaks of Salmonella infections associated with chicken challenging to investigate, but whole genome sequencing is a powerful tool that can be used to assist investigators. Whole genome sequencing of pathogens isolated from clinical, environmental, and food samples is increasingly being used in multistate foodborne outbreak investigations to determine with unprecedented resolution how closely related these isolates are to one another genetically. In 2014, federal and state health officials investigated an outbreak of 146 Salmonella Heidelberg infections in 24 states. A follow-up analysis was conducted after the conclusion of the investigation in which 27 clinical and 24 food isolates from the outbreak underwent whole genome sequencing. These isolates formed seven clades, the largest of which contained clinical isolates from a subcluster of case patients who attended a catered party. One isolate from a chicken processed by a large producer was closely related genetically (zero to three single-nucleotide polymorphism differences) to the clinical isolates from these subcluster case patients. Chicken from this large producer was also present in the kitchen of the caterer on the day before the event, thus providing additional evidence that the chicken from this producer was the outbreak source. This investigation highlights how whole genome sequencing can be used with epidemiologic and traceback evidence to identify chicken sources of foodborne outbreaks.

scholarly journals Corrigendum and follow-up: Whole genome sequencing of multiple CRISPR-edited mouse lines suggests no excess mutations

2017 ◽  
Author(s):  
Kellie A. Schaefer ◽  
Benjamin W Darbro ◽  
Diana F. Colgan ◽  
Stephen H. Tsang ◽  
Alexander G. Bassuk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Mouse Line ◽  
Genome Data ◽  
Parental Lines ◽  
Mouse Lines

Our previous publication suggested CRISPR-Cas9 editing at the zygotic stage might unexpectedly introduce a multitude of subtle but unintended mutations, an interpretation that not surprisingly raised numerous questions. The key issue is that since parental lines were not available, might the reported variants have been inherited? To expand upon the limited available whole genome data on whether CRISPR-edited mice show more genetic variation, whole-genome sequencing was performed on two other mouse lines that had undergone a CRISPR-editing procedure. Again, parents were not available for either the Capn5 nor Fblim1 CRISPR-edited mouse lines, so strain controls were examined. Additionally, we also include verification of variants detected in the initial mouse line. Taken together, these whole-genome-sequencing-level results support the idea that in specific cases, CRISPR-Cas9 editing can precisely edit the genome at the organismal level and may not introduce numerous, unintended, off-target mutations.

scholarly journals Infection, recovery and re-infection of farmed mink with SARS-CoV-2

2021 ◽  
Author(s):  
Thomas Bruun Rasmussen ◽  
Jannik Fonager ◽  
Charlotte Sværke Jørgensen ◽  
Ria Lassaunière ◽  
Anne Sofie Hammer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Protein Gene ◽  
Virus Detection ◽  
Spike Protein ◽  
Whole Genome ◽  
Initial Infection ◽  
Follow Up Studies ◽  
Additional Sequence

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene. The infected mink recovered and after free-testing of the mink, the animals remained seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2.

scholarly journals Got Acetylene: A personal research retrospective

FEMS Microbes ◽  
2021 ◽  
Author(s):  
Ronald S Oremland
Keyword(s):  
Solar System ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Whole Genome ◽  
Outer Solar System ◽  
Cassini Mission ◽  
Personal Research ◽  
Made In

Abstract In research, sometimes sheer happenstance and serendipity make for an unexpected discovery. Once revealed and if interesting enough, such a finding and its follow-up investigations can lead to advances by others that leave its originators ‘scooped’ and mulling about what next to do with their unpublished data. Specifically what journals could it still be published in and be perceived as original. This is what occurred with us nearly 40 years ago with regard to our follow-up observations of acetylene fermentation and led us to concoct a ‘cock and bull’ story. We hypothesized about a plausible role for acetylene metabolism in the primordial biogeochemistry of Earth and the possibility of acetylene serving as a key life-sustaining substrate for alien microbes dwelling in the orbs of the outer solar system. With the passage of time advances were made in whole genome sequencing coupled with major in silico progress in bioinformatics. In parallel came the results of explorations of the outer solar system (i.e. the Cassini mission to Saturn and its moons). It now appears that these somewhat harebrained ideas of ours, arisen at first out of a sense of desperation, actually ring true in fact, and particularly well in song: “Tell a tale of cock and bull, Of convincing detail full Tale tremendous, Heav'n defend us! What a tale of cock and bull!” From ‘Yeoman of the Guard’ by Gilbert & Sullivan.

scholarly journals The O-Antigen Epitope Governs Susceptibility to Colistin in Salmonella enterica

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Vito Ricci ◽  
Dexian Zhang ◽  
Christopher Teale ◽  
Laura J. V. Piddock
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Content Type ◽  
O Antigen ◽  
Antigen Epitope ◽  
Group B ◽  
O Antigens ◽  
Group D

ABSTRACT Group D and group B Salmonella enterica serovars differ in their susceptibility to colistin with the former frequently intrinsically resistant (MIC > 2 μg/ml); however, the mechanism has not been described. Here, we show that the O-antigen epitope in group D Salmonella governs the levels of colistin susceptibility. Substitution of the rfbJ gene in a group B Salmonella with the rfbSE genes from a group D Salmonella conferred a decrease in susceptibility to colistin. The presence of dideoxyhexose, abequose, and the deoxymannose, tyvelose, differentiate the Salmonella group B and group D O antigens, respectively. We hypothesize that the subtle difference between abequose and tyvelose hinders the colistin molecule from reaching its target. Whole-genome sequencing also revealed that increased colistin susceptibility in a group D Salmonella veterinary isolate was due to a defect in the O-antigen polymerase protein, Rfc. This study shows that two different mechanisms that influence the presence and composition of O antigens affect colistin susceptibility in Salmonella enterica. IMPORTANCE Some serovars of Salmonella, namely, those belonging to group D, appear to show a degree of intrinsic resistance to colistin. This observed intrinsic colistin resistance is of concern since this last-resort drug might no longer be effective for treating severe human infections with the most common Salmonella serovar, Salmonella enterica serovar Enteritidis. Here, we show that the O-antigen epitope in group D Salmonella governs the levels of colistin susceptibility. Using whole-genome sequencing, we also revealed that increased colistin susceptibility in a group D Salmonella veterinary isolate was due to a defect in the O-antigen polymerase protein, Rfc. In summary, we show that two different mechanisms that influence the presence and composition of O antigens affect colistin susceptibility in Salmonella enterica.

scholarly journals Whole Genome Sequencing and Custom Liquid Biopsy Markers in Sarcomas

2021 ◽  
Author(s):  
Felix Haglund de Flon ◽  
Cecilia Arthur ◽  
Hero Nikdin Awier ◽  
Yi Chen ◽  
Jesper Eisfeldt ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Fusion Gene ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Liquid Biopsies ◽  
Prognostic Information ◽  
Genetic Changes ◽  
Rare Tumours

Abstract Background: Sarcomas are rare tumours with heterogeneous clinical behaviour including varying rates of metastasis. Clinical treatment and follow-up rely on crude grading systems with uncertain accuracy for individual patients. Whole genome sequencing (WGS) detects both structural variation and single nucleotide variants and may thus add important diagnostic/prognostic information. Liquid biopsies (LB) may potentially identify hematogenous spread and treatment response rate but further evaluation in sarcomas is needed. Methods: In this study we explore the performance of individualized LB in four patients with different types of sarcomas. Fresh frozen tumour tissue was sequenced using WGS and whole transcriptome sequencing. Three putative driver variants or one fusion gene were selected per case and custom digital droplet PCR (ddPCR) assays were designed, evaluated on tumour DNA and used to assess levels of cell free tumour DNA in plasma taken prior to surgery. Results: In LB, ddPCR identified three variants in one patient with metastatic disease. The remaining three patients had negative LBs and were without disease at follow-up (>18 months after surgery). Conclusions: WGS is a powerful tool to detect all types of genetic changes in sarcoma and can facilitate clinical diagnosis/classification while custom LB may add prognostic information.

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