scholarly journals Prognostic Utility of Whole-Genome Sequencing and Polymerase Chain Reaction Tests of Ocular Fluids in Postprocedural Endophthalmitis

2020 ◽  
Vol 217 ◽  
pp. 325-334 ◽  
Author(s):  
Cecilia S. Lee ◽  
Bryan Hong ◽  
Sundeep K. Kasi ◽  
Christopher Aderman ◽  
Katherine E. Talcott ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Chain Reaction ◽  
Ocular Fluids ◽  
Prognostic Utility ◽  
Polymerase Chain

scholarly journals SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021

2021 ◽  
Author(s):  
Katsutoshi Nagano ◽  
Chihiro Tani-Sassa ◽  
Yumi Iwasaki ◽  
Yuna Takatsuki ◽  
Sonoka Yuasa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Disease Severity ◽  
Genome Sequencing ◽  
Melting Curve ◽  
Melting Curve Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Crucial Issue ◽  
Chain Reaction ◽  
Polymerase Chain

Background: The spread of SARS-CoV-2 variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID-19 for the N501Y and E484K mutations associated with SARS-CoV-2. Study design: Nasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription-polymerase chain reaction with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples were also subjected to whole genome sequencing. Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. Results: The ratio of cases showing the 501N+484K mutation rapidly increased from 8% in February to 46% in March. Whole genome sequencing revealed that the viruses with 501N+484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants were not found. Conclusions: We found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021.

scholarly journals Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Assèta Kagambèga ◽  
Lari M. Hiott ◽  
David S. Boyle ◽  
Elizabeth A. McMillan ◽  
Poonam Sharma ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Sub Saharan Africa ◽  
Whole Genome ◽  
Chain Reaction ◽  
Food Borne ◽  
Polymerase Chain ◽  
Sub Saharan

Abstract Background Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0. Results Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data. Conclusion We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.

scholarly journals In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms

2020 ◽  
Vol 189 (8) ◽  
pp. 841-849
Author(s):  
Fermín Acosta ◽  
Ana Fernández-Cruz ◽  
Sandra R Maus ◽  
Pedro J Sola-Campoy ◽  
Mercedes Marín ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Outbreak Strain ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Extensively Drug Resistant ◽  
Polymerase Chain

Abstract In 2013–2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011–2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.

scholarly journals Molecular Typing of Methicillin-sensitive and Methicillin-resistant Staphylococcus aureus: What Epidemiologists need to know from Plasmid Analysis to Whole Genome Sequencing.

2016 ◽  
Vol 6 (1) ◽  
pp. 31-43
Author(s):  
Ibrahim A. Al-Zahrani
Keyword(s):  
Staphylococcus Aureus ◽  
Polymerase Chain Reaction ◽  
Molecular Typing ◽  
Gel Electrophoresis ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Pulsed Field Gel Electrophoresis ◽  
Whole Genome ◽  
Chain Reaction ◽  
Methicillin Resistant ◽  
Polymerase Chain

Methicillin-resistant Staphylococcus aureus is an important nosocomial pathogen. The early identification of an outbreak, making use of a rapid, precise and simple methicillin-resistant Staphylococcus aureus typing technique, can lead to prompt and effective precautions that avoid further spread of the infection. Pulsed-field gel electrophoresis is considered the gold standard for methicillin-resistant Staphylococcus aureus typing and has been recently supported by multilocus sequence typing. SmaI-multiplex polymerase chain reaction typing is a novel polymerase chain reaction -based technique that combines the principles of pulsed-field gel electrophoresis, with simplicity of polymerase chain reaction and can be used in many routine clinical laboratories. Whole genome sequencing typing is a second generation sequencing technology and may ultimately replace the traditional molecular typing methods. This review aims to survey existing molecular typing techniques for Staphylococcus aureus and to discuss information for each method in order to aid researchers and clinical professionals in the selection and implementation of an optimal technique.

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