Whole Genome Sequence Analysis and Population Genomics of Group A Streptococci

2020 ◽  
pp. 81-111
Author(s):  
Jake A. Lacey ◽  
Taylah B. James ◽  
Steven Y. C. Tong ◽  
Mark R. Davies
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Population Genomics ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Group A Streptococci ◽  
Genome Sequence Analysis ◽  
Group A

Whole-genome sequence analysis of G3 and G14 equine group A rotaviruses isolated in the late 1990s and 2009-2010

2015 ◽  
Vol 160 (5) ◽  
pp. 1171-1179 ◽  
Author(s):  
Manabu Nemoto ◽  
Makoto Nagai ◽  
Hiroshi Tsunemitsu ◽  
Tsutomu Omatsu ◽  
Tetsuya Furuya ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Group A Rotaviruses ◽  
Group A

30-OR: Whole Genome Sequence Analysis of Type 2 Diabetes Risk in 44,713 Humans of Diverse Ancestry in the TOPMed Study

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 30-OR
Author(s):  
HEATHER M. HIGHLAND ◽  
JENNIFER WESSEL ◽  
ALISA MANNING ◽  
Keyword(s):  
Type 2 Diabetes ◽  
Sequence Analysis ◽  
Genome Sequence ◽  
Diabetes Risk ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis

scholarly journals Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Sarah Flohr ◽  
Alban Ramette ◽  
Philipp K A Agyeman ◽  
Andrea Duppenthaler ◽  
Cordula Scherer ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Surgical Therapy ◽  
Skin Infection ◽  
Whole Genome Sequence ◽  
Factitious Disorder ◽  
Whole Genome ◽  
Mycobacterium Chelonae ◽  
Genome Sequence Analysis ◽  
Adequate Therapy

Abstract Mycobacterium chelonae infections usually resolve with adequate therapy. We report the case of an adolescent with a chronic and progressive M chelonae infection refractory to combined antimicrobial and surgical therapy. Whole genome sequence analysis of consecutive isolates distinguished reinfection from recurrence and contributed to the diagnosis of a factitious disorder.

scholarly journals Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada

PLoS ONE ◽  
2017 ◽  
Vol 12 (10) ◽  
pp. e0185656 ◽  
Author(s):  
Andrea D. Tyler ◽  
Elaine Randell ◽  
Maureen Baikie ◽  
Kym Antonation ◽  
Debra Janella ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Sequence Analysis ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis

Prevalence and Molecular Characterization of Novel Pathogenic Strains of Macrococcus Caseolyticus Isolated From External Wounds of Donkeys in Khartoum State –Sudan

2021 ◽  
Author(s):  
Dania Ali ◽  
Mushal Allam ◽  
Hisham Altayb ◽  
Dalia Mursi ◽  
M. A Abdalla ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Resistant Genes ◽  
Different Seasons ◽  
Novel Alleles

Abstract A pathogenic strains of Macrococcus caseolyticus was isolated from wounds infection during investigation on donkeys in Khartoum State. Samples were collected from external wounds (head, abdomin, back and leg), during different seasons of the year. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified thirty-one virulent genes of disease and defense including methicillin resistant genes, TatR family and ANT(4’)-Ib. Plasmid rep22 wasidentified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel strain of M.caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain Daniasudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. The prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. Mice modling showen bacteremia and many clinical (swelling, allergy, wounds and loss of hair). Enlarged, hyperemia, adhesions and abscesses were observed in many organs. This represents the first report of pathogenic strains of M.caseolyticus worldwide.

scholarly journals Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma

Oncoscience ◽  
2015 ◽  
Vol 2 (7) ◽  
pp. 618-628 ◽  
Author(s):  
John M. Furgason ◽  
Robert F. Koncar ◽  
Sharon K. Michelhaugh ◽  
Fazlul H. Sarkar ◽  
Sandeep Mittal ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

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