scholarly journals Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197, Isolated from Hybrid Striped Bass (Morone sp.) in the United States

2017 ◽  
Vol 5 (29) ◽  
Author(s):  
Yuki Teru ◽  
Jun-ichi Hikima ◽  
Tomoya Kono ◽  
Masahiro Sakai ◽  
Tomokazu Takano ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Striped Bass ◽  
The United States ◽  
Whole Genome Sequence ◽  
Economic Damage ◽  
Whole Genome ◽  
Content Type ◽  
Photobacterium Damselae ◽  
Causative Bacterium

ABSTRACT Photobacterium damselae subsp. piscicida is a causative bacterium of fish pasteurellosis, which has caused serious economic damage to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida 91-197, isolated in the United States, suggests that this genome consists of two chromosomes and two plasmids.

scholarly journals Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

2016 ◽  
Vol 2 (7) ◽  
pp. e1501714 ◽  
Author(s):  
Bridgett M. vonHoldt ◽  
James A. Cahill ◽  
Zhenxin Fan ◽  
Ilan Gronau ◽  
Jacqueline Robinson ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
North American ◽  
Sequence Data ◽  
The United States ◽  
Geographic Range ◽  
Whole Genome Sequence ◽  
Gray Wolf ◽  
Whole Genome ◽  
Eastern Wolf

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.

scholarly journals Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Sopio Chochua ◽  
Ben J. Metcalf ◽  
Zhongya Li ◽  
Joy Rivers ◽  
Saundra Mathis ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Group A Streptococci ◽  
Phylogenetic Clustering ◽  
Streptolysin O ◽  
Group A

ABSTRACTGroup A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing. Predictions were made for genotype, GAS carbohydrate, antimicrobial resistance, surface proteins (M family, fibronectin binding, T, R28), secreted virulence proteins (Sda1, Sic, exotoxins), hyaluronate capsule, and an upregulatedngaoperon (encodes NADase and streptolysin O) promoter (Pnga3). Sixty-four M protein gene (emm) types were identified among 69 clonal complexes (CCs), including one CC ofStreptococcus dysgalactiaesubsp.equisimilis.emmtypes predicted the presence or absence of activesofdeterminants and were segregated intosof-positive orsof-negative genetic complexes. Only one “emmtype switch” between strains was apparent.sof-negative strains showed a propensity to cause infections in the first quarter of the year, whilesof+strain infections were more likely in summer. Of 1,454 isolates, 808 (55.6%) were Pnga3 positive and 637 (78.9%) were accounted for by typesemm1,emm89, andemm12. Theoretical coverage of a 30-valent M vaccine combined with an M-related protein (Mrp) vaccine encompassed 98% of the isolates. WGS data predicted that 15.3, 13.8, 12.7, and 0.6% of the isolates were nonsusceptible to tetracycline, erythromycin plus clindamycin, erythromycin, and fluoroquinolones, respectively, with only 19 discordant phenotypic results. Close phylogenetic clustering ofemm59isolates was consistent with recent regional emergence. This study revealed strain traits informative for GAS disease incidence tracking, outbreak detection, vaccine strategy, and antimicrobial therapy.IMPORTANCEThe current population-based WGS data from GAS strains causing invasive disease in the United States provide insights important for prevention and control strategies. Strain distribution data support recently proposed multivalent M type-specific and conserved M-like protein vaccine formulations that could potentially protect against nearly all invasive U.S. strains. The three most prevalent clonal complexes share key polymorphisms in thengaoperon encoding two secreted virulence factors (NADase and streptolysin O) that have been previously associated with high strain virulence and transmissibility. We find thatStreptococcus pyogenesis phylogenetically subdivided into loosely defined multilocus sequence type-based clusters consisting of solelysof-negative orsof-positive strains; withsof-negative strains demonstrating differential seasonal preference for infection, consistent with the recently demonstrated differential seasonal preference based on phylogenetic clustering of full-length M proteins. This might relate to the differences in GAS strain compositions found in different geographic settings and could further inform prevention strategies.

scholarly journals Whole-Genome Sequence of High Salt and Heavy Metal-Tolerant Bacillus stratosphericus Strain 5Co, Isolated from Lichen Usnea florida in Central Florida, United States

2017 ◽  
Vol 5 (24) ◽  
Author(s):  
Pushpa Lata ◽  
Subramaniam S. Govindarajan ◽  
Feng Qi ◽  
Jian-Liang Li ◽  
Santosh K. Maurya ◽  
...  
Keyword(s):  
United States ◽  
Heavy Metal ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences ◽  
Content Type ◽  
Central Florida

ABSTRACT Bacillus stratosphericus strain 5Co was isolated from lichen Usnea florida in central Florida, United States. Here, we report a draft genome sequence of this strain, which consists of 159 contigs spanning 3,628,496 bp, with a G+C content of 41.3% and comprises 3,729 predicted coding sequences.

scholarly journals Complete Genome Sequence of Photobacterium damselae subsp. piscicida Strain OT-51443 Isolated from Yellowtail (Seriola quinqueradiata) in Japan

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Takashi Aoki ◽  
Yuki Teru ◽  
Natsuki Morimoto ◽  
Tomoya Kono ◽  
Masahiro Sakai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Seriola Quinqueradiata ◽  
Photobacterium Damselae ◽  
Economic Damages

ABSTRACT Pseudotuberculosis caused by infection of Photobacterium damselae subsp. piscicida has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida strain OT-51443, isolated in Japan, was determined and suggests that this genome consists of two chromosomes and five plasmids.

scholarly journals Whole-Genome Sequence Analysis of CTX-M Containing Escherichia coli Isolates from Retail Meats and Cattle in the United States

2018 ◽  
Vol 24 (7) ◽  
pp. 939-948 ◽  
Author(s):  
Daniel A. Tadesse ◽  
Cong Li ◽  
Sampa Mukherjee ◽  
Chih-Hao Hsu ◽  
Sonya Bodeis Jones ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genome Sequence ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Retail Meats

scholarly journals First Complete Genome Sequence of a Feline Morbillivirus Isolate from Germany

2018 ◽  
Vol 6 (16) ◽  
pp. e00244-18 ◽  
Author(s):  
Michael Sieg ◽  
Annett Vahlenkamp ◽  
Christoph Georg Baums ◽  
Thomas Wilhelm Vahlenkamp
Keyword(s):  
United States ◽  
Cell Culture ◽  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Cell Culture Isolation

ABSTRACT The first cell culture isolation and whole-genome sequence of a feline morbillivirus from Germany are described here. Phylogenetic analysis revealed highest similarity to isolates from Japan and a more distant relationship to strains from Italy, Hong Kong, and the United States. Therefore, feline morbilliviruses should be divided into two different genotypes.

scholarly journals Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region

2020 ◽  
Vol 58 (7) ◽  
Author(s):  
S. Wesley Long ◽  
Matthew Ojeda Saavedra ◽  
Paul A. Christensen ◽  
James M. Musser ◽  
Randall J. Olsen
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Clinical Laboratory ◽  
Draft Genome ◽  
The United States ◽  
Metropolitan Region ◽  
Whole Genome Sequence ◽  
Candida Auris ◽  
Content Type ◽  
African Clade

ABSTRACT Candida auris is a pathogen of considerable public health importance. It was first reported in 2009. Five clades, determined by genomic analysis and named by the distinct regions where they were initially identified, have been defined. We previously completed a draft genome sequence of an African clade (clade III) strain cultured from the urine of a patient hospitalized in the greater Houston metropolitan region (strain LOM). Although initially uncommon, reports of the African clade in the United States have grown to include a recent cluster in California. Here, we describe a second human C. auris infection in the Houston area. Whole-genome sequence analysis demonstrated the Houston patient isolates to be clonally related to one another but distantly related to other African clade organisms recovered in the United States or elsewhere. Infections in these patients were present on admission to the hospital and occurred several months apart. Taken together, the data demonstrate the emergence and persistence of a clonal C. auris population and highlights the importance of routine high-resolution genomic surveillance of emerging human pathogens in the clinical laboratory.

scholarly journals Complete Genome Sequence of the Arcobacter skirrowii Type Strain LMG 6621

2018 ◽  
Vol 7 (17) ◽  
Author(s):  
William G. Miller ◽  
Emma Yee
Keyword(s):  
Genome Sequence ◽  
Fecal Sample ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
The United Kingdom ◽  
Veterinary Importance

Arcobacter skirrowii is a species of veterinary importance, originally recovered from the feces, aborted fetuses, and preputial fluids of livestock. We present here the whole-genome sequence of the A. skirrowii type strain LMG 6621 (= 449/80T = CCUG 10374T), isolated in the United Kingdom from a lamb diarrheal fecal sample.

scholarly journals Corrected Genome Sequence of Acinetobacter baumannii Strain AB0057, an Antibiotic-Resistant Isolate from Lineage 1 of Global Clone 1

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Mohammad Hamidian ◽  
Pratap Venepally ◽  
Ruth M. Hall ◽  
Mark D. Adams
Keyword(s):  
United States ◽  
Acinetobacter Baumannii ◽  
Genome Sequence ◽  
The United States ◽  
Targeted Sequencing ◽  
Resistant Isolate ◽  
Illumina Hiseq ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Pcr Products

ABSTRACT Extensively antibiotic-resistant Acinetobacter baumannii isolate AB0057 recovered in the United States in 2004 was one of the first global clone 1 isolates to be completely sequenced. Here, the complete 4.05-Mb genome sequence (chromosome and one plasmid) has been revised using Illumina HiSeq data and targeted sequencing of PCR products.

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