Population-Sequencing as a Biomarker ofBurkholderia malleiandBurkholderia pseudomalleiEvolution through Microbial Forensic Analysis

Large-scale genomics projects are identifying biomarkers to detect human disease.B. pseudomalleiandB. malleiare two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

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Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2010.00688 ◽

2010 ◽

Vol 36 (4) ◽

pp. 688-694

Author(s):

Yi-Jun WANG ◽

Yan-Ping LÜ ◽

Qin XIE ◽

De-Xiang DENG ◽

Yun-Long BIAN

Keyword(s):

Sorghum Bicolor ◽

Gene Family ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Characterization ◽

I Gene

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SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Scientific Reports ◽

10.1038/s41598-019-55144-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Weili Cai ◽

Schyler Nunziata ◽

John Rascoe ◽

Michael J. Stulberg

Keyword(s):

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Coverage ◽

Metagenomic Sample ◽

Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

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Whole-Genome Sequence of Multidrug-ResistantPseudomonas aeruginosaStrain BAMCPA07-48, Isolated from a Combat Injury Wound

Genome Announcements ◽

10.1128/genomea.00547-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 2

Author(s):

Fatemeh Sanjar ◽

S. L. Rajasekhar Karna ◽

Tsute Chen ◽

Ping Chen ◽

Johnathan J. Abercrombie ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

Valuable Resource ◽

Combat Injury ◽

Pathogen Surveillance

We report here the complete genome sequence ofPseudomonas aeruginosastrain BAMCPA07-48, isolated from a combat injury wound. The closed genome sequence of this isolate is a valuable resource for pathogenome characterization ofP. aeruginosaassociated with wounds, which will aid in the development of a higher-resolution phylogenomic framework for molecular-guided pathogen-surveillance.

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

10.21203/rs.3.rs-867901/v1 ◽

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.

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Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients

Future Microbiology ◽

10.2217/fmb-2019-0038 ◽

2019 ◽

Vol 14 (16) ◽

pp. 1357-1367

Author(s):

Jumamurat R Bayjanov ◽

Miquel B Ekkelenkamp ◽

Malbert RC Rogers ◽

Rafael Cantón ◽

Barry J Benaissa-Trouw ◽

...

Keyword(s):

Cystic Fibrosis ◽

Core Genome ◽

Genetic Characterization ◽

Novel Species ◽

Antibiotic Resistance Genes ◽

Whole Genome Sequence ◽

Whole Genome ◽

Whole Genome Analysis ◽

Acquired Antibiotic Resistance

Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.

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Genome Sequence of Venturia oleaginea, the Causal Agent of Olive Leaf Scab

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0070-a ◽

2020 ◽

Vol 33 (9) ◽

pp. 1095-1097

Author(s):

Mohammed Y. Jaber ◽

Jiandong Bao ◽

Xiuqin Gao ◽

Limei Zhang ◽

Dou He ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Population Genetic ◽

Whole Genome Sequence ◽

Whole Genome ◽

Olive Leaf ◽

Spot Disease ◽

Host Interaction ◽

Fungal Biology

Olive leaf scab, also known as peacock spot disease, caused by Venturia oleaginea (syn. Spilocaea oleaginea and Fusicladium oleagineum) is the most widespread and economically important fungal disease attacking olive in production countries. Here, we report the first highly contiguous whole-genome sequence (46.08 Mb) of one isolate, YUN35, of V. oleaginea. The described genome sequence and annotation resource will be useful to study the fungal biology, pathogen-host interaction, characterization of genes of interest, and population genetic diversity.

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

Viruses ◽

10.3390/v12020183 ◽

2020 ◽

Vol 12 (2) ◽

pp. 183 ◽

Cited By ~ 11

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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Large-Scale Whole-Genome Sequencing Reveals the Genetic Architecture of Primary Membranoproliferative GN and C3 Glomerulopathy

Journal of the American Society of Nephrology ◽

10.1681/asn.2019040433 ◽

2020 ◽

Vol 31 (2) ◽

pp. 365-373 ◽

Cited By ~ 7

Author(s):

Adam P. Levine ◽

Melanie M.Y. Chan ◽

Omid Sadeghi-Alavijeh ◽

Edwin K.S. Wong ◽

H. Terence Cook ◽

...

Keyword(s):

Large Scale ◽

Rare Variants ◽

Alternative Pathway ◽

Atypical Hemolytic Uremic Syndrome ◽

Gene Mutations ◽

Whole Genome Sequence ◽

European Ancestry ◽

Whole Genome ◽

C3 Glomerulopathy ◽

Complement Gene

BackgroundPrimary membranoproliferative GN, including complement 3 (C3) glomerulopathy, is a rare, untreatable kidney disease characterized by glomerular complement deposition. Complement gene mutations can cause familial C3 glomerulopathy, and studies have reported rare variants in complement genes in nonfamilial primary membranoproliferative GN.MethodsWe analyzed whole-genome sequence data from 165 primary membranoproliferative GN cases and 10,250 individuals without the condition (controls) as part of the National Institutes of Health Research BioResource–Rare Diseases Study. We examined copy number, rare, and common variants.ResultsOur analysis included 146 primary membranoproliferative GN cases and 6442 controls who were unrelated and of European ancestry. We observed no significant enrichment of rare variants in candidate genes (genes encoding components of the complement alternative pathway and other genes associated with the related disease atypical hemolytic uremic syndrome; 6.8% in cases versus 5.9% in controls) or exome-wide. However, a significant common variant locus was identified at 6p21.32 (rs35406322) (P=3.29×10−8; odds ratio [OR], 1.93; 95% confidence interval [95% CI], 1.53 to 2.44), overlapping the HLA locus. Imputation of HLA types mapped this signal to a haplotype incorporating DQA1*05:01, DQB1*02:01, and DRB1*03:01 (P=1.21×10−8; OR, 2.19; 95% CI, 1.66 to 2.89). This finding was replicated by analysis of HLA serotypes in 338 individuals with membranoproliferative GN and 15,614 individuals with nonimmune renal failure.ConclusionsWe found that HLA type, but not rare complement gene variation, is associated with primary membranoproliferative GN. These findings challenge the paradigm of complement gene mutations typically causing primary membranoproliferative GN and implicate an underlying autoimmune mechanism in most cases.

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Whole genome sequence and phenotypic characterization of a Cbm+serotypeestrain ofStreptococcus mutans

Molecular Oral Microbiology ◽

10.1111/omi.12222 ◽

2018 ◽

Vol 33 (3) ◽

pp. 257-269 ◽

Cited By ~ 2

Author(s):

A. Avilés-Reyes ◽

I. A. Freires ◽

J.K. Kajfasz ◽

D. Barbieri ◽

J.H. Miller ◽

...

Keyword(s):

Genome Sequence ◽

Whole Genome Sequence ◽

Phenotypic Characterization ◽

Whole Genome

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Characterization of a Novel Alphaherpesvirus Isolated from the Fruit Bat Pteropus lylei in Vietnam

Journal of Virology ◽

10.1128/jvi.00673-20 ◽

2020 ◽

Vol 94 (18) ◽

Author(s):

Takuya Inagaki ◽

Souichi Yamada ◽

Hikaru Fujii ◽

Tomoki Yoshikawa ◽

Miho Shibamura ◽

...

Keyword(s):

Genome Sequence ◽

Lung Fibroblasts ◽

Whole Genome Sequence ◽

Replication Capacity ◽

Human Embryonic Lung ◽

Host Animal ◽

Entire Genome ◽

Fruit Bat ◽

Hsv 1

ABSTRACT Herpesviruses exist in nature within each host animal. Ten herpesviruses have been isolated from bats and their biological properties reported. A novel bat alphaherpesvirus, which we propose to name “Pteropus lylei-associated alphaherpesvirus (PLAHV),” was isolated from urine of the fruit bat Pteropus lylei in Vietnam and characterized. The entire genome sequence was determined to be 144,008 bp in length and predicted to include 72 genes. PLAHV was assigned to genus Simplexvirus with other bat alphaherpesviruses isolated from pteropodid bats in Southeast Asia and Africa. The replication capacity of PLAHV in several cells was evaluated in comparison with that of herpes simplex virus 1 (HSV-1). PLAHV replicated better in the bat-originated cell line and less in human embryonic lung fibroblasts than HSV-1 did. PLAHV was serologically related to another bat alphaherpesvirus, Pteropodid alphaherpesvirus 1 (PtAHV1), isolated from a Pteropus hypomelanus-related bat captured in Indonesia, but not with HSV-1. PLAHV caused lethal infection in mice. PLAHV was as susceptible to acyclovir as HSV-1 was. Characterization of this new member of bat alphaherpesviruses, PLAHV, expands the knowledge on bat-associated alphaherpesvirology. IMPORTANCE A novel bat alphaherpesvirus, Pteropus lylei-associated alphaherpesvirus (PLAHV), was isolated from urine of the fruit bat Pteropus lylei in Vietnam. The whole-genome sequence was determined and was predicted to include 72 open reading frames in the 144,008-bp genome. PLAHV is circulating in a species of fruit bats, Pteropus lylei, in Asia. This study expands the knowledge on bat-associated alphaherpesvirology.

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