scholarly journals High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity in Fecal Samples From Birds

2018 ◽  
Vol 9 ◽  
Author(s):  
Qian Zhang ◽  
Gabriel A. Al-Ghalith ◽  
Mayumi Kobayashi ◽  
Takahiro Segawa ◽  
Mitsuto Maeda ◽  
...  
Keyword(s):  
High Throughput ◽  
Variable Region ◽  
Fecal Samples ◽  
Short Variable Region

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

scholarly journals Broiler Campylobacter Contamination and Human Campylobacteriosis in Iceland

2008 ◽  
Vol 74 (21) ◽  
pp. 6483-6494 ◽  
Author(s):  
Kenneth A. Callicott ◽  
Hj�rd�s Har�ard�ttir ◽  
Frankl�n Georgsson ◽  
Jarle Reiersen ◽  
Vala Fri�riksd�ttir ◽  
...  
Keyword(s):  
Human Disease ◽  
Broiler Chicken ◽  
Variable Region ◽  
Time Frame ◽  
Lot Size ◽  
Individual Product ◽  
Contamination Levels ◽  
Multiple Clusters ◽  
Human Campylobacteriosis ◽  
Short Variable Region

ABSTRACT To examine whether there is a relationship between the degree of Campylobacter contamination observed in product lots of retail Icelandic broiler chicken carcasses and the incidence of human disease, 1,617 isolates from 327 individual product lots were genetically matched (using the flaA short variable region [SVR[) to 289 isolates from cases of human campylobacteriosis whose onset was within approximately 2 weeks from the date of processing. When there was genetic identity between broiler isolates and human isolates within the appropriate time frame, a retail product lot was classified as implicated in human disease. According to the results of this analysis, there were multiple clusters of human disease linked to the same process lot or lots. Implicated and nonimplicated retail product lots were compared for four lot descriptors: lot size, prevalence, mean contamination, and maximum contamination (as characterized by direct rinse plating). For retail product distributed fresh, Mann-Whitney U tests showed that implicated product lots had significantly (P = 0.0055) higher mean contamination than nonimplicated lots. The corresponding median values were 3.56 log CFU/carcass for implicated lots and 2.72 log CFU/carcass for nonimplicated lots. For frozen retail product, implicated lots were significantly (P = 0.0281) larger than nonimplicated lots. When the time frame was removed, retail product lots containing Campylobacter flaA SVR genotypes also seen in human disease had significantly higher mean and maximum contamination numbers than lots containing no genotypes seen in human disease for both fresh and frozen product. Our results suggest that cases of broiler-borne campylobacteriosis may occur in clusters and that the differences in mean contamination levels may provide a basis for regulatory action that is more specific than a presence-absence standard.

scholarly journals On the evolution and biogeography of Apple stem grooving capillovirus.

2020 ◽  
Author(s):  
Kamal Shujaei ◽  
Adrian John Gibbs ◽  
Mohammad Hajizadeh
Keyword(s):  
Coat Protein ◽  
Negative Selection ◽  
Variable Region ◽  
Genetic Evolution ◽  
Founder Effects ◽  
Factors Affecting ◽  
Northern India ◽  
Apple Stem ◽  
The Usa ◽  
Short Variable Region

Abstract Apple stem grooving Capillovirus (ASGV) has a wide host range, notably apples, pears and citrus. It is found worldwide. In this study, the published nucleotide sequences of the genomes of 60 isolates and of over 200 coat protein (CP) genes, including those of seven newly determined Iranian isolates, were analyzed. The non-recombinant genomes showed that sequences concatenated from the replicase genes (minus a short variable region), together with the movement and CP genes gave the best supported ML phylogenies, and these also correlated best with CP phylogenies, so that information from phylogenies of the genomic sequences could be augmented, with caution, by that from CP phylogenies. The basal ASGV population was only isolated from CP samples from Himachal Pradesh of northern India. Its progeny lineages diverged into populations in south and east Asia, especially China. The ASVG population in the USA probably came from a Chinese lineage, and the Eurasian one, including seven Iranian isolates, from Indian lineages. The analyses suggests that trade, negative selection and founder effects were the most important factors affecting the genetic evolution of ASGV.

Identification and characterization of the short variable region of the Japanese encephalitis virus 3′ NTR

Virus Genes ◽  
2011 ◽  
Vol 44 (2) ◽  
pp. 191-197 ◽  
Author(s):  
Fumihiro Kato ◽  
Akira Kotaki ◽  
Yukie Yamaguchi ◽  
Hajime Shiba ◽  
Kuniaki Hosono ◽  
...  
Keyword(s):  
Japanese Encephalitis Virus ◽  
Japanese Encephalitis ◽  
Variable Region ◽  
Encephalitis Virus ◽  
Identification And Characterization ◽  
Short Variable Region

scholarly journals Differentiation of Campylobacter Populations as Demonstrated by Flagellin Short Variable Region Sequences

2005 ◽  
Vol 71 (10) ◽  
pp. 6368-6374 ◽  
Author(s):  
Richard J. Meinersmann ◽  
Robert W. Phillips ◽  
Kelli L. Hiett ◽  
Paula Fedorka-Cray
Keyword(s):  
Population Structure ◽  
Synonymous Codon ◽  
Variable Region ◽  
Synonymous Codon Usage ◽  
Relative Synonymous Codon Usage ◽  
Clonal Population ◽  
Significant Differentiation ◽  
Clonal Population Structure ◽  
Usage Analysis ◽  
Short Variable Region

ABSTRACT The DNA sequence of the flaA short variable region (SVR) was used to analyze a random population of Campylobacter isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of C. jejuni and C. coli isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both C. jejuni and C. coli strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified C. jejuni, and the second group was characteristic for C. coli and the disparate alleles were not clustered. The data show that there is significant differentiation of Campylobacter populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from Campylobacter species other than C. jejuni and C. coli. It is evident that recombination within the flaA SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.

scholarly journals High-throughput UHPLC-MS to screen metabolites in feces for gut metabolic health

2021 ◽  
Author(s):  
Andressa de Zawadzki ◽  
Maja Thiele ◽  
Tommi Suvitaival ◽  
Asger Wretlind ◽  
Min Kim ◽  
...  
Keyword(s):  
High Throughput ◽  
Metabolic Diseases ◽  
Quality Data ◽  
High Quality Data ◽  
Fecal Samples ◽  
Heterogeneous Samples ◽  
Relative Standard ◽  
High Throughput Method ◽  
Related Liver Disease ◽  
Metabolite Detection

(1) Background: Feces are the product of our diets and have been linked to diseases of the gut, including Crohn's disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. (2) Methods: As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n= 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. (3) Results: MS analyses of the prepared fecal samples have shown reproducibility and coverage of n=28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD, LOQ and range of linearity. The average concentrations for 135 healthy participants are reported here for clinical applications. (4) Conclusions: our high-throughput method provides an efficient tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.

scholarly journals DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses

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