scholarly journals A Dynamic Whole-genome Database for Comparative Analyses, Molecular Epidemiology and Phenotypic Summary of Bacterial Pathogens

2013 ◽  
Keyword(s):  
Molecular Epidemiology ◽  
Bacterial Pathogens ◽  
Whole Genome ◽  
Genome Database ◽  
Comparative Analyses

scholarly journals The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

2008 ◽  
Vol 24 (23) ◽  
pp. 2803-2804 ◽  
Author(s):  
G. L. Winsor ◽  
B. Khaira ◽  
T. Van Rossum ◽  
R. Lo ◽  
M. D. Whiteside ◽  
...  
Keyword(s):  
Genome Database ◽  
Comparative Analyses ◽  
Flexible Queries

scholarly journals Correction for Quainoo et al., “Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis”

2017 ◽  
Vol 31 (1) ◽  
Author(s):  
Scott Quainoo ◽  
Jordy P. M. Coolen ◽  
Sacha A. F. T. van Hijum ◽  
Martijn A. Huynen ◽  
Willem J. G. Melchers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Pathogens ◽  
Whole Genome ◽  
Nosocomial Outbreak ◽  
The Future

scholarly journals Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates

2009 ◽  
Vol 19 (8) ◽  
pp. 1404-1418 ◽  
Author(s):  
K. S. Kassahn ◽  
V. T. Dang ◽  
S. J. Wilkins ◽  
A. C. Perkins ◽  
M. A. Ragan
Keyword(s):  
Gene Function ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Regulatory Control ◽  
Whole Genome ◽  
Comparative Analyses

scholarly journals Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina: TABLE 1 

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Claudia Carolina Carbonari ◽  
Nahuel Fittipaldi ◽  
Sarah Teatero ◽  
Taryn B. T. Athey ◽  
Luis Pianciola ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Whole Genome ◽  
Escherichia Coli O157 ◽  
Genome Sequences ◽  
High Quality ◽  
Human Infections

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.

scholarly journals Molecular Epidemiology of Bovine Coronavirus on the Basis of Comparative Analyses of the S Gene

2006 ◽  
Vol 44 (5) ◽  
pp. 1924-1924
Author(s):  
L. Liu ◽  
S. Hagglund ◽  
M. Hakhverdyan ◽  
S. Alenius ◽  
L. E. Larson ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Bovine Coronavirus ◽  
Comparative Analyses ◽  
S Gene

scholarly journals Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan

mSphere ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Tohru Miyoshi-Akiyama ◽  
Jatan Bahadur Sherchan ◽  
Yohei Doi ◽  
Maki Nagamatsu ◽  
Jeevan B. Sherchand ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Type ◽  
Whole Genome ◽  
Asian Countries ◽  
Content Type ◽  
E Coli ◽  
Global Spread ◽  
Low Prevalence

ABSTRACT The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia. The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region. IMPORTANCE The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia.

scholarly journals Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of InvasiveStaphylococcus aureusin Europe

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
David M. Aanensen ◽  
Edward J. Feil ◽  
Matthew T. G. Holden ◽  
Janina Dordel ◽  
Corin A. Yeats ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Bacterial Pathogens ◽  
Epidemiological Surveillance ◽  
Data Sets ◽  
Whole Genome ◽  
Bioinformatic Tools ◽  
Road Map

ABSTRACTThe implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasiveStaphylococcus aureusisolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show thatin silicopredictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools.IMPORTANCEThe spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.

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