scholarly journals Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms

2006 ◽  
Vol 16 (6) ◽  
pp. 757-767 ◽  
Author(s):  
W. Zhang
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Genomic Diversity ◽  
Escherichia Coli O157 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Strains of Escherichia coli O157:H7 Differ Primarily by Insertions or Deletions, Not Single-Nucleotide Polymorphisms

2002 ◽  
Vol 184 (7) ◽  
pp. 1873-1879 ◽  
Author(s):  
Indira T. Kudva ◽  
Peter S. Evans ◽  
Nicole T. Perna ◽  
Timothy J. Barrett ◽  
Frederick M. Ausubel ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Epidemiological Surveillance ◽  
Escherichia Coli O157 ◽  
Nucleotide Polymorphisms ◽  
Strain Variation ◽  
Single Nucleotide ◽  
E Coli ◽  
K 12 ◽  
Genetic Events

ABSTRACT Escherichia coli O157:H7 (O157) strains demonstrate varied pulsed-field gel electrophoresis patterns following XbaI digestion, which enable epidemiological surveillance of this important human pathogen. The genetic events underlying PFGE differences between strains, however, are not defined. We investigated the mechanisms for strain variation in O157 by recovering and examining nucleotide sequences flanking each of the XbaI restriction enzyme sites in the genome. Our analysis demonstrated that differences between O157 strains were due to discrete insertions or deletions that contained the XbaI sites polymorphic between strains rather than single-nucleotide polymorphisms in the XbaI sites themselves. These insertions and deletions were found to be uniquely localized within the regions of the genome that are specific to O157 compared to E. coli K-12 (O islands), suggesting that strain-to-strain variation occurs in these O islands. These results may be utilized to devise novel strain-typing tools for this pathogen.

scholarly journals Genomic surveillance of COVID-19 cases in Beijing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Pengcheng Du ◽  
Nan Ding ◽  
Jiarui Li ◽  
Fujie Zhang ◽  
Qi Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Frequency ◽  
Epidemiological Data ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Genomic Evolution ◽  
Single Nucleotide ◽  
Imported Cases ◽  
Single Nucleotide Variations ◽  
Local Transmission

Abstract The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.

scholarly journals Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

2006 ◽  
Vol 188 (12) ◽  
pp. 4453-4463 ◽  
Author(s):  
Patrick S. G. Chain ◽  
Ping Hu ◽  
Stephanie A. Malfatti ◽  
Lyndsay Radnedge ◽  
Frank Larimer ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Avirulent Strain ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

scholarly journals Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora

2018 ◽  
Author(s):  
Jasmina Uzunović ◽  
Emily B. Josephs ◽  
John R. Stinchcombe ◽  
Stephen I. Wright
Keyword(s):  
Gene Expression ◽  
Single Nucleotide Polymorphisms ◽  
Transposable Elements ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Mobile Dna ◽  
Gene Expression Variation ◽  
Single Nucleotide ◽  
Expression Variation ◽  
A Genome

AbstractTransposable elements (TEs) make up a significant portion of eukaryotic genomes, and thus are important drivers of genome evolution. However, the evolutionary forces controlling TE copy number and the extent to which TEs affect phenotypic variation on a genome-wide scale are still unclear. We characterised TE insertion polymorphism and its effects on gene expression in 124 whole genome sequences from a single population of Capsella grandiflora. The frequency of insertions was negatively correlated with distance to genes, as well as density of conserved non-coding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare single nucleotide polymorphisms (SNPs) contribute equally to up- and down-regulation, but have a weaker effect. Taken together, these results imply that TEs are a significant contributor to gene expression variation and can be more likely than rare SNPs to cause extreme changes in gene expression.Author SummaryTransposable elements (TEs), mobile DNA elements with the ability to excise from the genome and reinsert in new locations, are important components of genomic diversity. Due to their abundance and mobility, TEs play an influential role in genomic evolution, often deleterious. Here we show that TEs in a population of the plant Capsella grandiflora are most deleterious when they insert in genic and regulatory regions. We find that TEs indeed are associated with unusual levels of gene expression, predominantly decreased expression.Furthermore, this effect is stronger than the association of single nucleotide polymorphisms with gene expression variation, highlighting the importance of TE contribution to the maintenance of expression variation.

scholarly journals Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0131967 ◽  
Author(s):  
Sean M. Griffing ◽  
Duncan R. MacCannell ◽  
Amber J. Schmidtke ◽  
Molly M. Freeman ◽  
Eija Hyytiä-Trees ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Single Nucleotide Polymorphisms ◽  
Shiga Toxin ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs)

2007 ◽  
Vol 56 (10) ◽  
pp. 1363-1369 ◽  
Author(s):  
Sara Y. Tartof ◽  
Owen D. Solberg ◽  
Lee W. Riley
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphisms ◽  
Screening Test ◽  
Epidemiological Studies ◽  
Discriminatory Power ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Discriminatory Ability ◽  
E Coli

The application of genotyping techniques for subtyping uropathogenic Escherichia coli has contributed to better understanding of the epidemiology of community-acquired urinary tract infection (UTI). However, the current techniques are hampered by limited reproducibility, poor discriminatory power, labour-intensive performance or high cost. A screening test that is sequence-based would provide an inexpensive, reproducible way to subtype E. coli isolates. Such a test, if also discriminatory, would be highly useful for epidemiological studies. The discriminatory ability of 12 putative virulence genes (fimH, fliD, fliM, iha, motA, papA/H, kpsMTII, fepE, fimA, flgA, malG, purD) was evaluated based on single nucleotide polymorphisms (SNPs) in nine uropathogenic E. coli isolates, all previously found to belong to a single multilocus sequence type (MLST) complex (ST69). An additional 25 epidemiologically well-characterized E. coli isolates belonging to 12 distinct MLST clonal complexes were analysed for fimH SNP. None of the 12 genes except fimH were able to further discriminate the nine ST69-complex strains. Isolates belonging to the 12 non-ST69 MLST groups were separated into 10 fimH SNP subgroups. While fimH SNP analysis may not be an appropriate phylogenetic method, it offers discriminatory power similar to that of MLST and could be used as a simple, inexpensive screening test for epidemiological studies of uropathogenic E. coli.

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