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PMC:PMC3651199 JSONTXT

Divisions (21) JSON TSV

div. section text # proj. length # Ann.
0 TIAB Adaptive Mutations and Replacements of Virulence Traits in theEscherichia coliO104:H4 Outbreak Popul 1 2037 0 show
1 Introduction Since the beginning of May 2011 to the beginning of July 2011, we have witnessed the largest outbrea 1 4694 0 show
2 Results Whole-genome SNP Phylogeny We have sequenced the genome of three E. coli strains isolated prior to t 1 2488 0 show
3 Results Adaptive Nucleotide Substitutions in the Outbreak Strain Strain E112/10 differed from 2011C-3493 by 1 3627 0 show
4 Results Acquisition and Replacement of Virulence Traits To identify putative replacement events as well as t 1 6374 0 show
5 Discussion Strain E112/10, acquired by a Swede travelling in Tunisia a year prior to the outbreak is unique amo 1 7831 0 show
6 Materials and Methods Cultivation and DNA Isolation of Bacterial Strains All strains sequenced in this study were cultivat 1 458 0 show
7 Materials and Methods Publicly Available Sequences Unless otherwise stated, published sequences were retrieved from NCBI ( 1 1419 0 show
8 Materials and Methods Genome Sequencing, Assembly and Annotation The genomes of the 3 strains sequenced in this study were 1 2219 0 show
9 Materials and Methods Genome Mapping and SNP Calling All reads for all strains except those sequenced by PacBio technology 1 2125 0 show
10 Materials and Methods Phylogenetic Analysis A method similar to the one used by Pandya et al. [41] was used. All complete 1 968 0 show
11 Materials and Methods PAIs and VT2 Prophage Phylogenies An online blastn search to the nt database was performed with the 1 779 0 show
12 Caption-Figure 1 Phylogeny of E.coli and Salmonella genomes. Maximum-likelihood phylogenies (A) of all E. coli and Sa 1 755 0 show
13 Caption-Figure 2 Comparison of the genomes and plasmids of E.coli strains. Comparisons of (A) chromosomes and (B–C) p 1 973 0 show
14 Caption-Figure 3 Comparison of the agg genes in the outbreak strains and in other EAEC strains. Blast hits between th 1 383 0 show
15 Caption-Figure 4 Comparison of the second large putative plasmid found in E112/10 with related plasmids. Comparisons 1 361 0 show
16 Caption-Figure 5 Comparison of the gene order structures of pathogenicity island 1 (PAI1). Genes located inside PAI1 1 580 0 show
17 Caption-Figure 6 Comparison of the gene order structures of pathogenicity island 2 (PAI2). Genes located inside PAI2 1 844 0 show
18 Caption-Figure 7 Comparison of the gene order structures of the VT2 phages. Genes located inside the prophage are sho 1 696 0 show
19 Caption-Table 1 SNPs between E112/10 and the E. coli outbreak German isolates. 1 62 0 show
20 Caption-Table 2 Summary of the number of SNPs between E112/10 and the E. coli outbreak German isolates. 1 87 0 show