Genomics of Escherichia and Shigella

Perna, Nicole T.

doi:10.1007/978-1-4419-7686-4_5

Cited by 3 publications

(5 citation statements)

References 64 publications

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“…5). In agreement with the higher incidence of this sort of element in Shigella genomes than in E. coli genomes (34, 47, 48), the occurrence of these variants was prominent in the former.…”

Section: Resultssupporting

confidence: 72%

CRISPR-Cas Functional Module Exchange in Escherichia coli

Almendros

Mojica

Díez-Villaseñor

et al. 2014

mBio

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes constitute the CRISPR-Cas systems found in the Bacteria and Archaea domains. At least in some strains they provide an efficient barrier against transmissible genetic elements such as plasmids and viruses. Two CRISPR-Cas systems have been identified in Escherichia coli, pertaining to subtypes I-E (cas-E genes) and I-F (cas-F genes), respectively. In order to unveil the evolutionary dynamics of such systems, we analyzed the sequence variations in the CRISPR-Cas loci of a collection of 131 E. coli strains. Our results show that the strain grouping inferred from these CRISPR data slightly differs from the phylogeny of the species, suggesting the occurrence of recombinational events between CRISPR arrays. Moreover, we determined that the primary cas-E genes of E. coli were altogether replaced with a substantially different variant in a minor group of strains that include K-12. Insertion elements play an important role in this variability. This result underlines the interchange capacity of CRISPR-Cas constituents and hints that at least some functional aspects documented for the K-12 system may not apply to the vast majority of E. coli strains.

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“…5). In agreement with the higher incidence of this sort of element in Shigella genomes than in E. coli genomes (34, 47, 48), the occurrence of these variants was prominent in the former.…”

Section: Resultssupporting

confidence: 72%

CRISPR-Cas Functional Module Exchange in Escherichia coli

Almendros

Mojica

Díez-Villaseñor

et al. 2014

mBio

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“…Although not absolute, some preferential associations exist between certain phylogenetic groups and pathovars. As an example, extraintestinal pathogenic E. coli (ExPEC) strains belong more frequently to the B2 and D phylogroups, while enterohaemorrhagic E. coli (EHEC) strains most often belong to the E group, but also belong to B1 and A groups [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

“…coli (ExPEC) strains belong more frequently to the B2 and D phylogroups, while enterohaemorrhagic E. coli (EHEC) strains most often belong to the E group, but also belong to B1 and A groups [8].…”

Section: Introductionmentioning

confidence: 99%

Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems

et al. 2021

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Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli , is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.

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“…CC-BY-ND 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted March 22, 2021. ; https://doi.org/10.1101/2021.03.22.436425 doi: bioRxiv preprint B2 and D phylogroups while entero-hemorrhagic strains (EHEC) most often belong to the E group, but also belong to B1 and A groups (7).…”

Section: Introductionmentioning

confidence: 99%

“…Although not absolute, some preferential associations exist between certain phylogenetic groups and pathovars. As an example, Extraintestinal Pathogenic E. coli strains (ExPEC) belong more frequently to the B2 and D phylogroups while entero-hemorrhagic strains (EHEC) most often belong to the E group, but also belong to B1 and A groups (7).…”

Section: Introductionmentioning

confidence: 99%

LPS core type diversity in the Escherichia coli species and associations with phylogeny and virulence gene repertoire

So¹,

Branger²,

Dg³

et al. 2021

Preprint

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Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings, pathovars as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which 5 different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyze the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types while phylogroups B1, D and E strains were dominated by the R3 type and phylogroups B2 and C strains being dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clone of extra-intestinal pathogenic E. coli(ExPEC) strains. The origin of this uneven distribution is discussed but remains to be explained, as well as the consequences of carrying a specific core type on the physiology of the bacteria.

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Genomics of Escherichia and Shigella

Cited by 3 publications

References 64 publications

CRISPR-Cas Functional Module Exchange in Escherichia coli

CRISPR-Cas Functional Module Exchange in Escherichia coli

Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems

LPS core type diversity in the Escherichia coli species and associations with phylogeny and virulence gene repertoire

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