Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups

Abstract

In this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.

A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups

“…E. coli strains have been classified, revealing a variety of phylogenetic groups [ 42 ], the most prominent of which are A, B1, B2, D, E and S [ 43 , 44 ]. Commensal strains in humans belong mostly to phylogroup A [ 40 ], while pathogenic strains belong mostly to phylogroups B2 and D [ 44 , 45 ].…”

“…The enterohemorrhagic O157:H7 strains are in group E, whereas Shigella falls into the additional group S [ 46 ]. In a recent analysis, over 100,000 E. coli genomes were used for an extensive phylogenetic analysis [ 42 ]. This analysis allowed the more detailed definition of 14 phylogroups G, B2-1, B2-2, F, D1, D2, D3, E2, E1, A, C, B1, Shig1 and Shig2.…”

“…The phylogenetic analysis showed an early separation of phylogroup D (D1–3), followed by a separation of phylogroups F, G, B2-1 and B2-2 from the remaining groups. Eventually phylogroups E, A, S, C and B1 separated [ 42 ]. The analysis of gene gain, gene loss and gene duplication ratios showed significantly different gain/loss/duplication ratios of all phylogroups, even between phylogroups that are thought to share an ancestral history, highlighting the significant divergence across the different phylogroups [ 42 ].…”

“…Eventually phylogroups E, A, S, C and B1 separated [ 42 ]. The analysis of gene gain, gene loss and gene duplication ratios showed significantly different gain/loss/duplication ratios of all phylogroups, even between phylogroups that are thought to share an ancestral history, highlighting the significant divergence across the different phylogroups [ 42 ]. In this study, we restricted our analysis to the phylogroups A, B1, B2, D, E and S. Despite slightly less differentiation, our analysis still covers the divergence across the entire phylogenetic tree [ 42 ].…”

Funktion rätselhafter Retrons entschlüsselt

“…Für die meisten dieser unzähligen unterschiedlichen Gene ist keine Funktion bekannt. Selbst beim bestuntersuchten Mikroorganismus Escherichia coli K-12 ist für etwa ein Drittel der 4.500 Gene die Funktion unbekannt -und diese Zahl steigt nochmal signifi kant an, wenn man das Pangenom von E. coli mit über 100.000 verschiedenen Genclustern einbezieht [2]. Bei weniger gut untersuchten Mi kroorganismen ist diese Zahl noch deutlich höher [1].…”