Editing Escherichia coli (section)

===Phylogeny of ''E. coli'' strains===
{{Update|section|inaccurate=yes|reason=Cladogram uses an [[WP:OR|OR]] extension of Sims & Kim 2011, which is outdated anyways and should be replaced by Meier-Kolthoff et al. 2014 (fig 6).|talk=Phylogeny|date=January 2021}}
Many strains belonging to this species have been isolated and characterised. In addition to serotype (''vide supra''), they can be classified according to their [[phylogeny]], i.e. the inferred evolutionary history, as shown below where the species is divided into six groups as of 2014.<ref name="comparison02">{{cite journal | vauthors = Sims GE, Kim SH | title = Whole-genome phylogeny of ''Escherichia coli/Shigella'' group by feature frequency profiles (FFPs) | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 20 | pages = 8329–34 | date = May 2011 | pmid = 21536867 | pmc = 3100984 | doi = 10.1073/pnas.1105168108 | bibcode = 2011PNAS..108.8329S | doi-access = free }}</ref><ref name="pmid21713444">{{cite journal | vauthors = Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R | display-authors = 6 | title = Genome sequence analyses of two isolates from the recent ''Escherichia coli'' outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic ''Escherichia coli'' (EAHEC) | journal = Archives of Microbiology | volume = 193 | issue = 12 | pages = 883–91 | date = December 2011 | pmid = 21713444 | pmc = 3219860 | doi = 10.1007/s00203-011-0725-6 | bibcode = 2011ArMic.193..883B }}</ref> Particularly the use of [[Whole genome sequencing|whole genome sequences]] yields highly supported phylogenies.<ref name="Meier-Kolthoff14" /> The [[phylogroup]] structure remains robust to newer methods and sequences, which sometimes adds newer groups, giving 8 or 14 as of 2023.<ref>{{cite journal | vauthors = Koh XP, Shen Z, Woo CF, Yu Y, Lun HI, Cheung SW, Kwan JK, Lau SC | display-authors = 6 | title = Genetic and Ecological Diversity of ''Escherichia coli'' and Cryptic ''Escherichia'' Clades in Subtropical Aquatic Environments | journal = Frontiers in Microbiology | volume = 13 | pages = 811755 | date = 2022 | pmid = 35250929 | pmc = 8891540 | doi = 10.3389/fmicb.2022.811755 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW | title = Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups | journal = Communications Biology | volume = 4 | issue = 1 | pages = 117 | date = January 2021 | pmid = 33500552 | pmc = 7838162 | doi = 10.1038/s42003-020-01626-5 }}</ref>

The link between phylogenetic distance ("relatedness") and pathology is small,<ref name="Meier-Kolthoff14" /> ''e.g.'' the [[O157:H7]] serotype strains, which form a [[clade]] ("an exclusive group")—group E below—are all enterohaemorragic strains (EHEC), but not all EHEC strains are closely related. In fact, four different species of ''Shigella'' are nested among ''E. coli'' strains (''vide supra''), while ''[[Escherichia albertii|E. albertii]]'' and ''[[Escherichia fergusonii|E. fergusonii]]'' are outside this group. Indeed, all ''Shigella'' species were placed within a single subspecies of ''E. coli'' in a phylogenomic study that included the type strain.<ref name="Meier-Kolthoff14" /> All commonly used [[Escherichia coli (molecular biology)|research strains]] of ''E. coli'' belong to group A and are derived mainly from Clifton's K-12 strain (λ<sup>+</sup> F<sup>+</sup>; O16) and to a lesser degree from [[Félix d'Herelle|d'Herelle]]'s "[[Bacillus coli]]" strain (B strain; O7).

There have been multiple proposals to revise the taxonomy to match phylogeny.<ref name="Meier-Kolthoff14" /> However, all these proposals need to face the fact that ''Shigella'' remains a widely used name in medicine and find ways to reduce any confusion that can stem from renaming.<ref>{{cite journal |vauthors = Cobo-Simón M, Hart R, Ochman H |title = Escherichia Coli: What Is and Which Are? |journal = Molecular Biology and Evolution |volume = 40 |issue = 1 |pages = msac273 |date = January 2023 |pmid = 36585846 |pmc = 9830988 |doi = 10.1093/molbev/msac273 }}</ref>

{{clade|style=font-size:80%;line-height:80%
 |1=''[[Salmonella enterica]]''
 |2={{clade
  |1=[[Escherichia albertii|''E. albertii'']]
  |2={{clade
   |1=[[Escherichia fergusonii|''E. fergusonii'']]
   |2={{clade
     |1={{clade
      |label1=Group&nbsp;B2
      |1={{clade
       |1=[[E. coli SE15|''E. coli'' SE15]] (O150:H5. Commensal)
       |2=[[E. coli E2348/69|''E. coli'' E2348/69]] (O127:H6. Enteropathogenic)
      }}
     |2={{clade
      |1=[[E. coli ED1a|''E. coli'' ED1a]] O81 (Commensal)
      |2={{clade
       |1={{clade
        |1=[[E. coli CFT083|''E. coli'' CFT083]] (O6:K2:H1. UPEC)
        |2={{clade
         |1=[[E. coli APEC O1|''E. coli'' APEC O1]] (O1:K12:H7. APEC
         |2=[[E. coli UTI89|''E. coli'' UTI89]] O18:K1:H7. UPEC)
         |3=[[E. coli S88|''E. coli'' S88]]  (O45:K1. Extracellular pathogenic)
         }}
        }}
       |2={{clade
        |1=[[E. coli F11|''E. coli'' F11]]
        |2=[[E. coli 536|''E. coli'' 536]]
        }}
       }}
      }}
    |3={{clade
     |label1=Group&nbsp;D
     |1={{clade
      |1=[[E. coli UMN026|''E. coli'' UMN026]] (O17:K52:H18. Extracellular pathogenic)
      |2={{clade
       |1=[[E. coli SMS-3-5|''E. coli'']] (O19:H34. Extracellular pathogenic)
       |2=[[E. coli IAI39|''E. coli'']] (O7:K1. Extracellular pathogenic)
       }}
      }}
     |2={{clade
      |label1=Group&nbsp;E
      |1={{clade
       |1={{clade
        |1=[[E. coli EDL933|''E. coli'' EDL933]] (O157:H7  EHEC)
        |2=[[E. coli Sakai|''E. coli'' Sakai]] (O157:H7 EHEC)
        }}
       |2={{clade
        |1=[[E. coli EC4115|''E. coli'' EC4115]] (O157:H7 EHEC)
        |2=[[E. coli TW14359|''E. coli'' TW14359]] (O157:H7 EHEC)
        }}
       }}
      |2={{clade
       |label1=Shigella
       |1={{clade
        |1={{clade
         |1=''[[Shigella dysenteriae]]''
         |2={{clade
          |1=''[[Shigella sonnei]]''
          |2={{clade
           |1=''[[Shigella boydii]]''
           |2=''[[Shigella flexneri]]''
           }}
          }}
         }}
        }}
       |2={{clade
        |label1=Group&nbsp;B1
        |1={{clade
         |1={{clade
          |1=[[E. coli E24377A|''E. coli'' E24377A]] (O139:H28. Enterotoxigenic)
          |2={{clade
           |1={{clade
            |1={{clade
             |1=[[E. coli E110019|''E. coli'' E110019]] <!-- what is this? -->
             |2={{clade
              |1=[[E. coli 11368|''E. coli'' 11368]] (O26:H11. EHEC)
              |2=[[E. coli 11128|''E. coli'' 11128]] (O111:H-. EHEC)
              }}
             }}
            |2={{clade
             |1={{clade
              |1=[[E. coli IAI1|''E. coli'' IAI1]] O8 (Commensal)
              |2=[[E. coli 53638|''E. coli'' 53638]] (EIEC)
              }}
             |2={{clade
              |1=[[E. coli SE11|''E. coli'' SE11]] (O152:H28. Commensal)
              |2=[[E. coli B7A|''E. coli'' B7A]]
              }}
             }}
            }}
           |2={{clade
            |1={{clade
             |1={{clade
              |1=[[E. coli 12009|''E. coli'' 12009]] (O103:H2. EHEC)
              |2=[[E. coli O104:H4|''E. coli'' GOS1]] (O104:H4 EAHEC) German 2011 outbreak
              }}
             |2=[[E. coli E22|''E. coli'' E22]]
             }}
            |2={{clade
             |1=[[E. coli Oslo O103|''E. coli'' Oslo O103]]
             |2=[[E. coli 55989|''E. coli'' 55989]] (O128:H2. Enteroaggressive)
             }}
            }}
           }}
          }}
         }}
        |label2=Group&nbsp;A
        |2={{clade
         |1={{clade
          |1=[[E. coli HS|''E. coli'' HS]] (O9:H4. Commensal)
          |2=[[E. coli ATCC8739|''E. coli'' ATCC8739]] (O146. Crook's E.coli used in phage work in the 1950s)
          }}
         |2={{clade
          |label1=K-12 strain derivatives
          |1={{clade
           |1=[[E. coli K-12 W3110|''E. coli'' K-12 W3110]] (O16. λ<sup>−</sup> F<sup>−</sup> "wild type" molecular biology strain)
           |2=[[E. coli K-12 DH10b|''E. coli'' K-12 DH10b]] (O16. high electrocompetency molecular biology strain)
           |3=[[E. coli K-12 DH1|''E. coli'' K-12 DH1]]  (O16. high chemical competency molecular biology strain)
           |4=[[E. coli K-12 MG1655|''E. coli'' K-12 MG1655]] (O16. λ<sup>−</sup> F<sup>−</sup> "wild type" molecular biology strain)
           |5=[[E. coli BW2952|''E. coli'' BW2952]] (O16. competent molecular biology strain)
           }}
          |2={{clade
            |1=[[E. coli 101-1|''E. coli'' 101-1]] (O? H?. EAEC)
            |label2=B strain derivatives
            |2={{clade
             |1=[[E. coli B REL606|''E. coli'' B REL606]] (O7. high competency molecular biology strain)
             |2=[[E. coli BL21-DE3|''E. coli'' BL21-DE3]] (O7. expression molecular biology strain with T7 polymerase for pET system)
            }}
           }}
          }}
         }}
        }}
       }}
      }}
     }}
    }}
   }}
  }}
 }}
}}