Computational protocol: CRISPR1 analysis of naturalized surface water and fecal Escherichia coli suggests common origin

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Protocol publication

[…] Phylogenetic reconstruction was based on the seven‐gene multilocus sequence typing (MLST) protocol described elsewhere ( Forward and reverse sequences for each of the seven genes (aspC, clpX, fadD, icdA, lysP, mdh, and uidA) were assembled using the Staden package v3.3 (Hinxton, UK). (Staden et al. ). New alleles and sequence types were submitted to the Shigatox EcMLST database (Qi et al. ). For each E. coli strain, consensus sequences for each of the seven genes were concatenated and aligned using MUSCLE (default parameters) (Edgar ) as implemented from within Mega5 (Tamura et al. ). The alignment was imported into SplitsTree4 v.4.13.1 (Tubingen, Germany) and analyzed according to the Neighbour‐Net algorithm (default parameters) (Huson and Bryant ). MLST data of representative E. coli strains from the ECOR collection, clade ET1, and several additional non‐phylogroup B1 strains from the Milk River were included in the analysis for comparison purposes (Table S1). MLST sequences for reference strains from the ECOR collection were obtained from the Shigatox EcMLST database. Dr. Seth Walk (Montana State University, Bozeman, MT) kindly provided the MLST sequences for the reference clade ET–1 strains. […]

Pipeline specifications

Software tools MUSCLE, MEGA, SplitsTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Escherichia coli