Computational protocol: Identification and detection of three new F17 fimbrial variants in Escherichia coli strains isolated from cattle

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Protocol publication

[…] The localization of the F17 gene cluster on the genome of E. coli MHI813 was determined by nucleotide basic local alignment search tool (BLASTn) analyses on E. coli MHI813 whole genome shotgun (wgs) sequences (taxonomy ID: 754089, GenBank:AFDZ0100000000.1) using the nucleotidic sequences of the already described F17 variants. The genetic environment of the F17 cluster on the genome was determined using BLASTn analysis of E. coli MHI813 wgs sequence carrying F17 cluster on the entire nucleotide collection database. All automatic annotations of coding sequences located in the vicinity of the F17 cluster were also checked with Artemis software (Wellcome Trust Sanger Institute, Hinxton, UK) and BLASTx analyses. The F17 cluster on pVir68 plasmid sequence (GenBank accession number: CP001162.1) was analyzed by BLASTn and f17A gene on pVir68 sequence was compared with f17Ac and f17Ad genes from 31A and 111KH86 reference strains by alignment with ClustalX2 software. [...] Two primers were designed with Primer3Plus software for specific PCR detection of the new variants F17e-A and F17-G3: 5′-CTGACTCCATTTACCATTGAGC-3′ for F17e-A and 5′-GCCAAATAGTGGATATGAAACAAC-3′ for F17-G3. These primers were set up in addition to the currently available multiplex PCR protocol for the detection of all known variants of F17-A and F17-G []. […]

Pipeline specifications

Software tools BLASTN, BLASTX, Clustal W, Primer3
Applications WGS analysis, qPCR
Organisms Escherichia coli, Bos taurus, Ovis aries
Diseases Dysentery, Bacillary