基本信息

Using FimTyper to identify the FimH type in fully or partially sequenced isolates of Escherichia coli

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The fimH gene is part of the fim operon, which encodes a surface organelle named type 1 fimbriae found in most Escherichia coli strains. The FimH protein is located at the tip of the fimbrial structure and serves as a d-mannose-specific adhesin, which aids in immobilizing the bacterium on both biotic and abiotic surfaces. 

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FimTyper, a tool that has been developed to identify fimH alleles from either simple Sanger-generated sequences or raw or assembled WGS data from E. coli genomes, enables researchers and primary investigators to rapidly detect the fimH allele in their data sets. The fimH allele database contained all previously identified fimH allele variants (n = 492) collected at the State University of New York and used for conventional typing. The database was constructed as a single FASTA file and implemented in a BLAST-based PERL script. The default setting for minimum percent identity and minimum length of a hit to be reported by BLAST were chosen as 95% and 60%, respectively, to reduce false-positive hits caused by reporting of small fragments unrelated to the fimH gene.

补充信息

Related links:

https://bitbucket.org/genomicepidemiology/fimtyper

参考文献

Roer L, Tchesnokova V, Allesøe R, et al. Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles. J Clin Microbiol. 2017;55(8):2538-2543. doi:10.1128/JCM.00737-17