This script allows to get Enterobacter cloacae complex hsp60 cluster from a multi-Fasta file.

Perl programming language and NCBI-Blast+ are needed to run the proram. If you are using Linux Ubuntu/Debian, you can use the following command to install NCBI-Baslt+:

sudo apt update
sudo apt install ncbi-blast+

The script can be used as follows (the first argument is the input file, the second argument is the database file used by Blast, and the last argument is the %identity used to filter Blast output):

perl hsp60ECCtool.pl input_example.fasta database.fasta 80.00

The program will generate a result.tsv file with information on ECC clades found, and a blastOut file (output produced by blast)

hsp60ECCtool is a program dedicated to Enterobacter cloacae complex (ECC) that detects and identifies the partial coding sequence of hps60. It is based on the BLASTn algorithm and a specific dataset (based on sorted hsp60 sequences collected from GenBank ECC assemblies). The program helps users to clearly identify the hsp60 cluster and associated members of the Enterobacter cloacae complex.

• The tested strain(s) must be identified as belonging to the complex by a traditional method (API 20E, mass spectrometry...) before hsp60 typing.
• Partial amplification of the gene coding for hsp60 should be performed according to the initiale approach proposed by Hoffmann H. and Roggenkamp A. (2003).
• Hsp60 cluster assignment was done according to the original research article and additional analysis provided by Berouthy R. et al. (2018) and Pot M. et al. (2021).
• Associated species names are given according to Sutton GG. et al. (2018) and Wu W. et al. (2020).
• Best results are given in the hsp60ECCtool Result output. UD : Undefined Cluster (see in Figure S1 in the supplementary material provided by Pot M. et al. (2020)); NA : - Not Attributed in the related research paper. Without whole-genome sequencing and additional analyses, the precise species identification remains indicative and should be taken with caution.