LisSero

In silico serogroup and binary typing prediction for Listeria monocytogenes

Authors

• Jason Kwong (@kwongjc) - GitHub: kwongj
• Torsten Seemann (@torstenseemann) - GitHub: tseemann

Dependencies

• Python 3.6+
• BLAST 2.6.0

Installation

pip3 install lissero

Installing BLAST 2.6.0

Brew:

brew install blast

Conda:

conda install -c bioconda blast 

In silico serogrouping for Listeria monocytogenes

LisSero is based on a method of predicting serogroup for Listeria monocytogenes using PCR, as described by Doumith et al (see References). It detects the presence or absence of 5 DNA regions (lmo1118, lmo0737, ORF2110, ORF2819 and Prs). The patterns obtained reflect the four main serotypes (1/2a, 1/2b, 1/2c, and 4b) obtained from food and human sources.

The patterns are not based on genes involved in somatic (O) or flagellar (H) biosynthesis, and are not specific to just one serotype, but rather to a group of serotypes.

If only Prs is detected, these isolates are often serotype 4a or 4c, though LisSero reports these as "Nontypable".

In silico binary typing for Listeria monocytogenes

Using the method described by Huang et al (2007), where eight fragments are multiplexed. Each fragment has a unique number (1, 2, 4, 8, 16, 32, 64, and 128). The Binary Type is defined as the sum of the numbers of the present fragments.

Therefore, a sample with fragments 1, 4, and 16 would have a binary type of 21.

Usage

Bugs

Please submit via the GitHub issues page: https://github.com/MDU-PHL/LisSero/issues

Software Licence

GPLv2: https://github.com/MDU-PHL/LisSero/blob/master/LICENSE

References

• Doumith et al. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22.

• Huang et al. Binary typing of Listeria monocytogenes isolates from patients and food through multiplex PCR and reverse line hybridisation. SA, Australia, 2007; 136–137.