Listeria monocytogenes is a food-borne pathogen that causes listeriosis, an illness with a high mortality rate that primarily affects immunocompromised people. Next generation sequencing is commonly used for monitoring L. monocytogenes, creating the need for an in silico serotyping method. In this study, a tool was developed for in silico serotyping of L. monocytogenes based on molecular serotyping markers from literature including markers from Doumith et al., 2004.
A dataset of 560 L. monocytogenes genomes with known serotype was created, containing publicly available genomes from all 14 known serotypes. This dataset was then used to validate 32 markers from literature for serotyping in silico. Six markers were found to be capable of identifying Lineage III isolates (serotype 4a, 4c or 4b) with 98.7-100% specificity and 78.1-97.6% sensitivity. A maker for the recently discovered serotype 4h had 100% sensitivity and specificity, although only 3 of these isolates were included in the dataset. Three markers previously reported for further separating serogroups IIa or IIc were found to be non-useful. Other markers were redundant to those in Doumith et al., 2004, and performed similarly or worse.
Markers were also tested to separate non-1/2 serotypes in serogroups IIa, IIb and IIc, which were found to have 99.2% specificity but only 51.0% sensitivity. Similarly, serotype 4d was differentiated from within serogroup IVb with 100% specificity but only 45.5% sensitivity.
Using the well-performing markers, the tool was used to serotype 46,866 publicly available L. monocytogenes genomes. 99.3% of genomes were typeable, with the majority in serogroups IIa (41.9%) and IVb (29.5%), which contain serotypes 1/2a and 4b respectively, the most common in human infections.
This tool improves on existing methods based on a molecular typing scheme by Doumith et al., 2004 and will be of use for serotyping L. monocytogenes from genome sequence data with compatible results to PCR and antisera serotyping.