In silico Multilocus Sequence Typing of Listeria monocytogenes

In silico MLST was performed to identify clonal complex (CC) and sequence type (ST) on CLC genomic workbench (Qiagen, Redwood City, CA, USA) using seven housekeeping genes of L. monocytogenes, including ABC transporter (abcZ), beta-glucosidase (bglA), catalase (cat), succinyl diaminopimelate dessucinylase (dapE), d-amino acid aminotransferase (dat), l-lactate dehydrogenase (ldh), and histidine kinase (lhkA). An allele number was assigned to the sequence of each allele and CC determined based on the definition of Ragon et al. (2008) (link) and the Pasteur MLST database.¹ WGS data were further subjected to cgMLST cluster identification on Ridom SeqSphere + v9.0 (Ridom GmbH, Germany) (L. monocytogenes cgMLST scheme, 1701 loci) (Ruppitsch et al., 2015 (link)). The cluster distance threshold for the core genome was 10 allele differences. Epidemic clones of ECI, ECII, ECIII and ECIV (Chen and Knabel, 2007 (link)) were downloaded from the NCBI website.