Computational protocol: Isolation and characterization of Listeria species from rodents in natural environments in China

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Protocol publication

[…] L. monocytogenes serotype was identified by a combination of multiplex PCR and traditional slide agglutination. The multiplex PCR was performed by targeting the genes lmo0737, lmo1118, ORF2110, ORF2819 and Listeria-specific prs described by Doumith et al. When the serogroups were identified, only the antiserum against somatic antigens was used. MLST based on seven house-keeping genes (abcZ, bglA, cat, dapE, dat, ldh and lhkA) was performed according to the method of Ragon et al. The scheme and genotypic data are available at http://bigsdb.web.pasteur.fr/listeria/. Minimum spanning tree analysis was inferred using BioNumerics (Version 5.10, Applied Maths, Belgium). PFGE of the L. monocytogenes strains was performed using the primary restriction enzyme AscI according to the standard operating procedure by PulseNet of Centers for Disease Control and Prevention. Similarities between the digestion profiles of strains were analyzed by unweighted pair group method with arithmetic mean using BioNumerics software (Version 5.10, Applied Maths). […]

Pipeline specifications

Software tools BIGSdb, BioNumerics
Application De novo sequencing analysis
Organisms Homo sapiens, Listeria monocytogenes, Listeria ivanovii, Listeria innocua
Chemicals Oxacillin