Scientific Publications by FDA Staff

Appl Environ Microbiol 2016 Sep 30;82(20):6258-72

Core genome multilocus sequence typing for the identification of globally distributed clonal groups and differentiation of outbreak strains of Listeria monocytogenes.

Chen Y, Gonzalez-Escalona N, Hammack TS, Allard M, Strain EA, Brown EW

Many listeriosis outbreaks were caused by a few globally distributed clonal groups, designated as clonal complexes or epidemic clones of Listeria monocytogenes, several of which have been defined by classic multi-locus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had varying degree of diversity at the whole genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically-unrelated strains of the same clonal group, which cannot be achieved using classic MLST schemes. Precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST that can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed varying degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiologic evidence to define a listeriosis outbreak. IMPORTANCE: The concept of clonal complex or epidemic clone defined by classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST schemes can be used for simultaneous identification of clonal groups and differentiation among individual outbreak strains and epidemiologically-unrelated strains of the same clonal group. We further developed lineage-specific cgMLST schemes that targeted more genomic regions than the species-specific cgMLST schemes. Our data revealed the genome level diversity of clonal groups defined by classic MLST schemes. Our identification of the United States and international outbreaks as caused by major clonal groups can contribute to further understanding of the global epidemiology of L. monocytogenes.