The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data

Table 1 Adjusted Wallace coefficient and 95 % confidence intervals

	CGST	PFGE + Ribo	PFGE	ApaI	AscI	Ribotype	MLST
CGST		0.657 (0.400–0.914)	0.657 (0.400–0.914)	0.828 (0.645–1.000)	0.827 (0.644–1.000)	1.000 (1.000–1.000)	1.000 (1.000–1.000)
PFGE + Ribo	0.120 (0.019–0.222)		1.000 (1.000–1.000)	1.000 (1.000–1.000)	1.000 (1.000–1.000)	1.000 (1.000–1.000)	0.977 (0.955–0.999)
PFGE	0.120 (0.019–0.222)	1.000 (1.000–1.000)		1.000 (1.000–1.000)	1.000 (1.000–1.000)	1.000 (1.000–1.000)	0.977 (0.955–0.999)
ApaI	0.128 (0.024–0.233)	0.845 (0.743–0.947)	0.845 (0.743–0.947)		0.844 (0.741–0.947)	0.980 (0.962–0.999)	0.931 (0.896–0.967)
AscI	0.118 (0.017–0.220)	0.781 (0.711–0.851)	0.781 (0.711–0.851)	0.780 (0.709–0.850)		0.982 (0.965–0.999)	0.982 (0.965–0.999)
Ribotype	0.046 (0.000–0.095)	0.251 (0.137–0.365)	0.251 (0.137–0.365)	0.291 (0.171–0.412)	0.316 (0.207–0.425)		0.787 (0.641–0.932)
MLST	0.048 (0.000–0.099)	0.256 (0.144–0.368)	0.256 (0.144–0.368)	0.289 (0.168–0.410)	0.329 (0.223–0.436)	0.820 (0.683–0.957)

The Wallace coefficient measures agreement between groupings made with different typing methods. Row headers indicate methods from which two random samples were drawn and column headers identify the methods that were compared. The probabilities that two samples grouped together with one method (rows) will also be grouped together with another method (columns) are shown along with 95 % confidence intervals (parentheses)
ApaI and AscI data were combined to generate the PFGE category and ApaI, AscI, and Ribotype data were combined to generate the PFGE + Ribo category

ISSN: 1471-2180