Table 6.

Proposed criteria and practices for SNP-based epidemiological outbreak inclusion or exclusion.

Ideal case
PRIMARY CRITERIA
Highly credible exposure	Point source (clustered in time and space), pathogen isolated from incriminated vehicle
High quality sequencing	Contig numbers should be comparable to previous assemblies performed with the same assembly method, minimum coverage required will depend on technology used
Mobilome exclusion	Data focus on the most immutable part of the genome, most commonly the genome backbone
SNP validation	Second method, PCR confirmation or re-sequencing to validate mutations in discriminatory SNPs
SECONDARY CRITERIA
Collection of multiple isolates from cases for accurate attribution	The larger the sample that demonstrates homogeneity, the greater the likelihood of a common source
	If a common PFGE/MLVA type is present in the same region, confirmation that allelic differences exist between outbreak strain and background non-outbreak strains
SNP calling	Reference and outbreak based SNP comparisons
	Allelic frequency >=0.9
	Base and mapping quality control
Novel SNP	If a tolerance is set at >0 for SNPs as a cut point for assigning isolates as being from the same source, a SNP that is not in the database (i.e., apparently de novo) would be given more credence than one that has been described previously, and which probably represents a different lineage or located in a known polymorphic gene, such as rpoS
QUESTIONABLE CRITERIA
Variances in the complementary mobilome, such as presence of plasmids and phages	Loci of likely mobile origin are not reliable as a differentiating trait for epidemiologic purposes
BEST PRACTICES IN REPORTING RESULTS
Report exclusion criteria	A list of loci and regions that were excluded from SNP discovery
Provide list of SNP loci and alleles	Provide information on location of SNP, product, resulting codon change
Provide reads	Deposition of sequences and strain associated metadata in public repositories