Prophages in Listeria monocytogenes contain single-nucleotide polymorphisms that differentiate outbreak clones within epidemic clones.

A fragment end ligation-mediated PCR strategy was used to analyze the AscI pulsed-field gel electrophoresis patterns of Listeria monocytogenes epidemic clone II (ECII), which led to the identification of single-nucleotide polymorphisms (SNPs) in prophage regions that differentiated the two ECII outbreak clones. SNPs in prophages that differentiated the outbreak clones of ECIII and -IV were also identified.