Molecular characterization of endemic salmonella infections ... - Evira

Enterobacterial repetitive intergenic consensus (ERIC)-PCR
A highly conserved, repetitive element, about 126 bp in length, was identified in Salmonella.
However, the chromosomal locations of these enterobacterial repetitive intergenic consensus
(ERIC) sequences may differ between and within different species and strains, providing a basis
for typing (Grimont et al 2000). The DNA fingerprints obtained by ERIC-PCR are not very complex,
and making finer distinctions between the strains are more difficult (Versalovic et al 1991).
The use of ERIC-PCR for subtyping Salmonellae was first described by Kerouanton et al (1996),
but it could not subdivide 32 strains of S. Dublin. In a study by Burr et al (1998), ERIC-PCR
produced unique fingerprints for almost all 89 Salmonella isolates belonging to 22 serotypes, but
these fingerprints did not identify the serotypes. Furthermore, ERIC-PCR was found to be valuable
in the analysis of S. Typhimurium, S. Virchow, S. Enteritidis, S. Abortusequi, S. Choleraesuis, S.
Bareilly and S. Dublin (Bennasar et al 2000; Chmielewski et al 2002; Saxena et al 2002). However,
it was not able to differentiate between Argentinian strains of S. Infantis (Merino et al 2003).
Repetitive extragenic palindromic (REP)-PCR
Repetitive extragenic palindromic (REP) consensus sequences of 38 bp have been identified in
Salmonella, and among other enteric bacteria. Fingerprints of different bacterial genomes can be
produced by using these sequences as efficient primer binding sites in PCR reactions. The
complex DNA fingerprints are reproducible and diagnostic for specific strains (Versalovic et al
1991).
REP-PCR was first used for the typing of Salmonellae in 1996, when only one type was detected in
32 strains of S. Dublin (Kerouanton et al 1996). In contrast, REP-PCR was useful in the analysis of
isolates of S. Saintpaul, S. Typhimurium, S. Virchow, S. Enteritidis and S. Infantis (Beyer et al
1998; Bennasar et al 2000; Chmielewski et al 2002; Merino et al 2003). Modified REP-PCR typing
with the ERIC2 and BOXA1R primers was highly reproducible in the retrospective analysis of an
outbreak of S. Infantis. It also distinguished between the serovars (Johnson et al 2001). In a study
with 68 Salmonella isolates of ten different serovars, both PFGE and REP-PCR were able to
differentiate among isolates of the same serovar, but REP-PCR using BOX, ERIC, and REP
primers had a greater discriminatory capacity than PFGE in differentiating closely related isolates.
It was suggested that REP-PCR would therefore be the preferred method in transmission studies
of Salmonella, in those cases in which an individual isolate needs to be traced back to a specific
source (Weigel et al 2004). Woo and Lee (2006) also suggested that REP-PCR (using ERIC and
REP primers) may be preferred to PFGE as the most suitable method. In another study, REP-PCR
with the primers ERIC and (GTG)5 were compared with each other with regard to their
discriminatory power between serotypes. The reproducibility was poor between different PCR runs
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