Molecular characterization of endemic salmonella infections ... - Evira

Genomic sequences derived from temperate phages in S. Typhimurium were used to design
primer sets, which were used to analyse sequence variations of prophage loci. The typing was
based on the presence or absence of an amplified product. This multiple amplification of phage
locus typing (MAPLT) was more discriminatory than PFGE and MLST with the housekeeping
genes (fhuA, sucA, tonB, manB, glnA), regardless of phage type (Ross and Heuzenroeder 2005b).
Multiple-locus variable-number tandem-repeats analysis (MLVA) and variable number of tandem
repeats (VNTR)
The variable number of tandem repeats (VNTR) belong to a class of repetitive DNA that appears to
contain a high level of polymorphism, thereby giving the VNTR-based typing a high discriminatory
capacity (Lindstedt et al 2003). The multiple-locus variable-number tandem-repeats analysis
(MLVA) is based on capillary separation of multiplexed PCR products from VNTR loci in the
bacterial genome. These PCR products are labeled with fluorescent dyes (Lindstedt et al 2003,
2004). The VNTR-based method has a greatly superior discrimination within the highly
homogenous S. Typhimurium DT104 phage type compared to those of XbaI PFGE, AFLP and
integron pattern analyses (Lindstedt et al 2003). These authors also observed a high correlation
between MLVA clusters and PFGE clusters of S. Typhimurium (Lindstedt et al 2003, 2004).
However, the MLVA method is not suitable for predicting phage types, as it does not group all the
similar phage types within the same MLVA clusters, even though a correlation with the S.
Typhimurium phage types was found (Lindstedt et al 2004). MLVA was effective in identifying a
regional outbreak of S. Typhimurium DT12 in Denmark and locating its source, whereas the
routinely used PFGE did not discriminate between the isolates (Torpdahl et al 2006). MLVA was
evaluated, and compared with PFGE and phage typing, for subtyping S. Enteritidis. It was
concluded that MLVA was more discriminatory than PFGE and phage typing among nonepidemiologically
in addition to epidemiologically linked isolates. MLVA also was found to have
good reproducibility (Boxrud et al 2007).
2.5.2.7 DNA microarray
The DNA microarray methodology allows assessment of differences and changes in bacterial
genomic contents. It has been widely used for comparative Salmonella research since genomic
comparison of S. enterica serovars and S. bongori were performed by Chan et al in 2003. Porwollik
et al (2004) found that gene contents sometimes differed more within a serovar than between
serovars. The Salmonella strains that share a distinct profile of gene content are called genovars.
Two distinct groups among 13 strains of serovar Typhimurium DT104 were identified by a
prototype DNA microarray developed for strain differentiation (Pelludat et al 2005). Cooke et al
(2007) used microarrays to detect genes that exhibit significant genetic variation in S.Typhimurium,
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