Broad spectrum microarray for fingerprint-based bacterial species identification
In developed countries, Salmonella enterica subspecies 1 serovars Enteritidis and Typhimurium range among the most common causes of bacterial food-borne infections. The surveillance and typing of epidemic Salmonella strains are important tools in epidemiology. Usually, Salmonella enterica subspecies 1 serovars are differentiated by serotyping for diagnostic purposes. Further differentiation is done by phage typing as well as molecular typing techniques. Here we have designed and evaluated a prototype DNA microarray as a tool for serovar Typhimurium strain differentiation. It harbors 83 serovar Typhimurium probes obtained by differential subtractive hybridization and from the public database. The microarray yielded reproducible hybridization patterns in repeated hybridizations with chromosomal DNA of the same strain and could differentiate five serovar Typhimurium reference strains (DT204, DT104, DT208, DT36, and LT2). Furthermore, the microarray identified two distinct groups among 13 serovar Typhimurium DT104 strains. This correlated with observations from pulsed-field gel electrophoresis analysis. Twenty-three further serovar Typhimurium strains were analyzed to explore future directions for optimization of the simple 83-probe DNA microarray. The data presented here demonstrate that DNA microarrays harboring small numbers of selected probes are promising tools for serovar Typhimurium strain typing.