Purpose: To develop improved fast laboratory diagnostic techniques with the combination of bioinformatics analysis and biological experiment validation for the control of this pathogen. And to develop genotyping method for determining the sources of outbreaks and for understanding the epidemiology of sporadic cases acquired from various sources to meet the increasing demand of Salmonella surveillance.
Methods: Specific molecular detection targets for the species of Salmonella enterica, its serogroups A to D, and even 8 serotypes were identified based on the analysis results from bioinformatics platform (SMM-system) and PCR assays. Using the multilocus sequence typing (MLST), 25 Salmonella isolates from 5 chicken farms, 121 Salmonella food isolates from 13 countries or regions, and 353 Salmonella clinic isolates from Shanghai CDC were subtyped.
Results: Based on these targets, several multiplex and real-time PCR systems have been developed for the identification and differentiation of this bacterium. Further functional analysis showed that Salmonella enterica-specific target genes were related with its survival and pathogenesis; Salmonella serogroup-specific target genes were associated with sugar synthesis and metabolism or O-actetyl transfer; and Salmonella serovar-specific target genes were involved in DNA repair or phage encoded protein. Using MLST, the farm isolates, isolates from different countries or regions, and clinic isolates demonstrated 6, 42 and 12 sequence types, respectively. In addition, the discriminatory power of MLST (D = 0.947) was close to that of the serotyping method. The close evolutionary relationship between food and clinical isolates suggested that the patients might have been infected by the contaminated food. It was concluded that MLST has been an alternative method for the analysis of Salmonella population structure, an evolutionary and epidemiological tool for this pathogen.
Significance: The methods developed in this study can help to the fast laboratory diagnosing of Salmonella, to determining the sources of outbreaks and to understanding the epidemiology of sporadic cases acquired from various sources.