title: Genome-Scale Screening and Validation of Targets for Identification of Salmonella enterica and Serovar Prediction.
abstract: Salmonella enterica is the most common foodborne pathogen worldwide, with 2,500 recognized serovars. Detection of S. enterica and its classification into serovars are essential for food safety surveillance and clinical diagnosis. The PCR method is useful for these applications because of its rapidity and high accuracy. We obtained 412 candidate detection targets for S. enterica using a comparative genomics mining approach. Gene ontology (GO) functional enrichment analysis of these candidate targets revealed that the GO term with the largest number of unigenes with known function (38 of 177, 21.5%) was significantly involved in pathogenesis (P < 10(-24)). All the candidate targets were then evaluated by PCR assays. Fifteen targets showed high specificity for the detection of S. enterica by verification with 151 S. enterica strains and 34 non-Salmonella strains. The phylogenetic trees of verified targets were highly comparable with those of housekeeping genes, especially for differentiating S. enterica strains into serovars. The serovar prediction ability was validated by sequencing one target (S9) for 39 S. enterica strains belonging to six serovars. Identical mutation sites existed in the same serovar, and different mutation sites were found in diverse serovars. Our findings revealed that 15 verified targets can be potentially used for molecular detection, and some of them can be used for serotyping of S. enterica strains.
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Xiujuan
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Lida
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Chunlei
authors.initials: C
authors.lastname: Shi
authors.affiliation: U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA.
authors.forename: Pina M
authors.initials: PM
authors.lastname: Fratamico
authors.affiliation: College of Food Science and Engineering, Northwest Agriculture and Forestry University, Shaanxi Yangling, People's Republic of China.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA.
authors.forename: George C
authors.initials: GC
authors.lastname: Paoli
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Dan
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Zhuang
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Wang
authors.affiliation: Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China. xmshi@sjtu.edu.cn.
authors.forename: Xianming
authors.initials: X
authors.lastname: Shi
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005516:Food Microbiology / Q000379:methods*; D063990:Gene Ontology; D005798:Genes, Bacterial; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D019779:Salmonella enterica / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012680:Sensitivity and Specificity; D065288:Serogroup; D012703:Serotyping
chemical_list: D004269:DNA, Bacterial