{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T16:03:39Z","timestamp":1790265819206,"version":"4.1.0"},"reference-count":33,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2012,6,1]],"date-time":"2012-06-01T00:00:00Z","timestamp":1338508800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2012,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>With the advent of high-throughput DNA sequencing, more than 4,000 bacterial genomes have been sequenced and are publicly available. We report a user-friendly web platform, ssGeneFinder Webserver (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/147.8.74.24\/ssGeneFinder\/\">http:\/\/147.8.74.24\/ssGeneFinder\/<\/jats:ext-link>), which is updated weekly for the automated pangenomic selection of specific targets for direct PCR detection and the identification of clinically important bacteria without the need of gene sequencing. To apply the ssGeneFinder Webserver for identifying specific targets for<jats:named-content content-type=\"genus-species\">Salmonella enterica<\/jats:named-content>serovar Typhi, we analyzed 11<jats:italic>S<\/jats:italic>. Typhi genomes, generated two specific targets, and validated them using 40<jats:italic>S<\/jats:italic>. Typhi, 110 non-Typhi<jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>serovars (serovar Paratyphi A,<jats:italic>n<\/jats:italic>= 4; Paratyphi B,<jats:italic>n<\/jats:italic>= 1; Typhimurium,<jats:italic>n<\/jats:italic>= 5; Enteritidis,<jats:italic>n<\/jats:italic>= 12; non-Paratyphi group A,<jats:italic>n<\/jats:italic>= 6; non-Paratyphi group B,<jats:italic>n<\/jats:italic>= 29; non-Paratyphi group C,<jats:italic>n<\/jats:italic>= 12; non-Typhi group D,<jats:italic>n<\/jats:italic>= 35; group E and others,<jats:italic>n<\/jats:italic>= 6), 115<jats:named-content content-type=\"genus-species\">Enterobacteriaceae<\/jats:named-content>isolates (<jats:named-content content-type=\"genus-species\">Escherichia<\/jats:named-content>,<jats:italic>n<\/jats:italic>= 78;<jats:named-content content-type=\"genus-species\">Shigella<\/jats:named-content>,<jats:italic>n<\/jats:italic>= 2;<jats:named-content content-type=\"genus-species\">Klebsiella<\/jats:named-content>,<jats:italic>n<\/jats:italic>= 13;<jats:named-content content-type=\"genus-species\">Enterobacter<\/jats:named-content>,<jats:italic>n<\/jats:italic>= 9; others,<jats:italic>n<\/jats:italic>= 13), and 66 human stool samples that were culture negative for<jats:italic>S<\/jats:italic>. Typhi. Both targets successfully detected all typical and atypical<jats:italic>S<\/jats:italic>. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2O<jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>antiserum, and the Vi-negative attenuated vaccine strain Ty21a. No false positive was detected from any of the bacterial isolates and stool samples. DNA sequencing confirmed the identity of all positive amplicons. The PCR assays have detection limits as low as 100 CFU per reaction and were tested using spiked stool samples. Using a pangenomic approach, ssGeneFinder Webserver generated targets specific to<jats:italic>S<\/jats:italic>. Typhi. These and other validated targets should be applicable to the identification and direct PCR detection of bacterial pathogens from uncultured, mixed, and environmental samples.<\/jats:p>","DOI":"10.1128\/jcm.06843-11","type":"journal-article","created":{"date-parts":[[2012,3,23]],"date-time":"2012-03-23T03:29:56Z","timestamp":1332473396000},"page":"1905-1911","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":23,"title":["Automated Pangenomic Analysis in Target Selection for PCR Detection and Identification of Bacteria by Use of ssGeneFinder Webserver and Its Application to Salmonella enterica Serovar Typhi"],"prefix":"10.1128","volume":"50","author":[{"given":"Chi-Chun","family":"Ho","sequence":"first","affiliation":[{"name":"Department of Microbiology, The University of Hong Kong, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan K. L.","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cindy W. S.","family":"Tse","sequence":"additional","affiliation":[{"name":"Department of Pathology, Kwong Wah Hospital, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwok-Yung","family":"Yuen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The University of Hong Kong, Hong Kong, China"},{"name":"State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China"},{"name":"Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China"},{"name":"Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna K. P.","family":"Lau","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The University of Hong Kong, Hong Kong, China"},{"name":"State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China"},{"name":"Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China"},{"name":"Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick C. Y.","family":"Woo","sequence":"additional","affiliation":[{"name":"Department of Microbiology, The University of Hong Kong, Hong Kong, China"},{"name":"State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China"},{"name":"Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China"},{"name":"Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02147-07"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01794-09"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/clinids\/6.3.345"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.257.5073.1050"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/31159"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02418-10"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.15.3.416-418.1982"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02215-09"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00025-07"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01702-10"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05062-11"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00701-06"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(00)04403-2"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05088-11"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.3.1470-1472.2005"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02095-08"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/146.6.724"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00431-11"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.5.1885-1889.2004"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.17.5883-5898.2004"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01586"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcp.2008.04.002"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.1.225-228.1999"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/468037a"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01627-09"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02071-09"},{"key":"e_1_3_3_28_2","doi-asserted-by":"crossref","DOI":"10.1128\/9781555816728","volume-title":"Manual of clinical microbiology","author":"Versalovic J","year":"2011","unstructured":"VersalovicJ (ed). 2011. Manual of clinical microbiology, 10th ed. ASM Press, Washington, DC.","edition":"10"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijfoodmicro.2008.01.006"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.3.1190-1194.2001"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000416"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01750-09"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.3.805-810.2002"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02350-10"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.06843-11","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.06843-11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T10:33:11Z","timestamp":1687343591000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.06843-11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6]]},"references-count":33,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2012,6]]}},"alternative-id":["10.1128\/JCM.06843-11"],"URL":"https:\/\/doi.org\/10.1128\/jcm.06843-11","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,6]]},"assertion":[{"value":"2011-12-30","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-03-11","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-06-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}