ArticleJournal of clinical microbiology2012
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.
Article in Journal of clinical microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 24 citations in OpenAlex.
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- RUCS: rapid identification of PCR primers for unique core sequences.Bioinformatics (Oxford, England) · 2017Article
- Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR.PloS one · 2015Article
- An efficient alternative marker for specific identification of Mycobacterium tuberculosis.World journal of microbiology & biotechnology · 2014Article
- Romance of the three domains: how cladistics transformed the classification of cellular organisms.Protein & cell · 2013Review
- Pan-PCR, a computational method for designing bacterium-typing assays based on whole-genome sequence data.Journal of clinical microbiology · 2013Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 (http://147.8.74.24/ssGeneFinder/), 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 Salmonella enterica serovar Typhi, we analyzed 11 S. Typhi genomes, generated two specific targets, and validated them using 40 S. Typhi, 110 non-Typhi Salmonella serovars (serovar Paratyphi A, n = 4; Paratyphi B, n = 1; Typhimurium, n = 5; Enteritidis, n = 12; non-Paratyphi group A, n = 6; non-Paratyphi group B, n = 29; non-Paratyphi group C, n = 12; non-Typhi group D, n = 35; group E and others, n = 6), 115 Enterobacteriaceae isolates (Escherichia, n = 78; Shigella, n = 2; Klebsiella, n = 13; Enterobacter, n = 9; others, n = 13), and 66 human stool samples that were culture negative for S. Typhi. Both targets successfully detected all typical and atypical S. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2O Salmonella 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 S. 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.
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