Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex Polymerase Chain Reaction Assay

Ou, Hong Yu and Ju, C.T.S. and Thong, Kwai Lin and Ahmad, Norazah and Deng, Z.X. and Barer, Michael R. and Rajakumar, Kumar (2007) Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex Polymerase Chain Reaction Assay. Journal of Molecular Diagnostics, 9 (5). pp. 624-630. ISSN 1525-1578

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Official URL: https://doi.org/10.2353/jmoldx.2007.070064

Abstract

The use of pathogen genome sequence data for the control and management of infections remains an ongoing challenge. We describe a broadly applicable, web-enabled approach that can be used to develop bacteria-specific polymerase chain reaction (PCR) assays. Salmonella enterica Paratyphi A has emerged as a major cause of enteric fever in Asia. Culture-based diagnosis is slow and frequently negative in patients with suspected typhoid and paratyphoid fever, potentially compromising patient management and public health. We used the MobilomeFINDER web-server to perform in silico subtractive hybridization, thus identifying 43 protein-coding sequences (CDSs) that were present in two Paratyphi A strains but not in other sequenced Salmonella genomes. After exclusion of 29 CDSs found to be variably present in Paratyphi A strains by microarray hybridization and grouping of remaining CDSs by genomic location, four dispersed targets (stkF, spa2473, spa2539, hsdM) were used to develop a highly discriminatory multiplex PCR assay. All 52 Paratyphi A strains within the diverse panel investigated produced one of two pathognomonic four-band signatures. Given rapid and ongoing expansion of DNA and comparative genomics databases, our universally accessible web-server-supported do-it-yourself approach offers the potential to contribute significantly to the rapid development of species-, serovar-, or pathotype-specific PCR assays targeting pre-existing and emerging bacterial pathogens.

Item Type: Article
Uncontrolled Keywords: Translational Genomics; Salmonella enterica Serovar Paratyphi; Multiplex Polymerase Chain Reaction Assay
Subjects: Q Science > Q Science (General)
Q Science > QH Natural history
Q Science > QR Microbiology
Divisions: Faculty of Science > Institute of Biological Sciences
Depositing User: miss munirah saadom
Date Deposited: 28 Dec 2012 05:15
Last Modified: 15 Oct 2018 03:16
URI: http://eprints.um.edu.my/id/eprint/5646

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