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Journal of Clinical Microbiology, August 2009, p. 2435-2441, Vol. 47, No. 8
0095-1137/09/$08.00+0     doi:10.1128/JCM.00327-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Reliable Means of Diagnosis and Serovar Determination of Blood-Borne Salmonella Strains: Quick PCR Amplification of Unique Genomic Loci by Novel Primer Sets{triangledown}

Arvindhan Govindasamy Nagarajan,# Guruswamy Karnam,# Amit Lahiri, Uday Sankar Allam, and Dipshikha Chakravortty*

Centre for Infectious Disease Research and Biosafety Laboratories, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India

Received 13 February 2009/ Returned for modification 1 May 2009/ Accepted 8 June 2009

Typhoid fever is becoming an ever increasing threat in the developing countries. We have improved considerably upon the existing PCR-based diagnosis method by designing primers against a region that is unique to Salmonella enterica subsp. enterica serovar Typhi and Salmonella enterica subsp. enterica serovar Paratyphi A, corresponding to the STY0312 gene in S. Typhi and its homolog SPA2476 in S. Paratyphi A. An additional set of primers amplify another region in S. Typhi CT18 and S. Typhi Ty2 corresponding to the region between genes STY0313 to STY0316 but which is absent in S. Paratyphi A. The possibility of a false-negative result arising due to mutation in hypervariable genes has been reduced by targeting a gene unique to typhoidal Salmonella serovars as a diagnostic marker. The amplified region has been tested for genomic stability by amplifying the region from clinical isolates of patients from various geographical locations in India, thereby showing that this region is potentially stable. These set of primers can also differentiate between S. Typhi CT18, S. Typhi Ty2, and S. Paratyphi A, which have stable deletions in this specific locus. The PCR assay designed in this study has a sensitivity of 95% compared to the Widal test which has a sensitivity of only 63%. As observed, in certain cases, the PCR assay was more sensitive than the blood culture test was, as the PCR-based detection could also detect dead bacteria.

* Corresponding author. Mailing address: Centre for Infectious Disease Research and Biosafety Laboratories, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India. Phone: 91-80-22932986. Fax: 91-80-23602697. E-mail: dipa{at}mcbl.iisc.ernet.in

{triangledown} Published ahead of print on 17 June 2009.

# A.N. and G.K. made equal contributions to this study.

Journal of Clinical Microbiology, August 2009, p. 2435-2441, Vol. 47, No. 8
0095-1137/09/$08.00+0     doi:10.1128/JCM.00327-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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