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Journal of Clinical Microbiology, August 2005, p. 3688-3698, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3688-3698.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected Salmonella enterica Serotypes

Sharinne Sukhnanand,1 Sam Alcaine,1 Lorin D. Warnick,2 Wan-Lin Su,1 Jessica Hof,1 Mary Pat J. Craver,1 Patrick McDonough,2 Kathryn J. Boor,1 and Martin Wiedmann1*

Department of Food Science,1 Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 148532

Received 16 September 2004/ Accepted 17 April 2005

While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This "three-gene sequence typing scheme" allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.

* Corresponding author. Mailing address: Department of Food Science, 412 Stocking Hall, Cornell University, Ithaca, NY 14853. Phone: (607) 254-2838. Fax: (607) 254-4868. E-mail: mw16{at}cornell.edu.

Journal of Clinical Microbiology, August 2005, p. 3688-3698, Vol. 43, No. 8
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.8.3688-3698.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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