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Journal of Bacteriology, April 2005, p. 2638-2650, Vol. 187, No. 8
0021-9193/05/$08.00+0     doi:10.1128/JB.187.8.2638-2650.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Diversity of Genome Structure in Salmonella enterica Serovar Typhi Populations{dagger}

Sushma Kothapalli,1 Satheesh Nair,1 Suneetha Alokam,1 Tikki Pang,2 Rasik Khakhria,3,{ddagger} David Woodward,3 Wendy Johnson,4 Bruce A. D. Stocker,5,§ Kenneth E. Sanderson,1* and Shu-Lin Liu1,6,7

Department of Biological Sciences,1 Department of Microbiology and Infectious Diseases, University of Calgary, Calgary,6 Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Health Canada,3 Cangene Corporation, Winnipeg, Manitoba, Canada,4 Research Policy and Cooperation, World Health Organization, Geneva, Switzerland,2 Department of Medical Microbiology, Stanford University, Stanford, California,5 Department of Microbiology Peking University School of Basic Medical Sciences, Beijing, China7

Received 24 September 2004/ Accepted 6 January 2005

The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.

* Corresponding author. Mailing address for Kenneth E. Sanderson: Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada. Phone: (403) 220-6792. Fax: (403) 289-9311. E-mail: kesander{at}ucalgary.ca Mailing address for Shu-Lin Liu: Department of Microbiology and Infectious Diseases, University of Calgary, Calgary T2N 1N4, Canada. Phone: (403) 220-3799. Fax: (403) 270-2772. E-mail: slliu{at}ucalgary.ca.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Present address: 32 Amberwood Crescent, Nepean, Ontario,Canada.

§ Deceased.

Journal of Bacteriology, April 2005, p. 2638-2650, Vol. 187, No. 8
0021-9193/05/$08.00+0     doi:10.1128/JB.187.8.2638-2650.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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