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Prophage Sequences Defining Hot Spots of Genome Variation in Salmonella enterica Serovar Typhimurium Can Be Used To Discriminate between Field Isolates

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom,¹ Health Protection Agency Centre for Infections, 61 Colindale Avenue, London NW9 5EQ, United Kingdom,² Scottish Salmonella Reference Laboratory, Stobhill Hospital, 133 Balornock Road, Glasgow G21 3UW, Scotland,³ SAC Veterinary Services and Animal Health Group, Drummondhill, Stratherrick Road, Inverness IV2 4JZ, Scotland⁴

Received 4 April 2007/ Returned for modification 10 May 2007/ Accepted 14 May 2007

Sixty-one Salmonella enterica serovar Typhimurium isolates of animal and human origin, matched by phage type, antimicrobial resistance pattern, and place of isolation, were analyzed by microbiological and molecular techniques, including pulsed-field gel electrophoresis (PFGE) and plasmid profiling. PFGE identified 10 profiles that clustered by phage type and antibiotic resistance pattern with human and animal isolates distributed among different PFGE profiles. Genomic DNA was purified from 23 representative strains and hybridized to the composite Salmonella DNA microarray, and specific genomic regions that exhibited significant variation between isolates were identified. Bioinformatic analysis showed that variable regions of DNA were associated with prophage-like elements. Subsequently, simple multiplex PCR assays were designed on the basis of these variable regions that could be used to discriminate between S. enterica serovar Typhimurium isolates from the same geographical region. These multiplex PCR assays, based on prophage-like elements and Salmonella genomic island 1, provide a simple method for identifying new variants of S. enterica serovar Typhimurium in the field.

Published ahead of print on 23 May 2007.