Development and application of molecular typing methods for Salmonella spp - the UK experience

Abstract

For the identification and typing of salmonellas the policy of the Laboratory of Enteric Pathogens is to use a hierarchical approach based in the first instance on phenotypic subdivion, supplemented when appropriate by methods based on the analysis of plasmid DNA and chromosomal DNA (genotyping). Plasmid DNA-based methods include plasmid profile typing, plasmid fingerprinting and the identification of plasmid-encoded salmonella plasmid virulence (spv) genes. Genotyping methods include ribotyping, insertion sequence (IS) 200 fingerprinting and pulsed-field gel electrophoresis (PFGE). In addition to providing a genomic fingerprint PFGE can be used in conjunction with gene probing to locate specific DNA sequences of interest such as rRNA or antibiotic resistance genes. More recently the applicability of a range of PCR-based methods including rep-PCR, ERIC-PCR and RAP-D have been assessed. For the investigation of antibiotic resistance recent advances in the PCR mapping of integrons coupled with direct sequencing of amplifield gene products has added a new dimension to our understanding of the epidemiology of chromosomally-located resistance genes in key serotypes and phage types. The strengths and weaknesses of genomic fingerprinting will be discussed with particular reference to recent international outbreaks of Salmonella agona, S. anatum and multiresistant S. typhimurium DT 104 (DT 104). In relation to DT 104, the use of integron analysis by PCR to investigate the epidemiology of multiple antibiotic resistance genes in this key phage type will also be discussed.