Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona.

This study describes the characterization of the recently described Salmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285-291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised approximately 87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.

Molecular tools for the characterisation of antibiotic-resistant bacteria.

This review will discuss a number of molecular tools which are currently used as well as some innovative approaches for the characterisation of antibiotic-resistant bacterial strains. Various methods involved in the detection and characterisation of genes and mutations associated with antibiotic resistance and that are used for strain typing as part of epidemiological studies, are described. Furthermore, a few examples are discussed in which the results of both gene and strain characterisation are combined to investigate the underlying mechanism of the spread of antibiotic resistance. Some of the available molecular techniques are heavily supported by the existence of databases on the Internet. These databases either contain a fast growing amount of sequence information or a large number of allelic or fingerprint profiles. The current progress in applied DNA technology and the ongoing projects on the elucidation of the whole genomic sequence of bacterial species have lead and will further lead to the development and application of sophisticated new strategies for the analysis of antibiotic resistant bacterial strains.

AFLP allows the identification of genomic markers of ruminant Chlamydia psittaci strains useful for typing and epidemiological studies.

Amplified fragment length polymorphism (AFLP), a novel method for molecular typing, was evaluated for its ability to differentiate among a group of highly related Chlamydia psittaci strains isolated from ruminants and belonging to serotype 1. A total set of 12 strains were included in this study, 10 strains inducing abortion in ruminants and 2 strains from faecal samples. For the AFLP analysis, the total purified genomic DNA of each strain was submitted to a one-step digestion-ligation reaction for 3 h at 37 degrees C. DNA was digested with a single restriction endonuclease Mspl and ligated to specially constructed adapters. Subsequently, restricted fragments were selectively amplified under high stringency PCR conditions using primers complementary to the adapters. Amplified products were then resolved on agarose gel electrophoresis. The method is easy to perform, fast and reproducible. AFLP enabled characterization of C. psittaci strains at the infra-subspecific level. Thus, AFLP led to the identification of a cluster of strains on the basis of their AFLP patterns, constituted by French chlamydial isolates. It also permitted differentiation among strains in relation to host origin and to clinical syndromes. These data confirmed the highly discriminative power of AFLP towards the differentiation of closely related ruminant C. psittaci strains. The analysis will need to be applied to more samples to check the usefulness of AFLP markers in epidemiological and evolutionary studies.