[Genotyping of isolates of bacteria and Candida]

Strain differentiation of Staphylococcus species, Streptococcus pneumoniae, Escherichia coli, Clostridium difficile, and Candida species was performed by restriction endonuclease analysis (REA) of genomic DNA with HinfI or HaeIII followed by conventional agarose gel electrophoresis. REA of 19 methicillin-resistant S. aureus isolates and 19 methicillin-susceptible S. aureus isolates revealed 8, and 14 patterns, respectively. Fifty-three isolates of S. epidermidis were divided into 39 groups on the basis of REA pattern. REA patterns obtained from different strains of the same species were more similar than those from different Staphylococcus species. A total of 67 patterns were noted among 215 S. pneumoniae isolates. There was some correlation between the REA patterns and serotypes. In addition, all 61 isolates showing the pattern 6 (serotype 19) were penicillin-resistant. Sixteen isolates of E. coli O157 and 18 isolates of E. coli O25 were analyzed by REA with HaeIII. Among 14 epidemiologically unrelated E. coli O157:H7 isolates, REA patterns were either identical or differed only by a few fragment bands. REA patterns of 7 isolates of heat stable enterotoxin producing E. coli O25 from an outbreak were identical. Eight distinct REA patterns were noted among 7 toxigenic C. difficile strains, and one to two strains were included in each group. Candida strains belonging to different six Candida species were analysed by REA. All C. albicans isolates (148 strains) showed one to four bright bands ranging from 4 to 8kb in size, and these strains were divided into 37 groups according to the REA patterns. Each Candida strain showed species-specific REA patterns. Twenty-one isolates of Mycobacterium tuberculosis complex were analyzed by PCR with primer complementary to the inverted repeat of IS6110(IS6110-PCR). The results of PCR of 19 M. tuberculosis isolates and 2 M. bovis BCG isolates revealed 15 patterns, and 1 pattern, respectively. Our results demonstrated that REA of genomic DNA with HinfI or HaeIII was a useful tool for strain differentiation. By comparing the species-specific REA patterns of reference strains, clinical isolates of Candida and Staphylococci could be identified to the species level if they could not be identified by routine biochemical methods. Because IS6110-PCR is simple and rapid to perform, it seems to be a good screening method to differentiate M. tuberculosis strains.