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Bacteroides  spp. are opportunist pathogens that cause blood and soft tissue infections and are often resistant to antimicrobial agents. We have developed a combined PCR-restriction fragment length polymorphism (RFLP) technique to characterize the 16S rRNA gene for identification purposes and the nitroimidazole resistance ( nim ) gene for detection of resistance to the major antimicrobial agent used to treat  Bacteroides infections: metronidazole (MTZ). PCR-RFLP analysis of 16S ribosomal (rDNA) with  Hpa II and  Taq I produced profiles that enabled discrimination of type strains and identification of 70 test strains to the species level. The 16S rDNA PCR-RFLP identification results agreed with routine phenotypic testing for 62 of the strains. The discrepancies between phenotypic and PCR-RFLP methods for eight strains were resolved by 16S rDNA sequencing in three cases, but five strains remain unidentified. The presence of  nim  genes was indicated by PCR in 25 of 28 strains that exhibited reduced sensitivity to MTZ. PCR-RFLP of the  nim  gene products identified the four reported genes ( nimA , - B , - C , and - D ) and indicated the presence of a previously unreported  nim  gene in 5 strains. This novel nim  gene exhibited 75% DNA sequence similarity with nimB . These rapid, accurate, and inexpensive methods should enable improved identification of Bacteroides  spp. and the detection of MTZ resistance determinants.

PCR-Restriction Fragment Length Polymorphism Analysis for Identification of Bacteroides spp. and Characterization of Nitroimidazole Resistance Genes