Detection of genomic variation in Providencia stuartii clinical isolates by analysis of DNA restriction fragment length polymorphisms containing rRNA cistrons

Abstract

Chromosomal DNA from 26 strains of Providencia stuartii isolated mainly in hospitals in the United Kingdom and reference strains of P. stuartii, P. rustigianii, and Proteus vulgaris were digested with the restriction endonucleases EcoRI and HindIII. After electrophoresis in agarose gels, the fragments were subjected to Southern blot hybridization analysis with a biotin-labeled cDNA probe transcribed from a mixture of 16S and 23S rRNA from P. stuartii NCTC 11800T. The pattern of bands (the rDNA fingerprint), which depended on restriction fragment length polymorphism containing rRNA genes, was used as a measure of minor genomic variation within and between species. The P. stuartii clinical isolates had similar total digest patterns, but the rDNA fingerprints revealed some heterogeneity between strains, with EcoRI digests providing better strain discrimination than HindIII. Such rDNA fingerprints comprised between five and seven bands with sizes in the range of 5 to 28 kilobases. The 11 different EcoRI patterns were compared by numerical analysis, and several groups or subgroups of strains were identified. Over half (15 of 26) of the urease-negative isolates (subgroups Aa and Ab) had patterns that differed only by the presence or absence of a 25-kilobase band. Urease-negative strains from other clinical material were more heterogeneous in their patterns. No correlation was apparent between strain pattern group and urease production or geographic location of isolate. The P. stuartii rDNA fingerprints were quite distinct from those of allied Providencia and Proteus species and provided a more sensitive measure of minor genomic differences than total DNA digests did.

Molecular characterization of Haemophilus ducreyi by ribosomal DNA fingerprinting

“…Because rRNA has been more highly conserved during evolution than the rest of the genome (7), the advantage of ribotyping over the use of randomly cloned DNA fragments is that a single probe can be used to study rRNA gene restriction fragments from many different bacterial species. rRNA from E. coli is a broad-spectrum probe that has been used in the study of the molecular epidemiology of different bacteria (14,20). The analysis of rRNA gene restriction patterns has been successfully applied to several bacterial species, including H. influenzae biogroup aegyptius (8), Acholeplasma laidlawii, Mycoplasma hominis, and Mycoplasma pneumoniae (25).…”

Comparison of methods for discrimination between strains of Listeria monocytogenes from epidemiological surveys

“…Numerous studies have demonstrated the utility of DNA fingerprinting for epidemiological analysis of phenotypically indistinguishable microbial pathogens (1,4,15,18,19,22,36,(38)(39)(40). Ribotyping, based on restriction fragment length polymorphisms in the chromosomal DNA containing rRNA genes, has also been used as a means of detecting interspecies and interstrain differences (13,14,24). Fingerprinting and ribotyping do not rely on phenotypic expression, are sensitive to minor genomic differences, and offer a precise means for characterizing species and differentiating closely related strains.…”

Differentiation of Clostridium difficile, Clostridium bifermentans, Clostridium sordellii, and Clostridium perfringens from Diarrheal Stool by API ZYM and API LRA Oxidase Test

“…All C. perfringens strains studied constantly exhibited activities 2, 3,4,11,12,13,14,16,17, and two strains (66%) showed additional activities like: 9, 10, 15, 18, that yielded the biochemical pattern of this group of microorganisms, more specific and typical. So for this species the system correctly identified 100% of the strains tested.…”