Development of a species-specific DNA probe for Moraxella (Branhamella) catarrhalis

Species-specific and ubiquitous-DNA-based assays for rapid identification of Staphylococcus aureus

Staphylococcus aureus is the cause of serious infections in humans, including endocarditis, deep-seated abscesses, and bacteremia, which lead to toxic and septic shock syndromes. Rapid and direct identification of this bacterium specifically and ubiquitously directly from clinical specimens would be useful in improving the diagnosis of S. aureus infections in the clinical microbiology laboratory. A wide variety of kits based on biochemical characteristics efficiently identify S. aureus, but the rapidity and the accuracy of each of these methods combined with testing of clinically relevant antibiotic resistance genes need to be improved. On the basis of hybridization assays with randomly selected clones from an S. aureus genomic library, we have identified a chromosomal DNA fragment which is specific for S. aureus and which detected all 82 S. aureus isolates tested. This 442-bp fragment was sequenced and was used to design a set of PCR amplification primers. The PCR assay was also specific and ubiquitous for the identification from bacterial cultures of 195 clinical strains of S. aureus isolated from a variety of anatomical sites and obtained from hospitals throughout the world. The PCR assay that we have developed is simple and can be performed in about 1 h. This DNA-based test provides a novel diagnostic tool for the diagnosis of S. aureus infections.

Fastidious gram-negative bacteria: meeting the diagnostic challenge with nucleic acid analysis

The extended panorama of fastidious Gram-negative bacteria (FGNB) as opportunistic etiological agents of infectious diseases in immunocompromised patients is largely due to improved medical expertise and technology. The heightened awareness of infectious diseases due to FGNB species mandates comprehensive classification and identification systems as a basis for rapid and reliable diagnostics. The most useful approaches are combinations of nucleic acid techniques such as hybridization, genetic transformation, amplification and base sequence analysis with selected conventional criteria. Among these approaches, the widely distributed feature of natural competence in these organisms facilitates the use of the biological method of genetic transformation as a valuable addition to the more common nucleic acid techniques. We describe the development of the taxonomy of FGNB through the last four decades, with particular emphasis on the families Neisseriaceae, Moraxellaceae, and Pasteurellaceae.

Epidemiological typing of Moraxella catarrhalis by pulsed field gel electrophoresis

Pulsed field gel electrophoresis (pfge) was used to compare 59 strains of Moraxella catarrhalis to evaluate pfge for the epidemiological typing of this organism. pfge-generated patterns were compared with those obtained by small fragment restriction enzyme analysis (rea) and species-specific probe hybridization. The strains used in the study were isolated from various geographic locations and included proven epidemiologically related strains. pfge yielded more unique patterns than dna-dna hybridization - 30 versus 18, respectively - but fewer than rea, which generated 45 unique patterns. Strains that demonstrated the same rea pattern or dna-dna hybridization pattern did not always demonstrate the same pfge pattern. For example, in 23 epidemiologically unrelated strains that shared six rea patterns, pfge differentiated the isolates into 12 patterns. Conversely, strains that demonstrated the same pfge pattern did not always demonstrate the same rea pattern or hybridization pattern. For example, in 42 strains that shared 13 pfge patterns, rea differentiated the isolates into 31 patterns and dna-dna hybridization differentiated them into 16 patterns. However, compared with rea, pfge yielded less complex patterns that were more easily comparable, and compared with dna-dna hybridization, pfge was technically easier.

Epidemiological typing of Moraxella catarrhalis by using DNA probes

Small-fragment restriction enzyme analysis and DNA-DNA hybridization were used to compare 60 strains of Moraxella catarrhalis isolated from various geographic locations. Restriction enzyme analysis with HaeIII resulted in 46 different patterns, 7 of which were shared by more than one isolate. Hybridizations with two DNA probes resulted in 18 different patterns, 11 of which were shared by more than one isolate. Strains with the same restriction enzyme pattern always had the same hybridization pattern. However, of the 50 strains that shared the 11 hybridization patterns, 39 could be further differentiated by restriction enzyme analysis. We found that hybridization is a method that is specific for the epidemiological typing of M. catarrhalis, but because of limited sensitivity, combination with small-fragment restriction enzyme analysis may be necessary to better determine the relatedness of strains.

Identification of toxigenic Clostridium difficile strains using a toxin B gene-specific oligonucleotide probe

We describe the use of a new specific synthetic oligonucleotide probe, deduced from the sequence of the gene for Clostridium difficile toxin B, to identify toxigenic strains of C. difficile. This probe does not hybridize to the DNA of non-toxigenic strains of C. difficile nor to DNA isolated from different Clostridium species, including C. sordellii. None of the enteric pathogenic bacteria tested were seen to hybridize with the probe. A preliminary study of direct probing of faecal specimens indicates a potential for the use of this DNA probe in the clinical laboratory for the rapid identification of toxigenic strains of C. difficile.

Isolation and characterization of a species-specific DNA probe for Candida albicans

As a model for the isolation of species-specific sequences of DNA, we isolated and characterized a species-specific DNA fragment from the Candida albicans genome. We used a series of differential colony hybridization experiments, in which a C. albicans genomic library was hybridized with genomic DNA probes from related organisms to minimize the number of potentially specific C. albicans DNA fragments to be tested. Six clones were tested by dot blot analysis, and one of them, a 1348 bp EcoRI DNA fragment, was confirmed as specific for C. albicans. This species-specific fragment could be utilized as a DNA probe for rapid, sensitive, and specific diagnosis of C. albicans DNA in clinical specimens.