M. E. Frazier

Use of pulsed field gel electrophoresis to differentiate Coxiella burnetii strains

Pulsed field gradient gel electrophoresis (PFGE) provides a powerful technique for the analysis of bacterial genomic DNA by allowing the resolution of DNA fragments as large as 9000 kilobase pairs (kbp). When isolates of Coxiella burnetii were examined using this method, the restriction enzymes Not I and Sfi I gave the fewest and most easily resolved fragments. Sfi I cuts the genome of the Priscilla isolate of C. burnetii into 15 DNA fragments ranging in size from 320 to 18 kbp, and Not I cuts the DNA of this isolate into 20 fragments from 293 to 10 kbp in size. Analysis of the undigested DNA and summing of the Sfi I restriction fragments both indicate that the C. burnetii DNA contains approximately 1600 kbp, or is about one-third the size of the DNA in Escherichia coli. Comparisons of isolates revealed that the numbers and patterns of DNA fragments observed correlate with proposed strain designations. Because PFGE allows the reproducible separation of restriction endonuclease-digested C. burnetii DNA fragments into precise bands, it greatly facilitates the selection of large DNA fragments for cloning. Bands harvested from the gel can be cloned. Clone banks are invaluable for identifying the location of specific genes and landmarks and providing material for future experiments, including DNA sequencing. Yeast artificial chromosome (YAC) cloning vectors can accept fragments as large as 500 kbp. The fragmentation patterns of C. burnetii that we have obtained with infrequent-cutting enzymes are small enough to be cloned into YAC vectors. Using a PFGE selection method means that only small libraries would have to be created and screened. Thus, the results of these experiments also demonstrate the applicability of PFGE for deriving a physical map of C. burnetii chromosomal DNA. Development of such a macrorestriction map will facilitate genetic and molecular studies with C. burnetii.

Strategy for detection and differentiation of Coxiella burnetii strains using the polymerase chain reaction.

A method for the rapid detection of Coxiella burnetii and differentiation between strains that cause endocarditis and those that cause acute Q fever is based on the observation that the different strains contain unique plasmid sequences. This method employs the polymerase chain reaction (PCR) and requires knowledge of specific DNA sequences in the region (target) of DNA to be amplified. To detect and differentiate between C. burnetii isolates, two sets of primers are required. The first set was derived from a fragment of plasmid QpH1 which has been detected in all C. burnetii isolates. A second PCR reaction was conducted using primers specific for DNA sequences that are shared only by QpRS plasmid-containing strains of C. burnetii. The first reaction detects the presence of C. burnetii. The second PCR is necessary to determine whether the isolate contains DNA sequences associated with strains causing chronic disease. These procedures detect as few as one to ten organisms.

DNA probes for the identification of Coxiella burnetii strains.

Isolation of Coxiella Burnetii in the standard laboratory setting is hazardous; therefore most diagnoses are based on retrospective detection of a rising antibody titer to C. burnetti. As a result, this disease is usually undiagnosed or misdiagnosed. Methods for the rapid detection of C. burnetti have now been developed that utilize specific hybridization of labeled DNA probes to nucleic acid in clinical samples. One method detects the presence of C. burnetii 16S ribosomal RNA (rRNA); another uses plasmid sequences. We have developed a probe that detects C. burnetii and one that differentiates between Coxiella strains capable of causing chronic disease and those that cause the acute form. Using these probes, C. burnetii can be identified in blood, urine, and tissue samples. The plasmid-derived probes detect as few as 10(4) organisms and less than 1 ng of Coxiella DNA. A third method differentiates between chronic (endocarditis-causing) strains and those that cause acute Q fever. This method uses the polymerase chain reaction (PCR), in which the target regions of DNA are amplified by iterative cycles of Taq I DNA polymerase chain extension to produce up to a 10(6) amplification of the target sequences. When Southern blotting is used in conjunction with PCR, the test detects as few as 2-9 C. burnetti cells.

Genomic Analysis of Phase I and II Coxiella burnetii with Restriction Endonucleases

Restriction endonuclease-digested DNAs from several isolates of phase I and phase II Coxiella burnetii were compared using agarose gel electrophoresis and soft-laser scanning densitometry. Our results demonstrate that the two phases are, as previously assumed, alternative phases of the same organism. Although the restriction endonuclease digestion revealed genetic differences between clonal isolates of phase I and phase II C. burnetii Nine Mile strain, these differences do not appear to be related to antigenic phase variation. However, analyses of the fragment patterns generated by restriction enzyme digestion suggest potential grouping of the different isolates.