The genome of Bartonella bacilliformis was shown to be a single circular DNA molecule of about 1,600 kbp having six NotI, four SfiI, and two CeuI sites. A physical map of the DNA was constructed by contour-clamped homogeneous electric field pulsed-field gel electrophoresis of DNA restriction fragments. rRNA operons, the invasion-associated locus, and a flagellin gene were located on the map by hybridization.Bartonella bacilliformis is a flagellated, highly motile, hemotrophic, gram-negative bacterium (6, 13) which is transmitted to humans by sand fly bites (4,6,7,13). It is the causative agent of Carrión's disease, an endemic disease in certain areas of Columbia, Ecuador, Peru, Bolivia, and Chile (4). To facilitate study of this interesting bacterium, we have constructed an initial physical map of its DNA by pulsed-field gel electrophoresis (PFGE) of NotI, SfiI, and CeuI restriction fragments.Number and sizes of restriction fragments. B. bacilliformis, grown to 1 ϫ 10 8 to 2 ϫ 10 8 bacteria per ml as previously described (9), was washed with phosphate-buffered saline (PBS), resuspended in 1 ml of PBS, mixed with 1 ml of molten 2% pulsed-field agarose (Bio-Rad Laboratories, Richmond, Calif.), and poured into a commercial plastic mold (Bio-Rad, Richmond, Calif.) designed to form thin agarose slabs. The bacteria were lysed within the agarose slabs by soaking the slabs in 1% sodium dodecyl sulfate-proteinase K (1 mg/ml)-TBE (89 mM Tris, 89 mM boric acid, 2 mM EDTA [pH 8.0]) for 48 h at 37ЊC, rinsing them with 10 changes of TBE, soaking them in 100% ice-cold acetone for 20 min, and rinsing them with 5 changes of TBE. The processed slabs were stored in 0.5 M EDTA at 4ЊC. Digestions were performed on small agarose plugs (9 by 1 by 1 mm) cut from the slabs. The plugs were washed and placed into microcentrifuge tubes. Restriction endonuclease digestions were performed under conditions recommended by New England Biolabs (Beverly, Mass.). After electrophoresis, the DNA was initially visualized with ethidium bromide. In later experiments, 32 P labeling of DNA within the agarose slabs was accomplished by including dATP, dTTP, dGTP (25 nM each), [ 32 P]dCTP (25 Ci/ml), and Taq polymerase (12.5 U/ml) in the restriction digestion reaction mixtures; unincorporated radioactive material was removed by washing before electrophoresis. After electrophoresis, the DNA was stained with ethidium bromide, photographed, nicked, vacuum transferred to a nylon membrane, and autoradiographed.Digestion with SfiI produced four DNA fragments, S1 to S4 (Fig. 1A, lane 3), with sizes of 753, 602, 247, and Ͻ50 kbp, respectively, measured by PFGE with a CHEF-DRII or -DRIII apparatus (Bio-Rad, Hercules, Calif.). By standard gel electrophoresis, the size of the fourth band was shown to be 15 kbp. NotI digestion produced six fragments, N1 to N6 (Fig. 1B, lane 3), with sizes of 544, 444, 354, 116, 109, and 50 kbp, respectively, by PFGE. The sums of the fragment sizes were 1,617 kbp for both SfiI and NotI digestions; this exact agreement, while convenien...