Candida species are the most common cause of opportunistic fungal infection worldwide. We report the genome sequences of six Candida species and compare these and related pathogens and nonpathogens. There are significant expansions of cell wall, secreted, and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the Mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/alpha2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine to serine genetic code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the C. albicans gene catalog, identifying many new genes.

A second high-frequency switching system was identified in selected pathogenic strains in the dimorphic yeast Candida albicans. In the characterized strain WO-1, cells switched heritably, reversibly, and at a high frequency (-10-2) between two phenotypes readily distinguishable by the size, shape, and color of colonies formed on agar at 25°C. In this system, referred to as the "white-opaque transition," cells formed either "white" hemispherical colonies, which were similar to the ones formed by standard laboratory strains of C. albicans, or "opaque" colonies, which were larger, flatter, and grey. At least three other heritable colony phenotypes were generated by WO-1 and included one irregular-wrinkle and two fuzzy colony phenotypes. The basis of the white-opaque transition appears to be a fundamental difference in cellular morphology. White cells were similar in shape, size, and budding pattern to cells of common laboratory strains. In dramatic contrast, opaque cells were bean shaped and exhibited three times the volume and twice the mass of white cells, even though these alternative phenotypes contained the same amount of DNA and a single nucleus in the log phase. In addition to differences in morphology, white and opaque cells differed in their generation time, in their sensitivity to low and high temperatures, and in their capacity to form hypae. The possible molecular mechanisms involved in high-frequency switching in the white-opaque transition are considered.Recently, we demonstrated that a common laboratory strain of the dimorphic yeast Candida albicans was capable of switching heritably, reversibly, and at a high frequency among at least seven general phenotypes distinguishable by colony morphology (17; D. R. Soll, B. Slutsky, S. Mackenzie, C. Langtimm, and M. Staebell, J. Oral Pathol., in press). In this system, cells of the parent strain switched spontaneously at a frequency of roughly io-4. A low dose of UV light, which killed less than 10% of the cell population, stimulated a 200-fold increase in this initial frequency. Whether spontaneous or UV induced, once the original strain switched, it continued to switch spontaneously and reversibly between variant colony phenotypes at a frequency of 10-2. Revertants to the original colony phenotype which exhibited a decrease in switching frequency from 10-2 to i0' were also obtained (17; Soll et al., in press).In examining the switching capabilities of strains of C. albicans isolated from patients with systemic infections, we have discovered a second switching system, which we will refer to as the "white-opaque transition." In this system, cells switch heritably, at a high frequency, and reversibly between two phenotypes which generate alternative colony morphologies distinguishable by colony size, shape, and color. In the "white" phenotype, cells form colonies which are white and hemispherical. In the "opaque" phenotype, cells form colonies which are larger, flatter, and opaque, or grey. The differences in colony shape and tone appear to be the result of a...

In this study we established the usefulness of DNA fingerprinting for the epidemiology of tuberculosis on the basis of the DNA polymorphism generated by the insertion sequence (IS) IS986. Although clinical isolates of Mycobacterium tuberculosis displayed a remarkably high degree of restriction fragment length polymorphism, we showed that transposition of this IS element is an extremely rare event in M. tuberculosis complex strains grown either in vitro or in vivo for long periods of time. The M. tuberculosis and Mycobacterium africanum strains tested in this study contained 6 to 17 IS copies. In the Mycobacterium bovis strains, the copy numbers ranged between 1 and 5, and all 27 M. bovis BCG strains investigated invariably contained a single IS copy. This copy was located at a unique chromosomal position, reinforcing the idea that the frequency of IS transposition is very low in M. tuberculosis complex strains. Various microepidemics are described in which each microepidemic corresponds to a particular fingerprint type. The extent of similarity between Dutch and African strains was quantitatively assessed by computer-assisted analysis of DNA fingerprints. The results indicate that M. tuberculosis strains from regions in central Africa, where tuberculosis is highly prevalent, are generally more related to each other than isolates from the Netherlands, where the transmission rate is low and where the majority of the tuberculosis cases are presumed to be the result of reactivation of previously contracted M. tuberculosis infections. MATERIALS AND METHODS Bacterial strains and plasmids. In this study, 222 M. tuberculosis strains, 5 Mycobacterium africanum strains, 24 M. bovis strains, and 27 M. bovis BCG strains were inves-2578 on September 28, 2020 by guest http://jcm.asm.org/ Downloaded from USE OF IS ELEMENTS IN TUBERCULOSIS EPIDEMIOLOGY 2579 TABLE 1. Bacterial strains used in this study Bacterial strain no. Species Origin Source or reference 5, 14, 15, 97, 164, 265, 266, 319-323 M. tuberculosis The Netherlands This laboratory 272-285 M. tuberculosis Czechoslovakia J. Ivanyib 34, 165, 302-316 M. tuberculosis The Netherlands P. G. H. Peerboomsc 324-333 M. tuberculosis Ruwanda F. Portaelsd 334-335 M. tuberculosis Central African Republic F. Portaelsd 336-343 M. tuberculosis Burundi F. Portaelsd 317-318 M. tuberculosis Belgium F. Portaelsd 116-126, 286-292 M. tuberculosis The Netherlands P. L. van Puttene 267-271, 108, 109, 111, 114 M. tuberculosis The Netherlands J. Steensmaf 295-301, 168-171 M. bovis The Netherlands This laboratory 149-152, 293, 294, 45, 106 M. bovis BCG5 The Netherlands This laboratory 44, 104 M. bovis BCG5 The Netherlands This laboratory 102 M. bovis BCG9 Organon Teknikah 103 M. bovis BCG5 Armand Frappier' a Strains used only for standard RFLP typing are not mentioned in this table.

Most strains of Candida albicans are capable of switching frequently and reversibly between a number of phenotypes distinguishable by colony morphology. A number of different switching systems have been defined according to the limited set of phenotypes in each switching repertoire, and each strain appears to possess a single system. Switching can affect many aspects of cellular physiology and morphology and appears to be a second level of phenotypic variability superimposed upon the bud-hypha transition. The most dramatic switching system so far identified is the "white-opaque transition." This system dramatizes the extraordinary effects switching can have on the budding cell phenotype, including the synthesis of opaque-specific antigens, the expression of white-specific and opaque-specific genes, and the genesis of unique cell wall structures. Switching has been demonstrated to occur at sites of infection and between episodes of recurrent vaginitis, and it may function to generate variability in commensal and infecting populations for adaptive reasons. Although the molecular mechanisms involved in the switch event are not understood, recent approaches to its elucidation are discussed and an epigenetic mechanism is proposed.

Upon homozygosis from a/a to a/a or a/a, Candida albicans must still switch from the 'white' to 'opaque' phenotype to mate. It was, therefore, surprising to discover that pheromone selectively upregulated mating-associated genes in mating-incompetent white cells without causing G1 arrest or shmoo formation. White cells, like opaque cells, possess pheromone receptors, although their distribution and redistribution upon pheromone treatment differ between the two cell types. In speculating about the possible role of the white cell pheromone response, it is hypothesized that in overlapping white a/a and a/a populations in nature, rare opaque cells, through the release of pheromone, signal majority white cells of opposite mating type to form a biofilm that facilitates mating. In support of this hypothesis, it is demonstrated that pheromone induces cohesiveness between white cells, minority opaque cells increase two-fold the thickness of majority white cell biofilms, and majority white cell biofilms facilitate minority opaque cell chemotropism. These results reveal a novel form of communication between switch phenotypes, analogous to the inductive events during embryogenesis in higher eukaryotes.