The phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16s ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthornonas theicoh, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16s rDNA sequences within the genusxanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.The phytopathogenic specialization and the broad host range of members of the genus Xanthomonas (30) have made these microorganisms the subject of numerous taxonomic studies (for a review, see reference 59). Traditional methods used for the detection and identification of xanthomonads, such as biochemical (55), serological, and pathogenicity tests (3, 4, 5, 31, 45, 48), have been extended by molecular methods based on protein profiling (57, 60) and fatty acid analysis (7, 63).Currently, molecular approaches are being used increasingly in studies of the taxonomy and epidemiology of Xanthomonas species (15, 19). This has led to the development of different probes for detection and identification by hybridization or by PCR amplification (17, 18, 20, 21, 24, 25, 27, 32,40) and to analyses of the genetic structures of field populations (1,4,26, 28, 29).A polyphasic approach, such as the approach described by Vandamme et al. (54), could utilize all of these methods to contribute to the classification of the genus Xanthomonas. In practice, however, DNA reassociation, which provides a measure of the overall similarity of chromosomal genomes, is generally used for species delineation. This strategy has been used by Vauterin et al. (58), who recently reclassified the genus Xanthomonas and recognized and described 20 genomic species.Ideally, a comparison of the complete nucleotide sequences of genomes would probably be the most informative technique and thus the best method for determining the overall taxonomic relatedness of bacterial taxa. As sequencing entire genomes on a routine basis for taxonomy purposes is still impractical, techniques such as the sequencing of "molecular chronometers" like rRNA genes have been developed during the las...
The clinical and environmental importance of Stenotrophomonas bacteria requires thorough, molecular studies on their epidemiology and taxonomy. In order to obtain a complete genomic profile of this genus, over I00 Stenotrophomonas maltophilia strains from various origins were investigated by AFLP fingerprinting. A subset of these strains was analysed by DNA hybridization and 16s rDNA sequencing. In contrast to their high phenotypic homogeneity, the strains were found to be very heterogeneous genotypically by AFLP fingerprinting. Nevertheless, ten cores of highly similar strains representing ten genomic groups were observed. The same groups could be retrieved by DNA hybridizations and also, partly, by 16s rDNA sequence analysis. The intergroup DNA similarities were too high to create confident species delineations, neither could the genomic groups be characterized by phenotypic features.1 Keywords: Stenotrophomonas maltophilia, genomic groups, AFLP fingerprinting 1 INTRODUCTIONStenotrophomonas maltophilia (Palleroni & Bradbury, 1993), formerly named Pseudomonas maltophilia (Hugh, 198 1) and Xanthomonas maltophilia (Swings et al., 1983), is a commonly found ubiquitous bacterium. It is increasingly prevalent in hospitals as an opportunistic human pathogen causing nosocomial infections. The numerous recent literature reports, dealing with S. maltophilia infections and outbreaks, emphasize the importance of this rapidly emerging clinical pathogen. S . maltophilia is a causal agent of infection and colonization of immunocompromised cancer and HIV patients and transplant recipients (Nagai, 1984; Roilides et al., 1992;Spencer, 1995) and has been reported as a cause of bacteraemia and infections of the respiratory tracts (Fisher et al., 1981) and urinary tracts (Vartivarian et al., 1996), post-operative infections (Fisher et al., 198 l), ocular infections (Penland & Wilhelmus, 1996) and a variety of other disease syndromes . The low outer membrane permeability and the ability to produce plactamases with broad-spectrum activity are responsible for the high degree of resistance towards most commonly used broad-spectrum antibiotics such as penicillins and carbapenems (Mett et al., 1988 ; LescoBornet & Bergogne-Berezin, 1997 ;Norrby, 1995 ;Sanders & Sanders, 1992). Retrospective studies have shown that S. maltophilia is the second most frequently isolated nosocomial bacterium after Pseudomonas aeruginosa (Zuravleff & Yu, 1982) and that its impact as a multidrug-resistant pathogen increases significantly (Heath & Currie, 1995;Suzuki et al., 1995). The growing clinical importance of S . maltophilia infections has recently been reviewed by Denton & Kerr (1 998). In the environment, S . maltophilia has been isolated as a growth promoting or symbiotic agent from the rhizosphere of plants and crops including chicory, wheat and crucifers (Debette & Blondeau, 1980;Juhnke et al., 1987) Yao et al., 1995) and PFGE (Yao et al., 1995), only a few strains from the same intensive care unit showed identical genomic profiles, thus sugge...
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