The group of bacteria is an important group including mammalian and

The group of bacteria is an important group including mammalian and insect pathogens, such as group, accessible at http://mlstoslo. types (1,2). MLST is usually thus a method that is unambiguous and truly portable among laboratories. Since the initial development of this technique for in 1998, MLST schemes have been developed for about 30 species including some of the most important bacterial pathogens, e.g. and the group (see (1) for a recent review). These MLST schemes have been used successfully to explore the population structure of bacteria, to study the evolution of their virulence properties, to identify antibiotic-resistant strains and epidemic clones, and for epidemiological surveillance. The group includes bacterial species that are of medical and/or economic importance, such as group, based on different sets of genes and isolates (5C10). The Priest scheme (8) is currently the most widely used. Studies with the various schemes have independently indicated that this group population is usually divided into three main phylogenetic clusters and that species are usually intermixed within the groups. One cluster contains the monomorphic 875446-37-0 manufacture isolates and a number of and strains, many of which are from clinical sources. A second heterogeneous cluster includes and isolates from various origins, while cold-tolerant and isolates belong to the third group. The individual MLST analyses have also revealed that this group population is usually weakly clonal overall due to numerous clinical and virulent isolates emerging from different phylogenetic positions (5C8,11C14), with the Rabbit polyclonal to ZNF544 exception of the cold-tolerant cluster that seems to exhibit a panmictic (or sexual) population structure, i.e. with frequent genetic exchanges between strains (9). Despite the overall congruence between the various MLST studies, the use of individual schemes with no gene overlap and very little strain overlap has produced a confusing situation and makes the results difficult to compare directly. Therefore, we recently proposed a combined scheme based on genes taken from three of the four schemes available by then and for which we created a web-based database accessible at the University of Oslo’s MLST server, http://mlstoslo.uio.no/ (5). Here, in order to provide the group research community with a common MLST resource, we have developed on the same website a database, SuperCAT, that compiles and integrates MLST data from all the published group schemes. In addition, we applied supertree reconstruction methods to build an integrated view of the group population and phylogeny. Below we describe the content and main features of the new database as well as the process of supertree building. 875446-37-0 manufacture DATABASE CONTENT AND IMPLEMENTATION The SuperCAT database provides information, sequence and phylogenetic data for all those bacterial isolates that have been typed using any of the five published MLST schemes for the group (Table 1). 875446-37-0 manufacture Strain information, when known, includes isolate description, source and geographical location of isolation, and the scheme(s) used for typing. The sequence data include the nucleotide sequences of the MLST loci examined in 875446-37-0 manufacture a given strain. SuperCAT also contains the phylogenetic supertree of the group reconstructed by combining the sequence data from all five schemes, as well as supertrees built 875446-37-0 manufacture for individual schemes. Information and sequences for isolates typed by the Priest and TourasseCHelgason schemes were retrieved from the databases devoted to these schemes at http://pubmlst.org/bcereus and http://mlstoslo.uio.no/, respectively. MLST data for additional strains not available in the pubmlst.org repository (strains from (15) are missing therein) and for the Helgason, Ko, and CandelonCSorokin schemes were taken from the published literature and the.

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