Resolving taxonomic confusion : establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae

Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family

Molecular regulation of epithelial tube size

In nature, epithelial tubes are vital structures in organ design and are required for transport of gases and liquids in organs, such as the vascular system, the vertebrate lung and the kidneys. The tubular epithelium is single layered, but is often reinforced by layers of muscular support. It constitutes an apical side facing the lumen and a basal side that contacts surrounding tissues. To ensure optimal flow, it is critical that the tubes are correctly sized and shaped. Epithelial tube growth depends on apical membrane enlargements, as well as sub-apical rearrangements, but the mechanisms involved in the regulation of size and shape of epithelial tubes are yet to be revealed. In this thesis the Drosophila respiratory (tracheal) system has been used as a model organ to identify essential genes and clarify the mechanisms involved in the making and shaping of tubes. Through genetic and molecular analyses, new biological concepts have been uncovered. The main tracheal tube, the dorsal trunk (DT), expands three-fold in diameter during a short interval followed by tube elongation. In this thesis we have dissected the roles of five genes in tube regulation, called kkv, knk rtv, dBest2 and DAAM. Analysis of kkv, knk and rtv led us to identify an unprecedented need for luminal matrix components in modeling tube shape. A chitinous luminal matrix is deposited in newly formed tubes and constitutes an expanding cord inside the tube that is required for uniform tube diameter growth. kkv is required for chitin synthesis while knk and rtv are needed for chitin filament assembly. If chitin is missing or fail to form an organized matrix, the expanding tubes develop severe local dilations and constrictions. The subsequent tube elongation requires dBest2 and DAAM. dBest2 encodes an apical chloride channel and is essential for lumen growth during elongation, suggesting that elongation is driven by an increased luminal osmotic pressure. DAAM has a function in actin organization. In the wild type trachea, actin filaments arrange as sub-apical rings perpendicular to tube length, thus allowing for lumen elongation, but not diametrical expansion, upon the increase in lumen pressure. In DAAM mutants, the actin rings are disorganized, thus lumen elongation is inhibited. The luminal chitin matrix has a second role at this stage by preventing excess tube elongation. A balance between combinatorial physical forces exerted by the lumen and sub-apical actin cytoskeleton determines final tube size

Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences

Raw Kymographs - Optical DNA Mapping

Supporting data for publication "The Resistomes of Six Carbapenem-Resistant Pathogens – A Critical Genotype-Phenotype Analysis."<br><br>Data provided as raw Kymographs (TIFF) from Optical DNA mapping experiments. File name indicates plasmid followed by molecule number within ().<strong><br></strong><strong></strong