Pneumokokkinfektsioon lapseeas

Streptococcus pneumoniae (pneumokokk) on üks olulisemaid bakteriaalse respiratoorse ja invasiivse infektsiooni tekitajaid lapseeas. Viimase kahekümne aasta jooksul kujunenud pneumokoki antibiootikumresistentsuse üheks peamiseks riskiteguriks peetakse liigset antibiootikumide tarvitamist. Ülevaateartiklis on käsitletud pneumokoki antibiootikumresistentsuse tekkemehhanisme ja levikut maailmas, samuti selle kliinilist tähendust ning tutvustatud ka antibakteriaalse ravi taktikat ja uusi profülaktikavõimalusi pneumokokkinfektsiooni korral. Eesti Arst 2003; 82 (2): 464–47

Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Towards a unified paradigm for sequence-based identification of fungi

Kõljalg, Urmas et al.The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.The North European Forest Mycologists network is acknowledged for support. Urmas Kõljalg and Kessy Abarenkov are supported by the Estonian Research Council grant no 8235.Peer reviewe

TÜ Kliinikumi ühendlaboris isoleeritud anaeroobide spekter ja ravimitundlikkus

2001.–2006. a analüüsiti TÜ Kliinikumi ühendlaboris kliinilistest materjalidest isoleeritud anaeroobide rühmi ja antibiootikumitundlikkust ning võrreldi neid parodontiidi patogeenide sarnaste andmetega. Kliinilistest materjalidest isoleeritud anaeroobsetest parodontiidi patogeenidest olid sagedasemad prevotellad ja fusobakterid. Anaeroobide antibiootikumitundlikkus oli suhteliselt kõrge. Metronidasool toimis hästi gramnegatiivsetesse pulkbakteritesse, kuid grampositiivsed kokid olid resistentsemad. Klindamütsiin ja ampitsilliin/sulbaktaam olid tõhusad kõikide anaeroobirühmade suhtes. Beetalaktamaasi produtseerivate mikroobide osakaal oli 7–54%. Sagedasemad beetalaktamaasi suhtes positiivsed mikroobid olid Porphyromonas spp. ja Prevotella spp. Parodontiidi anaeroobsed patogeenid osutusid kliinilistest isolaatidest antibiootikumitundlikumateks. Eesti Arst 2008; 87(11):834−84

The next generation fungal diversity researcher

Fungi are more important to our lives than is assumed by the general public. They can comprise both devastating pathogens and plant-associated mutualists in nature, and several species have also become important workhorses of biotechnology. Fungal diversity research has in a short time transcended from a low-tech research area to a method-intensive high-tech discipline. With the advent of the new genomic and post-genomic methodologies, large quantities of new fungal data are currently becoming available each year. Whilst these new data and methodologies may help modern fungal diversity researchers to explore and discover the yet hidden diversity within a context of biological processes and organismal diversity, they need to be reconciled with the traditional approaches. Such a synthesis is actually difficult to accomplish given the current discouraging situation of fungal biology education, especially in the areas of biodiversity and taxonomic research. The number of fungal diversity researchers and taxonomists in academic institutions is decreasing, as are opportunities for mycological education in international curricula. How can we educate and stimulate students to pursue a career in fungal diversity research and taxonomy and avoid the situation whereby only those few institutions with strong financial support are able to conduct excellent research? Our short answer is that we need a combination of increased specialization and increased collaboration, i.e. that scientists with specialized expertise (e.g., in data generation, compilation, interpretation, and communication) consistently work together to generate and deliver new fungal knowledge in a more integrative manner – closing the gap between both traditional and modern approaches and academic and non-academic environments. Here we discuss how this perspective could be implemented in the training of the ‘next generation fungal diversity researcher’

How to know unknown fungi: the role of a herbarium.

Published versio

Chitin mixed in potting soil alters lettuce growth, the survival of zoonotic bacteria on the leaves and associated rhizosphere microbiology

Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia colt O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves

Merging the genus Tomentella with Thelephora (Fungi, Thelephorales)

In this article we merge the genus Tomentella with Thelephora. As a result, 191 new combinations are made and 24 nomina nova are created. In addition, one new combination of Tomentellopsis and Polyozellus species are made, respectively