Towards Uniform Gene Bank Documentation In Europe – The Experience From The EFABISnet Project

In the EFABISnet project, a collaborative effort of EAAP, FAO and partners from 14 European countries, in cooperation with the European Regional Focal Point for Animal Genetic Resources (ERFP), national information systems for monitoring the animal genetic resources on breed level were established in Austria, Cyprus, Estonia, Georgia, Iceland, Ireland, Italy, Netherlands, Slovakia, Slovenia, Switzerland, and United Kingdom. The network was soon extended beyond the project plans, with the establishment of EFABIS databases in Finland, Greece, and Hungary. The network was then complemented by a set of inventories of national gene bank collections to strengthen the documentation of ex situ conservation programmes. These documentation systems were established by the National Focal Points for management of farm animal genetic resources. Here we present the experience gained in establishment of these national inventories of gene banks and their relevance to the Strategic Priority Areas of the Global Plan of Action which could be useful for other areas in the world

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.ISSN:2057-585

<i>Pseudomonas aeruginosa</i> intensive care unit outbreak:winnowing of transmissions with molecular and genomic typing

Bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 097831/Z/11/Z]. BJP, KO, MP, MTGH, GP and SHG are funded by the Chief Scientist Office through the Scottish Infection Research Network, a part of the SHAIPI consortium grant reference number SIRN/10.Background: Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical to base decisions on. Aim: We explore the usefulness of whole genome sequencing (WGS) in the investigation of a Pseudomonas aeruginosa outbreak describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. Methods: Six patient isolates and six environmental samples from an Intensive Care Unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS. Findings:  VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates giving greater assurance of the transmission route between wash hand basin (WHB) water and two patients supporting control measures employed. Conclusion:  WGS provided detailed information without need for further typing. When allied to epidemiological information it can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and reduction in costs.Publisher PDFPeer reviewe

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Publication history: Accepted - 29 March 2023; Published - 25 May 2023.Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.This work was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland (DAERA-NI) through its Evidence and Innovation programme – project no. 15/3/07. Additional funding was provided by the UK’s Biotechnology and Biological Sciences Research Council (BBSRC) – grant numbers BB/P0105598 and BB/M01262X. A. A. is supported by a Bolashak International Scholarship

Iodine Atoms: A New Molecular Feature for the Design of Potent Transthyretin Fibrillogenesis Inhibitors

The thyroid hormone and retinol transporter protein known as transthyretin (TTR) is in the origin of one of the 20 or so known amyloid diseases. TTR self assembles as a homotetramer leaving a central hydrophobic channel with two symmetrical binding sites. The aggregation pathway of TTR into amiloid fibrils is not yet well characterized but in vitro binding of thyroid hormones and other small organic molecules to TTR binding channel results in tetramer stabilization which prevents amyloid formation in an extent which is proportional to the binding constant. Up to now, TTR aggregation inhibitors have been designed looking at various structural features of this binding channel others than its ability to host iodine atoms. In the present work, greatly improved inhibitors have been designed and tested by taking into account that thyroid hormones are unique in human biochemistry owing to the presence of multiple iodine atoms in their molecules which are probed to interact with specific halogen binding domains sitting at the TTR binding channel. The new TTR fibrillogenesis inhibitors are based on the diflunisal core structure because diflunisal is a registered salicylate drug with NSAID activity now undergoing clinical trials for TTR amyloid diseases. Biochemical and biophysical evidence confirms that iodine atoms can be an important design feature in the search for candidate drugs for TTR related amyloidosis

SOURCES OF POLLUTION AS A HAZARD FOR RIVER ENVIRONMENT IN CASE OF FLOOD

In the case of flood the main damages on the environment may occur as a consequence of accidents at sources of pollution. The issue of pollution sources is a key area of environmental protection. While pollution from point sources can be disposed by suitable technology, for diffuse pollution are essential proposals of preventive measures, that creating conditions to prevent contamination. The paper presents results of evaluation the sources of pollution in Hornad river basin in the eastern Slovakia in flooded area. Environmental risk assessment methods can be particularly useful in evaluating whether uses are threatened when a stressor of concern is not expressed as a numeric criterion in water quality standards. The risk assessment framework can add value to watershed-based management

Genomic investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen

Funding: The Wellcome Trust [grants 098051 and 097831/Z/11/B (to J. M. B., S. R. H., H. M. B. S.-S., N. R. T.)], The Medical Research Council (grant number G1000413 [to J. M. B.]), The Special Trustees of the Royal Free London, National Health Service Foundation Trust (S. H. G., T. Mc. H., C. L.), and The University of St Andrews Medical School (S. H. G., K. O.).Background. Mycoplasma amphoriforme has been associated with infection in patients with Primary Antibody Deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community. Methods. The bacterial load was estimated in sequential sputum samples from nine patients by qPCR. The genomes of all available isolates, originating from patients in the UK, France and Tunisia, were sequenced along with the type strain. Genomic data was assembled, annotated and a high-resolution phylogenetic tree constructed. Results. By using high-resolution whole genome sequence data we show that patients can be chronically infected with M. amphoriforme manifesting as a relapsing remitting bacterial load interspersed by periods when the organism is undetectable. Importantly we demonstrate transmission of strains within a clinical environment. Antibiotic resistance mutations accumulate in isolates taken from patients who received multiple courses of antibiotics. Conclusions. Mycoplasma amphoriforme isolates form a closely related species responsible for a chronic relapsing and remitting infection in PAD patients in the UK and from immunocompetent patients in other countries. We provide strong evidence of transmission between patients attending the same clinic suggesting that screening and isolation may be necessary for susceptible patients. This work demonstrates the critical role that whole genome sequencing can play in unravelling the biology of a novel pathogen rapidly.Publisher PDFPeer reviewe

Characterization of glycoprotein C of HSZP strain of herpes simplex virus 1

Sequences of UL44 genes of strains HSZP, KOS and 17 of herpes simplex virus 1 (HSV-1) were determined and the amino acid sequences of corresponding glycoproteins (gC) were deduced. In comparison with the 17 strain, the HSZP strain showed specific changes in 3 nucleotides and in 2 amino acids (aa 139 and 147, both from Arg to Trp) in the antigenic locus LII. The change at aa 147 was situated within the GAG-binding epitope. In a similar comparison, KOS strain had changes in 3 nucleotides and 3 amino acids (aa 3, 14, and 300). The UL44 genes of HSZP and KOS strains were expressed in insect Sf-21 cells by means of the baculovirus (Bac-to-Bac(TM)) expression system. As shown by immunoblot analysis, both the recombinant baculoviruses (B1-HSZP and B6-KOS) expressed a glycosylated gC, the M-r of which (116 K) was lower than that of gC synthesized in Vero cells (129 K) infected with strains HSZP or KOS. In addition, smaller gC-specific proteins (of apparent M-r of 50-58 K and 98 K) corresponding to a non-glycosylated precursor polypeptide and/or incomplete forms of the partially glycosylated gC were found. When Balb/c mice were immunized with Sf-21 cells expressing gC, the recombinant gC-HSZP represented a more efficient immunogen possibly due to its stronger expression in these cells. The corresponding gC-HSZP antiserum reacted in enzyme-linked immunosorbent assay (ELISA) equally well with HSZP and KOS virion antigens and neutralized HSZP strain at a low titer. Both gC-HSZP and gC-KOS antisera detected the homologous as well as the heterologous gC antigens in Vero cells regardless whether infected with strains HSZP, KOS or 17, revealing the presence of gC from 6 to 16 hrs post infection (p.i.) in the cytoplasm, on the nuclear membrane and at the cell surface