Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    We will mail you new results for this query: keywords==Pathogens
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An update on radiotracer development for molecular imaging of bacterial infections
Welling, Mick M. ; Hensbergen, Albertus W. ; Bunschoten, Anton ; Velders, Aldrik H. ; Roestenberg, Meta ; Leeuwen, Fijs W.B. van - \ 2019
Clinical and Translational Imaging 7 (2019)2. - ISSN 2281-5872 - p. 105 - 124.
Infectious diseases - Molecular imaging - Nuclear medicine - Pathogens - Radiotracers

Background: Bacterial infections are still a major global healthcare problem. To combat the increasing antimicrobial resistance, early diagnosis of bacterial infections—including the identification of bacterial species—is needed to improve antibiotic stewardship and to help reduce the use of broad-spectrum antibiotics. To aid successful targeted antibiotic treatment, specific detection and localisation of infectious organisms is warranted. Nuclear medicine imaging approaches have been successfully used to diagnose bacterial infections and to differentiate between pathogen induced infections and sterile inflammatory processes. Aim: In this comprehensive review we present an overview of recent developments in radiolabelled bacterial imaging tracers. Methods: The PubMed/MEDLINE and Embase (OvidSP) literature databases were systematically searched for publications on SPECT and PET on specific imaging of bacterial using specific guidelines with MeSH-terms, truncations, and completion using cross-references. Tracers in literature that was extensively reviewed before 2016 were not included in this update. Where possible, the chemical structure of the radiolabelled compounds and clinical images were shown. Results: In 219 original articles pre-clinical and clinical imaging of bacterial infection with new tracers were included. In our view, the highest translational potential lies with tracers that are specific to target the pathogens: e.g., 99m Tc- and 68 Ga-labelled UBI 29–41 , 99m Tc-vancomycin, m-[ 18 F]-fluoro-PABA, [methyl- 11 C]-D-methionine, [ 18 F]-FDS, [ 18 F]-maltohexaose and [ 18 F]-maltotriose. An encouraging note is that some of these tracers have already been successfully evaluated in clinical settings. Conclusion: This review summarises updates in tracer development for specific (pre-clinical and clinical) imaging of bacterial infections. We propsed some promising tracers that are likely to become innovative standards in the clinical setting in the near feature.

Reprint of : Microbial food safety in the 21st century: Emerging challenges and foodborne pathogenic bacteria
Franz, Charles M.A.P. ; Besten, Heidy M.W. den; Böhnlein, Christina ; Gareis, Manfred ; Zwietering, Marcel H. ; Fusco, Vincenzina - \ 2019
Trends in Food Science and Technology 84 (2019). - ISSN 0924-2244 - p. 34 - 37.
Food safety - Microbial risk assessment - Pathogens
Exploring the unmapped DNA and RNA reads in a songbird genome
Laine, Veronika N. ; Gossmann, Toni I. ; Oers, Kees van; Visser, Marcel E. ; Groenen, Martien A.M. - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Contamination - DNA sequencing - Pathogens - RNA sequencing - Unmapped reads

Background: A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence. Results: Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma. Conclusions: Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

Cryptosporidium concentrations in rivers worldwide
Vermeulen, Lucie C. ; Hengel, Marijke van; Kroeze, Carolien ; Medema, Gertjan ; Spanier, J.E. ; Vliet, Michelle T.H. van; Hofstra, Nynke - \ 2019
Water Research 149 (2019). - ISSN 0043-1354 - p. 202 - 214.
Global - Model - Pathogens - Surface water - Transport - Water quality

Cryptosporidium is a leading cause of diarrhoea and infant mortality worldwide. A better understanding of the sources, fate and transport of Cryptosporidium via rivers is important for effective management of waterborne transmission, especially in the developing world. We present GloWPa-Crypto C1, the first global, spatially explicit model that computes Cryptosporidium concentrations in rivers, implemented on a 0.5 × 0.5° grid and monthly time step. To this end, we first modelled Cryptosporidium inputs to rivers from human faeces and animal manure. Next, we use modelled hydrology from a grid-based macroscale hydrological model (the Variable Infiltration Capacity model). Oocyst transport through the river network is modelled using a routing model, accounting for temperature- and solar radiation-dependent decay and sedimentation along the way. Monthly average oocyst concentrations are predicted to range from 10−6 to 102 oocysts L−1 in most places. Critical regions (‘hotspots’) with high concentrations include densely populated areas in India, China, Pakistan and Bangladesh, Nigeria, Algeria and South Africa, Mexico, Venezuela and some coastal areas of Brazil, several countries in Western and Eastern Europe (incl. The UK, Belgium and Macedonia), and the Middle East. Point sources (human faeces) appears to be a more dominant source of pollution than diffuse sources (mainly animal manure) in most world regions. Validation shows that GloWPa-Crypto medians are mostly within the range of observed concentrations. The model generally produces concentrations that are 1.5–2 log10 higher than the observations. This is likely predominantly due to the absence of recovery efficiency of the observations, which are therefore likely too low. Goodness of fit statistics are reasonable. Sensitivity analysis showed that the model is most sensitive to changes in input oocyst loads. GloWPa-Crypto C1 paves the way for many new opportunities at the global scale, including scenario analysis to investigate the impact of global change and management options on oocysts concentrations in rivers, and risk analysis to investigate human health risk.

Microbial food safety in the 21st century : Emerging challenges and foodborne pathogenic bacteria
Franz, Charles M.A.P. ; Besten, Heidy M.W. den; Böhnlein, Christina ; Gareis, Manfred ; Zwietering, Marcel H. ; Fusco, Vincenzina - \ 2018
Trends in Food Science and Technology 81 (2018). - ISSN 0924-2244 - p. 155 - 158.
Food safety - Microbial risk assessment - Pathogens
Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection
Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, Philippine ; Mable, Barbara K. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Arabidopsis lyrata - Balancing selection - Disease resistance - Genome scan - Mating system - Pathogens - Polymorphism - R-genes - RAD-seq

Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results: We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima's D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions: Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.

Natural Diversity in Heat Resistance of Bacteria and Bacterial Spores : Impact on Food Safety and Quality
Besten, Heidy M.W. Den; Wells-Bennik, Marjon H.J. ; Zwietering, Marcel H. - \ 2018
Annual Review of Food Science and Technology 9 (2018). - ISSN 1941-1413 - p. 383 - 410.
D-value - Pathogens - Spoilage organisms - Thermotolerance - Variability - z-value
Heat treatments are widely used in food processing often with the aim of reducing or eliminating spoilage microorganisms and pathogens in food products. The efficacy of applying heat to control microorganisms is challenged by the natural diversity of microorganisms with respect to their heat robustness. This review gives an overview of the variations in heat resistances of various species and strains, describes modeling approaches to quantify heat robustness, and addresses the relevance and impact of the natural diversity of microorganisms when assessing heat inactivation. This comparison of heat resistances of microorganisms facilitates the evaluation of which (groups of) organisms might be troublesome in a production process in which heat treatment is critical to reducing the microbial contaminants, and also allows fine-tuning of the process parameters. Various sources of microbiological variability are discussed and compared for a range of species, including spore-forming and non-spore-forming pathogens and spoilage organisms. This benchmarking of variability factors gives crucial information about the most important factors that should be included in risk assessments to realistically predict heat inactivation of bacteria and spores as part of the measures for controlling shelf life and safety of food products.
Foodborne pathogens and their risk exposure factors associated with farm vegetables in Rwanda
Ssemanda, James Noah ; Reij, Martine W. ; Middendorp, Gerrieke van; Bouw, El ; Plaats, Rozemarijn van der; Franz, Eelco ; Muvunyi, Claude Mambo ; Bagabe, Mark Cyubahiro ; Zwietering, Marcel H. ; Joosten, Han - \ 2018
Food Control 89 (2018). - ISSN 0956-7135 - p. 86 - 96.
Developing countries - Farming systems - Fresh produce - Global one health - Irrigation water - Pathogens
In this study, we tested farm vegetables and agricultural water for the presence of foodborne pathogens, and evaluated farming practices of vegetable farms in Rwanda. Farm vegetable samples were found to be contaminated with foodborne pathogens at considerably high rate (overall 15/99 = 15%). Specifically, the prevalence of pathogens in farm vegetables varied from 1.0% (1/99) for Listeria monocytogenes, 3.0% (3/99) for thermo-tolerant Campylobacter spp., 5.1% (5/99) for Salmonella spp. to 6.1% (6/99) pathogenic Escherichia coli. In agricultural water from rivers, lakes, lagoons, ground and marshlands, prevalence of DNA from pathogens varied from 3% (1/30) for Enteroinvasive E. coli (EIEC); 7% (2/30) for Enteroaggregative E. coli (EAEC); 13% (4/30) for Enterotoxigenic E. coli. (ETEC) and Vibrio cholera; 20% (6/30) for Yersinia pestis; 27% (8/30) for Francisella tularensis; 40% (12/30) for Cyclospora to 87% (26/30) for thermo-tolerant Campylobacter spp. DNA of the following pathogens was not detected (0/30) in water: entero pathogenic E. coli (EPEC), shiga toxin producing E. coli (STEC), Salmonella spp., L. monocytogenes, Burkholderia, Rickettsia, Toxoplasma gondii, Giardia lamblia, Cryptosporidium, Entamoeba histolytica and Hepatitis E. About farming practices, 60% of the visited vegetable farms practiced irrigation and all the water used was from un-protected sources (from marshlands [70%], rivers [18%], lakes [7%], runoff lagoons [5%]). Over 80% of the farms applied overhead irrigation methods and none of the farms had implemented measures to restrict the access of domestic and wild animals, while 50% of the farms used untreated manure. The reported high detection rate of foodborne pathogens DNA in agricultural water and the observed risky farming practices, provides a likely explanation of the reported prevalence of pathogens in farm vegetables and presents an important public health concern if these vegetables are to be consumed raw.
Grower perceptions of biotic and abiotic risks of potato production in South Africa
Waals, J.E. van der; Steyn, J.M. ; Franke, A.C. ; Haverkort, A.J. - \ 2016
Crop Protection 84 (2016). - ISSN 0261-2194 - p. 44 - 55.
Abiotic risks - Climate change - Grower knowledge - Pathogens - Pests - Potatoes - South Africa - Technology transfer

Growers' surveys took place in all sixteen potato growing regions of South Africa in 2013 and 2014. The agro-ecological climate of these regions is diverse and potato is produced in rainy or dry seasons, in winter or summer seasons, or year round. Growers were asked how often in ten years crops suffered more than 25% yield losses due to extreme weather events related to precipitation events such as hail, floods and droughts, and to temperature-related events such as frost and heat waves. Simultaneously they were asked their opinion about occurrence and severity of diseases caused by potato viruses, fungi and bacteria and pests such as nematodes, tuber moths, aphids and leaf miners. Weather related hazards resulted in losses over 25% virtually each year in the Gauteng growing region due to hail, frosts and floods; losses occurred less than once every five years, for example due to extremely high temperatures, in the Sandveld area where growers take a risk by producing potatoes in hot summers. Regarding the biotic factors, every pest or pathogen assessed was reported to occur on at least one farm in each growing region. Countrywide the lowest frequency of 50% was recorded for powdery scab whereas the insects tuber moths, leaf miners and aphids were reported most frequently, by between 88% and 98% of the growers. The complex of silver scurf and black dot resulted in the greatest yield losses in all growing regions, followed closely by tuber moth, early blight and the blackleg/soft rot disease complex. Yield losses due to potato virus Y, potato leaf roll virus and aphids were not reported as being very severe. When the growers' perceptions of severity of biotic factors were accumulated, significant differences between the regions appeared, with the Eastern Cape most prone with an accumulated score of 700 due to an array of pests and diseases, and the North-West with a score of only 50 mainly attributed to root knot nematodes. Growers were also asked how frequently biocides were applied to potato to control soil-borne organisms (nematicide and seed treatment), foliar fungi or insects. There were no significant correlations between frequency of biocide applications and severity of the disease as reflected in yield losses, most likely because growers use biocide applications as insurance against pests and diseases. This is common among crop farmers around the world. Although potato production in South Africa appears to carry more risks than production elsewhere, South African commercial potato growers are economically competitive when compared to growers in other areas of the globe, with comparable planting conditions and risks.

Presence of helminth eggs in domestic wastewater and its removal at low temperature UASB reactors in Peruvian highlands
Yaya-Beas, Rosa Elena ; Cadillo-La-Torre, Erika Alejandra ; Kujawa-Roeleveld, Katarzyna ; Lier, Jules B. van; Zeeman, Grietje - \ 2016
Water Research 90 (2016). - ISSN 0043-1354 - p. 286 - 293.
Helminth eggs - Municipal wastewater - Pathogens - Sludge bed filtration capacity - UASB reactor

This work studied the anaerobic sludge filtration capacity for pathogens reduction in a 29 L and 1.65 m height lab-scale UASB reactor treating domestic wastewater at low temperatures in the city of Puno (Peru). The anaerobic sludge filtration capacity was performed applying upflow velocities of 0.12, 0.14, 0.16, 0.20, 0.27 and 0.41 m/h. Results show that the HE removal varied between 89 and 95% and the most common specie was Ascaris lumbricoides. Faecal coliform and Escherichia coli removal varied in the range of 0.9-2.1 and 0.8-1.6 log10 respectively. Likely related to the low operational temperatures, the total COD removal varied between 37 and 62%. The best performance in terms of removal of HE, total COD and turbidity was obtained at the lowest upflow velocity of 0.12 m/h. In order to meet WHO standards for water reuse a post-treatment unit will be required to polish the effluent.

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