Genomic surveillance of selected infectious diseases in the Czech Republic
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PROVIDER: PRJEB62484 | ENA |
REPOSITORIES: ENA
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Project description:IntroductionThe study presents the results of the genomic surveillance of invasive meningococcal disease (IMD) in the Czech Republic for the period of 2015-2017.Material and methodsThe study set includes all available IMD isolates recovered in the Czech Republic and referred to the National Reference Laboratory for Meningococcal Infections in 2015-2017, a total of 89 Neissseria meningitidis isolates-from 2015 (n = 20), 2016 (n = 27), and from 2017 (n = 42). All isolates were studied by whole genome sequencing (WGS).ResultsSerogroup B (MenB) was the most common, followed by serogroups C, W, and Y. Altogether 17 clonal complexes were identified, the most common of which was hypervirulent complex cc11, followed by complexes cc32, cc41/44, cc269, and cc865. Over the three study years, hypervirulent cc11 (MenC) showed an upward trend. The WGS method showed two clearly differentiated clusters of N. meningitidis C: P1.5,2:F3-3:ST-11 (cc11). The first cluster is represented by nine isolates, all of which are from 2017. The second cluster consisted of five isolates from 2016 and eight isolates from 2017. Their genetic discordance is illustrated by the changing nadA allele and subsequently by the variance in BAST type. Clonal complex cc269 (MenB) also increased over the time frame. WGS identified the presence of MenB vaccine antigen genes in all B and non-B isolates of N. meningitidis. Altogether 49 different Bexsero antigen sequence types (BAST) were identified and 10 combinations of these have not been previously described in the PubMLST database.ConclusionsThe genomic surveillance of IMD in the Czech Republic provides data needed to update immunisation guidelines for this disease. WGS showed a higher discrimination power and provided more accurate data on molecular characteristics and genetic relationships among invasive N. meningitidis isolates.
| S-EPMC6622526 | biostudies-literature
Project description:The REVEALS model is a tool for recalculating pollen data into vegetation abundances on a regional scale. We explored the general effect of selected parameters by performing simulations and ascertained the best model setting for the Czech Republic using the shallowest samples from 120 fossil sites and data on actual regional vegetation (60 km radius). Vegetation proportions of 17 taxa were obtained by combining the CORINE Land Cover map with forest inventories, agricultural statistics and habitat mapping data. Our simulation shows that changing the site radius for all taxa substantially affects REVEALS estimates of taxa with heavy or light pollen grains. Decreasing the site radius has a similar effect as increasing the wind speed parameter. However, adjusting the site radius to 1 m for local taxa only (even taxa with light pollen) yields lower, more correct estimates despite their high pollen signal. Increasing the background radius does not affect the estimates significantly. Our comparison of estimates with actual vegetation in seven regions shows that the most accurate relative pollen productivity estimates (PPEs) come from Central Europe and Southern Sweden. The initial simulation and pollen data yielded unrealistic estimates for Abies under the default setting of the wind speed parameter (3 m/s). We therefore propose the setting of 4 m/s, which corresponds to the spring average in most regions of the Czech Republic studied. Ad hoc adjustment of PPEs with this setting improves the match 3-4-fold. We consider these values (apart from four exceptions) to be appropriate, because they are within the ranges of standard errors, so they are related to original PPEs. Setting a 1 m radius for local taxa (Alnus, Salix, Poaceae) significantly improves the match between estimates and actual vegetation. However, further adjustments to PPEs exceed the ranges of original values, so their relevance is uncertain.
| S-EPMC4061133 | biostudies-literature
Project description:Emerging infectious diseases, such as COVID-19, continue to pose significant threats to human beings and their surroundings. In addition, biological warfare, bioterrorism, biological accidents, and harmful consequences arising from dual-use biotechnology also pose a challenge for global biosecurity. Improving the early surveillance capabilities is necessary for building a common biosecurity shield for the global community of health for all. Furthermore, surveillance could provide early warning and situational awareness of biosecurity risks. However, current surveillance systems face enormous challenges, including technical shortages, fragmented management, and limited international cooperation. Detecting emerging biological risks caused by unknown or novel pathogens is of particular concern. Surveillance systems must be enhanced to effectively mitigate biosecurity risks. Thus, a global strategy of meaningful cooperation based on efficient integration of surveillance at all levels, including interdisciplinary integration of techniques and interdepartmental integration for effective management, is urgently needed. In this paper, we review the biosecurity risks by analyzing potential factors at all levels globally. In addition to describing biosecurity risks and their impact on global security, we also focus on analyzing the challenges to traditional surveillance and propose suggestions on how to integrate current technologies and resources to conduct effective global surveillance.
| S-EPMC8918423 | biostudies-literature
Project description:Czech Republic human listeriosis
| PRJEB37840 | ENA
Project description:The Korea Centers for Disease Control and Prevention (KCDC) operate infectious disease surveillance systems to monitor national disease incidence. Since 1954, Korea has collected data on various infectious diseases in accordance with the Infectious Disease Control and Prevention Act. All physicians (including those working in Oriental medicine) who diagnose a patient with an infectious disease or conduct a postmortem examination of an infectious disease case are obliged to report the disease to the system. These reported data are incorporated into the database of the National Infectious Disease Surveillance System, which has been providing web-based real-time surveillance data on infectious diseases since 2001. In addition, the KCDC analyzes reported data and publishes the Infectious Disease Surveillance Yearbook annually.
| S-EPMC4272235 | biostudies-literature
Project description:Emerging infectious diseases present a complex challenge to public health officials and governments; these challenges have been compounded by rapidly shifting patterns of human behaviour and globalisation. The increase in emerging infectious diseases has led to calls for new technologies and approaches for detection, tracking, reporting, and response. Internet-based surveillance systems offer a novel and developing means of monitoring conditions of public health concern, including emerging infectious diseases. We review studies that have exploited internet use and search trends to monitor two such diseases: influenza and dengue. Internet-based surveillance systems have good congruence with traditional surveillance approaches. Additionally, internet-based approaches are logistically and economically appealing. However, they do not have the capacity to replace traditional surveillance systems; they should not be viewed as an alternative, but rather an extension. Future research should focus on using data generated through internet-based surveillance and response systems to bolster the capacity of traditional surveillance systems for emerging infectious diseases.
| S-EPMC7185571 | biostudies-literature
Project description:BackgroundInfectious diseases remain a major public health problem worldwide. Hence, their surveillance is critical. Currently, many surveillance strategies and systems are in use around the world. An inventory of the data, surveillance strategies, and surveillance systems developed worldwide for the surveillance of infectious diseases is presented herein, with emphasis on the role of the microbiology laboratory in surveillance.MethodsThe data, strategies, and systems used around the world for the surveillance of infectious diseases and pathogens, along with current issues and trends, were reviewed.ResultsTwelve major classes of data were identified on the basis of their timing relative to infection, resources available, and type of surveillance. Two primary strategies were compared: disease-specific surveillance and syndromic surveillance. Finally, 262 systems implemented worldwide for the surveillance of infections were registered and briefly described, with a focus on those based on microbiological data from laboratories.ConclusionsThere is currently a wealth of available data on infections, which has been growing with the recent emergence of new technologies. Concurrently with the expansion of computer resources and networks, these data will allow the optimization of real-time detection and notification of infections.
| S-EPMC7110877 | biostudies-literature
Project description:Routine surveillance of STEC at the Belgian NRC STEC
| PRJEB54005 | ENA
Project description:We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of ccRCC.
2013-06-03 | GSE40435 | GEO