OBJECTIVES: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. METHODS: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. RESULTS: mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. CONCLUSIONS: Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.
- MeSH
- antibakteriální látky * farmakologie MeSH
- azithromycin * farmakologie MeSH
- bakteriální geny MeSH
- bakteriální léková rezistence * genetika MeSH
- epidemiologické monitorování MeSH
- Escherichia coli * účinky léků genetika MeSH
- genotyp MeSH
- infekce vyvolané Escherichia coli mikrobiologie MeSH
- makrolidy farmakologie MeSH
- maso * mikrobiologie MeSH
- mikrobiální testy citlivosti * MeSH
- plazmidy genetika MeSH
- prasata MeSH
- Salmonella * účinky léků genetika izolace a purifikace MeSH
- sekvenování celého genomu MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Názvy látek
- antibakteriální látky * MeSH
- azithromycin * MeSH
- makrolidy MeSH
Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.
- MeSH
- antibakteriální látky * farmakologie MeSH
- bakteriální léková rezistence * genetika MeSH
- genomika MeSH
- lidé MeSH
- Salmonella genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Geografické názvy
- Etiopie epidemiologie MeSH
- Názvy látek
- antibakteriální látky * MeSH
Technologies for the Internet of Things (IoT) are maturing, yet no common standards dictate their direction, leaving space for a plethora of research directions and opportunities. Among the most important IoT topics is security. When we design a robust system, it is important to know the available options for facing common tasks related to access control, authentication, and authorization. In this review, we systematically analyze 1622 peer-reviewed publications from October 2017 to December 2020 to find the taxonomy of security solutions. In addition, we assess and categorize current practices related to IoT security solutions, commonly involved technologies, and standards applied in recent research. This manuscript provides a practical road map to recent research, guiding the reader and providing an overview of recent research efforts.
- Klíčová slova
- Internet of Things, authentication, authorization, identity management, security, survey,
- MeSH
- internet věcí * MeSH
- internet MeSH
- zabezpečení počítačových systémů MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- systematický přehled MeSH
In August 2017, an increased incidence of Salmonella Bareilly was detected in the Czech Republic. An investigation was conducted with Slovakia to confirm the outbreak and identify the source. Probable outbreak cases were defined as cases with laboratory-confirmed S. Bareilly reported in either of the national surveillance systems, and/or the Czech and Slovak National Reference Laboratory databases from July 2017. Confirmed cases had the pulsed-field gel electrophoresis (PFGE) outbreak pulsotype or up to 5 alleles difference from outbreak cluster members by core genome multilocus sequence typing (cgMLST). PFGE and whole genome sequencing were used for isolate comparison. The same trawling questionnaire was used in both countries. By the end of October 2018, 325 cases were identified. Among 88 human S. Bareilly isolates analysed by PFGE, 82 (93%) shared an identical pulsotype; cgMLST of 17 S. Bareilly human isolates showed 1-2 allele difference. The trawling questionnaire excluded consumption of unusual or imported foods. In September 2018, an isolate closely related to the outbreak isolates was identified in a powdered egg product. A spray dryer was recognised as the contamination source and the production plant was closed. Using molecular typing methods, we detected a diffuse cross-border outbreak caused by S. Bareilly.
- Klíčová slova
- Salmonella Bareilly, WGS, food- and water-borne diseases, outbreak, powdered egg product, spray dryer,
- MeSH
- epidemický výskyt choroby * MeSH
- genom bakteriální MeSH
- lidé MeSH
- multilokusová sekvenční typizace MeSH
- pulzní gelová elektroforéza MeSH
- Salmonella * genetika MeSH
- sekvenování celého genomu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika epidemiologie MeSH
- Slovenská republika epidemiologie MeSH
It is important in software development to enforce proper restrictions on protected services and resources. Typically software services can be accessed through REST API endpoints where restrictions can be applied using the Role-Based Access Control (RBAC) model. However, RBAC policies can be inconsistent across services, and they require proper assessment. Currently, developers use penetration testing, which is a costly and cumbersome process for a large number of APIs. In addition, modern applications are split into individual microservices and lack a unified view in order to carry out automated RBAC assessment. Often, the process of constructing a centralized perspective of an application is done using Systematic Architecture Reconstruction (SAR). This article presents a novel approach to automated SAR to construct a centralized perspective for a microservice mesh based on their REST communication pattern. We utilize the generated views from SAR to propose an automated way to find RBAC inconsistencies.
- Klíčová slova
- Access control, Authorization, Microservices, RBAC, REST, Security, Static code analysis, Systematic architecture reconstruction,
- Publikační typ
- časopisecké články MeSH
Salmonella enterica subspecies enterica serotype Choleraesuis is a swine adapted serovar. S. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. S. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999-2000 and 2012-2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European S. Choleraesuis isolates including the Danish outbreak isolates. A total of 102 S. Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European S. Choleraesuis was estimated to have emerged in ∼1837 (95% credible interval, 1733-1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012-2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphisms (SNPs) differences (0-4 SNPs) can be observed between clonal strains isolated from different organs of the same animal. Proper disinfection of livestock vehicles and improved quality control of livestock feed could help to prevent future spread of S. Choleraesuis or other more serious infectious diseases such as African swine fever (ASF) in the European pig production system.
- Klíčová slova
- Kunzendorf, Salmonella Choleraesuis, antimicrobial resistance genes, epidemiology, phylogenetics, transmission, whole genome sequencing, wild boar,
- Publikační typ
- časopisecké články MeSH
Plant functional traits directly affect ecosystem functions. At the species level, trait combinations depend on trade-offs representing different ecological strategies, but at the community level trait combinations are expected to be decoupled from these trade-offs because different strategies can facilitate co-existence within communities. A key question is to what extent community-level trait composition is globally filtered and how well it is related to global versus local environmental drivers. Here, we perform a global, plot-level analysis of trait-environment relationships, using a database with more than 1.1 million vegetation plots and 26,632 plant species with trait information. Although we found a strong filtering of 17 functional traits, similar climate and soil conditions support communities differing greatly in mean trait values. The two main community trait axes that capture half of the global trait variation (plant stature and resource acquisitiveness) reflect the trade-offs at the species level but are weakly associated with climate and soil conditions at the global scale. Similarly, within-plot trait variation does not vary systematically with macro-environment. Our results indicate that, at fine spatial grain, macro-environmental drivers are much less important for functional trait composition than has been assumed from floristic analyses restricted to co-occurrence in large grid cells. Instead, trait combinations seem to be predominantly filtered by local-scale factors such as disturbance, fine-scale soil conditions, niche partitioning and biotic interactions.
Determination of long-term tropical cyclone (TC) variability is of enormous importance to society; however, changes in TC activity are poorly understood owing to discrepancies among various datasets and limited span of instrumental records. While the increasing intensity and frequency of TCs have been previously documented on a long-term scale using various proxy records, determination of their poleward migration has been based mostly on short-term instrumental data. Here we present a unique tree-ring-based approach for determination of long-term variability in TC activity via forest disturbance rates in northeast Asia (33-45°N). Our results indicate significant long-term changes in TC activity, with increased rates of disturbances in the northern latitudes over the past century. The disturbance frequency was stable over time in the southern latitudes, however. Our findings of increasing disturbance frequency in the areas formerly situated at the edge of TC activity provide evidence supporting the broad relevance of poleward migration of TCs. Our results significantly enhance our understanding of the effects of climate change on TCs and emphasize the need for determination of long-term variation of past TC activity to improve future TC projections.
- Klíčová slova
- North Pacific, dendrochronology, natural hazard, poleward migration, tropical cyclones,
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The globally observed trend of changing intensity of tropical cyclones over the past few decades emphasizes the need for a better understanding of the effects of such disturbance events in natural and inhabited areas. On the Korean Peninsula, typhoon intensity has increased over the past 100 years as evidenced by instrumental data recorded from 1904 until present. We examined how the increase in three weather characteristics (maximum hourly and daily precipitation, and maximum wind speed) during the typhoon activity affected old-growth oak forests. Quercus mongolica is a dominant species in the Korean mountains and the growth releases from 220 individuals from three sites along a latitudinal gradient (33-38°N) of decreasing typhoon activity were studied. Growth releases indicate tree-stand disturbance and improved light conditions for surviving trees. The trends in release events corresponded to spatiotemporal gradients in maximum wind speed and precipitation. A high positive correlation was found between the maximum values of typhoon characteristics and the proportion of trees showing release. A higher proportion of disturbed trees was found in the middle and southern parts of the Korean peninsula where typhoons are most intense. This shows that the releases are associated with typhoons and also indicates the differential impact of typhoons on the forests. Finally, we present a record of the changing proportion of trees showing release based on tree-rings for the period 1770-1979. The reconstruction revealed no trend during the period 1770-1879, while the rate of forest disturbances increased rapidly from 1880 to 1979. Our results suggest that if typhoon intensity rises, as is projected by some climatic models, the number of forest disturbance events will increase thus altering the disturbance regime and ecosystem processes.
- MeSH
- cyklonové bouře * MeSH
- dub (rod) * MeSH
- stromy * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Korejská republika MeSH
Understanding how past climate changes affected biodiversity is a key issue in contemporary ecology and conservation biology. These diversity changes are, however, difficult to reconstruct from paleoecological sources alone, because macrofossil and pollen records do not provide complete information about species assemblages. Ecologists therefore use information from modern analogues of past communities in order to get a better understanding of past diversity changes. Here we compare plant diversity, species traits and environment between late-glacial Abies, early-Holocene Quercus, and mid-Holocene warm-temperate Carpinus forest refugia on Jeju Island, Korea in order to provide insights into postglacial changes associated with their replacement. Based on detailed study of relict communities, we propose that the late-glacial open-canopy conifer forests in southern part of Korean Peninsula were rich in vascular plants, in particular of heliophilous herbs, whose dramatic decline was caused by the early Holocene invasion of dwarf bamboo into the understory of Quercus forests, followed by mid-Holocene expansion of strongly shading trees such as maple and hornbeam. This diversity loss was partly compensated in the Carpinus forests by an increase in shade-tolerant evergreen trees, shrubs and lianas. However, the pool of these species is much smaller than that of light-demanding herbs, and hence the total species richness is lower, both locally and in the whole area of the Carpinus and Quercus forests. The strongly shading tree species dominating in the hornbeam forests have higher leaf tissue N and P concentrations and smaller leaf dry matter content, which enhances litter decomposition and nutrient cycling and in turn favored the selection of highly competitive species in the shrub layer. This further reduced available light and caused almost complete disappearance of understory herbs, including dwarf bamboo.
- MeSH
- biodiverzita * MeSH
- ekosystém MeSH
- klimatické změny MeSH
- ledový příkrov MeSH
- sopečné erupce MeSH
- stromy anatomie a histologie klasifikace fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Korejská republika MeSH
