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69 results for “molecular epidemiology”
CHIKVnext: Molecular epidemiology of Chikungunya virus
<p>CHIKVnext is an interactive resource to study the evolution and global spread of Chikungunya virus (CHIKV), built on the Nextstrain platform.</p>
Fig. 3 in Epidemiology and molecular phylogeny of Babesia sp. in Little Penguins Eudyptula minor in Australia
Fig. 3. Agarose gel electrophoresis of amplification products obtained through nested PCR tests targeting the 18S rRNA gene of Babesia (primers Bab5.1/BabB followed by RLBF/RLBR) or the mitochondrial cytochrome b gene of Haemoproteus/Plasmodium (primers HaemNFI/HaemNR3 followed by HaemF/HaemR2). The following samples are represented: (a) captive-born little penguin chick, negative blood smear; (b) adult wild little penguin, negative blood smear; (c) Babesia-infected adult wild little penguin, as confirmed through blood smear; (d) Haemoproteus-infected adult tropical screech owl, as confirmed through blood smear; (e) Plasmodium-inoculated chicken, raised in arthropod-free environment; (f) blood parasite-free chicken, raised in arthropodfree environment.
Fig. 1 in Epidemiology and molecular phylogeny of Babesia sp. in Little Penguins Eudyptula minor in Australia
Fig. 1. Geographic distribution of sampling locations, southeast Australia. Site details are given in Table 1. The geographic distribution of little penguins (black area) is shown in the top right map (adapted from Marchant and Higgins, 1990).
Fig. 4 in Epidemiology and molecular phylogeny of Babesia sp. in Little Penguins Eudyptula minor in Australia
Fig. 4. Maximum likelihood phylogenetic tree of the 18S rRNA gene of the studied Babesia lineages. Lineages identified in this study are emphasized in red, and other avianinfecting lineages are emphasized in blue. For each lineage, the following information is provided: morphospecies (Genbank ascension number) host species. For avianinfecting lineages, the geographic location is also provided. Branch lengths are drawn proportionally to evolutionary distance (scale bar is shown). For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.
Fig. 2 in Epidemiology and molecular phylogeny of Babesia sp. in Little Penguins Eudyptula minor in Australia
Fig. 2. Babesia sp. in the blood smear of a little penguin. Individual details: TAS- 124, male, adult, moulting, sampled at "Darlington Foreshore" (Maria Island, Tasmania) in 21/02/2013, Genbank ascension number KP144323, Giemsa stain.
Fig. 1 in Molecular epidemiology and pathology of spirorchiid infection in green sea turtles (Chelonia mydas)
Fig. 1. Lesions associated with spirorchiid blood flukes in Chelonia mydas. a) Mild (score = 1) granulomatous lesions (G) and lymphocytic inflammation within the cerebral meninges of an adult green turtle, centred on a brown-shelled fluke ovum. HE stain, scale bar = 125 Mm b) Moderate (score = 3) granulomatous lesions (G) and lymphocytic inflammation within the cerebral meninges of an adult green turtle, centred on several brown-shelled fluke ova. HE stain, scale bar = 350 Mm c) Severe (score = 5) granulomatous lesions (G) and lymphocytic inflammation within the meninges of a small immature green turtle, centred on multiple numerous fluke ova. HE stain, scale bar = 350 Mm d) Severe (score = 5) granulomatous lesion (G) with necrotic centre protruding into the lumen of the aorta of an adult green turtle, with dense lymphocytic inflammation in surrounding tissues. Numerous adult flukes (Hapalotrema pambanensis) were recovered from the heart and major vessels. HE stain, scale bar = 1.7 mm. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 2 in Molecular epidemiology of Theileria equi in horses and their association with possible tick vectors in the state of Rio de Janeiro, Brazil
Fig. 2 Real-time polymerase chain reaction analytical sensitivity, showing the amplification curves of plasmid DNA, containing the Theileria equi 18S rRNA gene (∼1,600 bp), in serial dilutions (3–30,000 copies)
Fig. 1 in Molecular epidemiology of Theileria equi in horses and their association with possible tick vectors in the state of Rio de Janeiro, Brazil
Fig. 1 Standard curve plotted from serial decimal dilutions of plasmid DNA, containing the Theileria equi 18S rRNA gene (∼1,600 bp). The quantification cycle (Cq) value obtained by real-time polymerase chain reaction using Taqman system was plotted as a function of the initial number of plasmid copies
Molecular Epidemiology of Trypanosomatids and Trypanosoma cruzi in Primates from Peru
<p>Resultados de laboratorio para el diagnóstico de tripanosomatidos y <em>Tripanosoma cruzi </em>en primates Neotropicales en cautiverio y vida libre en Peru. El diagnostico se realizó mediante microscopia directa y PCR. Los resultados y metodología empleada fueron publicados en Aysanoa, E., Mayor, P., Mendoza, A.P. et al. EcoHealth (2017) 14: 732. https://doi.org/10.1007/s10393-017-1271-8</p>
Fig. 4 in Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization
Fig. 4. Distribution of the 93 positive wild boars in the study area and details of prevalence, provinces, regional and national parks.
Fig. 1 in Molecular identification and epidemiological data of Anisakis spp. (Nematoda: Anisakidae) larvae from Southeastern Pacific Ocean off Peru
Fig. 1. Scanning electron micrographs of Anisakis type I and II.1a and 2a. Cephalic end. Detail of the structures: oral cavity (oc), tooth (t), excretory pore (ep), subventral lip bulge (s). 1b. caudal end of Anisakis pegreffii. 2b. caudal end of Anisakis physeteris. Detail of the structures: anal pore (ap), mucron (m).
Fig. 2 in Molecular identification and epidemiological data of Anisakis spp. (Nematoda: Anisakidae) larvae from Southeastern Pacific Ocean off Peru
Fig. 2. Phylogenetic tree based on mtDNA cox2 gene sequences exploring the relationships among Anisakis species. The relationship was drawn using Bayesian inference (BI) and maximum likelihood (ML) methods. Posterior probability value (first) and nodal support is shown as bootstrap value (second) on the basis of 10 million generations for BI and 1000 replicates (only bootstrap values greater than 80% are shown) for ML, respectively. Scale bar indicate nucleotide substitutions per site. GenBank accession numbers are shown in parentheses. Hysterothylacium deardorffoverstreetorum was used as an outgroup.
Fig. 2 in Molecular and epidemiological surveillance of Plasmodium spp. during a mortality event affecting Humboldt penguins (Spheniscus humboldti) at a zoo in the UK
Fig. 2. Histopathology associated with mortality of a Humboldt penguin (Spheniscus humboldti) infected with Plasmodium sp. Penguin paraffinembedded heart tissue section (5 μm) stained with haematoxylin and eosin a. Four sites of chromogenic in situ hybridization with a Plasmodium-specific probe occurred in what appeared to be cardiac macrophages. Magnification: x10. b. Same Penguin heart tissue sections inspected under light microscopy. Magnification: x100. Exoerythrocytic meronts are seen breaking out of a cardiac macrophage (ellipse).
Fig. 3 in Molecular and epidemiological surveillance of Plasmodium spp. during a mortality event affecting Humboldt penguins (Spheniscus humboldti) at a zoo in the UK
Fig. 3. Temporal distribution of mosquito and Plasmodium spp. prevalence at Chester Zoo between May and November 2017. Continuous top line: total number of mosquitoes collected on a weekly basis; Continuous bottom line: total number of Plasmodium infections; Dashed line: parasite prevalence estimated as a proportion of infected mosquitoes of the total captured on a weekly basis.
Fig. 1 in Molecular and epidemiological surveillance of Plasmodium spp. during a mortality event affecting Humboldt penguins (Spheniscus humboldti) at a zoo in the UK
Fig. 1. Mosquito abundance and Plasmodium prevalence compared at ten sampling sites across Chester Zoo. The Chester Zoo site (zoo perimeter is outlined) overlaid with a heat map of total mosquito numbers trapped at 10 sampling sites. Locations of traps are indicated by numbers 1–7, 10–12 inclusive. The location of the penguin exhibit in 2017 is indicated by a penguin symbol. a. Mosquito abundance. b. Plasmodium prevalence in trapped mosquitoes. Heat maps were generated using Heatmapper with a Gaussian radius multiplier of 1.
Fig. 4 in Molecular and epidemiological surveillance of Plasmodium spp. during a mortality event affecting Humboldt penguins (Spheniscus humboldti) at a zoo in the UK
Fig. 4. Maximum likelihood phylogeny of Plasmodium spp. cytb sequences. The phylogeny was estimated from a 378bp multiple sequence alignment using a GTR+Γ+І model (α = 0.488; proportion of invariant sites = 0.248). The tree is rooted with an outgroup of Leucocytozoon sequences (boxed). Node accuracy is indicated by an SH-like log-Likelihood ratio metric; bootstrap values greater than 0.5 are displayed in the tree. Novel sequences obtained in this study are shaded with their corresponding reference sequence; P. matutinum (MK443241), P. vaughani (MK652243) and P. relictum (JN164731). The clusters contain sequences derived from penguins, mosquitoes or wild birds, which is indicated by a penguin, mosquito or a bird symbol. One wild bird sequence is present in the P. matutinum cluster (OM912814); and three (MW814062, MW814149, MW814045), two (MW814453, MW814028) and two (MW814503, MW814500) mosquito sequences are present in the P. matutinum, P vaughani and P. relictum clusters respectively. The rest of the sequences in those clusters correspond to 23 novel sequences from penguins infected in the UK, indicating their origin (CZ: Chester Zoo, LZ: London Zoo, PZ: Paignton Zoo, BZ: Blackpool Zoo, CWP: Cotswold Wildlife Park) and year of sampling, if not 2017. Other shade sequences correspond to recognized morphospecies. P. vaughani cluster represents 145 novel sequences, P. matutinum cluster represents 345 novel sequences and P. relictum clusters represents 31 novel sequences. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</p>
Fig. 2. Invaginated protoscoleces isolated from a in Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization
Fig. 2. Invaginated protoscoleces isolated from a fertile hydatid cyst.
Fig. 1 in Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization
Fig. 1. Liver with massive CE infection by Echinococcus granulosus sensu stricto.
Molecular epidemiology and risk factors for extended-spectrum β-lactamase-producing Enterobacterales in long-term care residents
<div class="abstract-content selected"> <p><strong class="sub-title"> Objectives: </strong> We aimed to assess the burden of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in Swiss long-term care facilities (LTCFs) to describe the molecular epidemiology, describe the intra-institutional and regional clusters of resistant pathogens, and identify independent institution- and resident-level factors associated with colonization.</p> <p><strong class="sub-title"> Design: </strong> Cross-sectional study.</p> <p><strong class="sub-title"> Setting and participants: </strong> From August to October 2019, we performed a point prevalence study among residents from 16 LTCFs in Western and Eastern Switzerland (8 per region).</p> <p><strong class="sub-title"> Methods: </strong> Residents underwent screening for ESBL-producing Enterobacterales (ESBL-E); whole-genome sequencing (WGS) was performed. We gathered institution-level (eg, number of beds, staff-resident ratio, alcoholic hand rub consumption) and resident-level [eg, anthropometric data, time in facility, dependency, health care exposure, antibiotic treatment, proton-pump inhibitor (PPI) use] characteristics. Factors associated with colonization were identified using a generalized linear model.</p> <p><strong class="sub-title"> Results: </strong> Among 1185 eligible residents, 606 (51%) consented to the study. ESBL-E prevalence was 11.6% (70/606), ranging from 1.9% to 33.3% between institutions, with a median of 12.5% in the West and 6.9% in the East (P = .03). Among 59 <em>Escherichia</em> <em>coli</em> (from 58 residents), multilocus sequence type (ST) 131 was most common (n = 43/59, 73%), predominantly its subclone H30R1 (n = 37/43, 86%). WGS data identified multiple intra-institutional and regional clusters. Independent risk factors for ESBL carriage were previous ESBL colonization [adjusted odds ratio (aOR) 23.5, 95% confidence interval (CI) 6.6–83.8, P < .001), male gender (aOR 2.6, 95% CI 1.5–4.6, P = .002), and use of PPIs (aOR 2.2, 95% CI 1.2–3.8, P = .01).</p> <p><strong class="sub-title"> Conclusions and implications: </strong> Overall ESBL-E prevalence in Swiss LTCF residents is low. Yet, we identified several clusters of residents with identical pathogens within the same institution. This implies that particularly affected institutions might benefit from targeted infection control interventions. PPI use was the only modifiable factor associated with carriage of ESBL producers. This study adds to the growing list of adverse outcomes associated with PPIs, calling for action to restrict their use in the long-term care setting.</p> </div>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.