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1.
  • Akaberi, Dario, et al. (författare)
  • Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach.
  • 2018
  • Ingår i: Infection Ecology & Epidemiology. - 2000-8686 .- 2000-8686. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Current combination treatments with direct-acting antiviral agents (DAAs) can cure more than 95% of hepatitis C virus (HCV) infections. However, resistance-associated substitutions (RASs) may emerge and can also be present in treatment-naïve patients. Methods, results and discussion: In this study, a semi-pan-genotypic population sequencing method was developed and used to assess all NS5B amino acid variants between residue positions 310 and 564. Our method successfully sequenced more than 90% of genotype (GT) 1a, 1b, 2b and 3a samples. By using the population sequencing method with a cut-off of 20%, we found the dasabuvir RASs A553V and C445F to be a baseline polymorphism of GT 2b (8 out of 8) and GT 3a (18 out of 18) sequences, respectively. In GT 1a and 1b treatment-naïve subjects (n=25), no high-fold resistance polymorphism/RASs were identified. We further predicted dasabuvir's binding pose with the NS5B polymerase using the in silico methods to elucidate the reasons associated with the resistance of clinically relevant RASs. Dasabuvir was docked at the palm-I site and was found to form hydrogen bonds with the residues S288, I447, Y448, N291 and D318. The RAS positions 316, 414, 448, 553 and 556 were found to constitute the dasabuvir binding pocket.
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2.
  • Anyango, Gladys, et al. (författare)
  • A survey of aflatoxin M1 contamination in raw milk produced in urban and peri-urban areas of Kisumu County, Kenya
  • 2018
  • Ingår i: Infection Ecology & Epidemiology. - : Taylor & Francis. - 2000-8686 .- 2000-8686. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • ABSTRACTBackground: Food safety is of increasing global concern, and a OneHealth issue requiring attention of many disciplines. Aflatoxins are toxins produced by fungi and found in foods and feeds, and exposure causes negative health effects in humans and animals. When lactating animals consume aflatoxin B1, the metabolite (AFM1) is transferred to milk.Methods: A cross-sectional study was designed to determine characteristics of smallholder dairy farming in urban and peri-urban areas of Kisumu and quantify AFM1 in milk. Data was collected from 97 randomly selected dairy farms on farming practices, milk production, and awareness about aflatoxins. Collected milk samples were analyzed using enzyme-linked immunosorbent assay for AFM1.Results: Average milk produced was 13 liters per day per household and mainly used for household consumption and sold to neighbours. Farmers mainly fed cows on forage and concentrates (62.9%). Levels of AFM1 ranged from below the detection limit to 151 ppt, with a mean of 29.67 p...
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3.
  • Atterby, Clara, et al. (författare)
  • Increased prevalence of antibiotic-resistant E. coli in gulls sampled in Southcentral Alaska is associated with urban environments
  • 2016
  • Ingår i: Infection Ecology & Epidemiology. - : Taylor & Francis. - 2000-8686 .- 2000-8686. ; 6:1, s. 1-7
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Antibiotic-resistant bacteria pose challenges to healthcare delivery systems globally; however, limited information is available regarding the prevalence and spread of such bacteria in the environment. The aim of this study was to compare the prevalence of antibiotic-resistant bacteria in large-bodied gulls (Larus spp.) at urban and remote locations in Southcentral Alaska to gain inference into the association between antibiotic resistance in wildlife and anthropogenically influenced habitats.METHODS: Escherichia coli was cultured (n=115 isolates) from fecal samples of gulls (n=160) collected from a remote location, Middleton Island, and a more urban setting on the Kenai Peninsula.RESULTS: Screening of E. coli from fecal samples collected from glaucous-winged gulls (Larus glaucescens) at Middleton Island revealed 8% of isolates were resistant to one or more antibiotics and 2% of the isolates were resistant to three or more antibiotics. In contrast, 55% of E. coli isolates derived from fecal samples collected from large-bodied gulls (i.e. glaucous, herring [Larus argentatus], and potentially hybrid gulls) on the Kenai Peninsula were resistant to one or more antibiotics and 22% were resistant to three or more antibiotics. In addition, total of 16% of the gull samples from locations on the Kenai Peninsula harbored extended-spectrum cephalosporin-resistant E. coli isolates (extended-spectrum beta-lactamases [ESBL] and plasmid-encoded AmpC [pAmpC]), in contrast to Middleton Island where no ESBL- or pAmpC-producing isolates were detected.CONCLUSION: Our findings indicate that increased prevalence of antibiotic resistance is associated with urban environments in Southcentral Alaska and presumably influenced by anthropogenic impacts. Further investigation is warranted to assess how migratory birds may maintain and spread antimicrobial-resistant bacteria of relevance to human and animal health.
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4.
  • Backhans, Annette, et al. (författare)
  • Rodents on pig and chicken farms - a potential threat to human and animal health
  • 2012
  • Ingår i: Infection Ecology and Epidemiology. - : Taylor & Francis Open: Creative Commons Attribution Non-Commercial / Co-Action Publishing. - 2000-8686. ; 2
  • Forskningsöversikt (refereegranskat)abstract
    • Rodents can cause major problems through spreading various diseases to animals and humans. The two main species of rodents most commonly found on farms around the world are the house mouse (Mus musculus) and the brown rat (Rattus norvegicus). Both species are omnivorous and can breed year-round under favourable conditions. This review describes the occurrence of pathogens in rodents on specialist pig and chicken farms, which are usually closed units with a high level of bio-security. However, wild rodents may be difficult to exclude completely, even from these sites, and can pose a risk of introducing and spreading pathogens. This article reviews current knowledge regarding rodents as a hazard for spreading disease on farms. Most literature available regards zoonotic pathogens, while the literature regarding pathogens that cause disease in farm animals is more limited.
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5.
  • Badrul, Hasan, et al. (författare)
  • Absence of vancomycin-resistant enterococci among highly ESBL-positive crows (Corvus splendens) foraging on hospital waste in Bangladesh
  • 2015
  • Ingår i: Infection Ecology & Epidemiology. - 2000-8686 .- 2000-8686. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND:Vancomycin-resistant enterococci (VRE) have emerged as a growing problem in hospitals; however, domesticated animals, poultry, and wild birds are acting as potential reservoirs. There is a knowledge gap in the Epidemiology of VRE from Bangladesh.METHODS:To study the prevalence of VRE and the mechanisms of resistance implicated among wild birds, 238 fecal samples were collected in 2010 from house crows (Corvus splendens) foraging on hospital waste in Bangladesh. Fecal samples were screened by analyzing color change in broth and screening for vanA and vanB resistant genes by PCR.RESULTS:Neither vanA nor vanB genes were detected from the fecal samples. The house crow does not seem to constitute a reservoir for VRE.CONCLUSION:The zero prevalence is an indication that foraging on hospital waste does not constitute a major risk of VRE carriage in house crows and this is the first study to focus on the prevalence of VRE from wild birds in Bangladesh.
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7.
  • Blomqvist, Maria, et al. (författare)
  • Chlamydia psittaci in birds of prey, Sweden
  • 2012
  • Ingår i: Infection Ecology and Epidemiology. - 2000-8686. ; 2, s. 8435-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Chlamydia psittaci is an intracellular bacterium primarily causing respiratory diseases in birds but may also be transmitted to other animals, including humans. The prevalence of the pathogen in wild birds in Sweden is largely unknown. Methods: DNA was extracted from cloacae swabs and screened for C. psittaci by using a 23S rRNA gene PCR assay. Partial 16S rRNA and ompA gene fragments were sequence determined and phylogenies were analysed by the neighbour-joining method. Results and conclusion: The C. psittaci prevalence was 1.3% in 319 Peregrine Falcons and White-tailed Sea Eagles, vulnerable top-predators in Sweden. 16S rRNA and ompA gene analysis showed that novel Chlamydia species, as well as novel C. psittaci strains, are to be found among wild birds.
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8.
  • Blomqvist, Maria, et al. (författare)
  • Chlamydophila psittaci in birds of prey, Sweden
  • 2012
  • Ingår i: Infection Ecology & Epidemiology. - 2000-8686 .- 2000-8686. ; 2
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Chlamydia psittaci is an intracellular bacterium primarily causing respiratory diseases in birds but may also be transmitted to other animals, including humans. The prevalence of the pathogen in wild birds in Sweden is largely unknown.Methods: DNA was extracted from cloacae swabs and screened for C. psittaci by using a 23S rRNA gene PCR assay. Partial 16S rRNA and ompA gene fragments were sequence determined and phylogenies were analysed by the neighbour-joining method.Results and conclusion: The C. psittaci prevalence was 1.3% in 319 Peregrine Falcons and White-tailed Sea Eagles, vulnerable top-predators in Sweden. 16S rRNA and ompA gene analysis showed that novel Chlamydia species, as well as novel C. psittaci strains, are to be found among wild birds.
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