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  • 1. Akaberi, Dario
    et al.
    Bergfors, Assar
    Kjellin, Midori
    Kameli, Nader
    Lidemalm, Louise
    Kolli, Bhavya
    Shafer, Robert W
    Palanisamy, Navaneethan
    Lennerstrand, Johan
    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.2018In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 8, no 1, article id 1528117Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Atterby, Clara
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ramey, Andrew M.
    Gustafsson Hall, Gabriel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Järhult, Josef
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Börjesson, Stefan
    Bonnedahl, Jonas
    Increased prevalence of antibiotic resistant E. coli in gulls sampled in Southcentral Alaska is associated with urban environments2016In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 6, no 1, article id 32334Article in journal (Refereed)
    Abstract [en]

    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.

  • 3.
    Badrul, Hasan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Järhult, Josef D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Absence of vancomycin-resistant enterococci among highly ESBL-positive crows (Corvus splendens) foraging on hospital waste in Bangladesh2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, article id 29761Article in journal (Refereed)
    Abstract [en]

    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.

  • 4. Bäck, Anne Tuiskunen
    et al.
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Dengue viruses: an overview.2013In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 3Article in journal (Refereed)
    Abstract [en]

    Dengue viruses (DENVs) cause the most common arthropod-borne viral disease in man with 50-100 million infections per year. Because of the lack of a vaccine and antiviral drugs, the sole measure of control is limiting the Aedes mosquito vectors. DENV infection can be asymptomatic or a self-limited, acute febrile disease ranging in severity. The classical form of dengue fever (DF) is characterized by high fever, headache, stomach ache, rash, myalgia, and arthralgia. Severe dengue, dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) are accompanied by thrombocytopenia, vascular leakage, and hypotension. DSS, which can be fatal, is characterized by systemic shock. Despite intensive research, the underlying mechanisms causing severe dengue is still not well understood partly due to the lack of appropriate animal models of infection and disease. However, even though it is clear that both viral and host factors play important roles in the course of infection, a fundamental knowledge gap still remains to be filled regarding host cell tropism, crucial host immune response mechanisms, and viral markers for virulence.

  • 5.
    Danielsson, Axel
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Palanisamy, Navaneethan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Golbob, Sultan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Yin, Hong
    Blomberg, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Hedlund, Johan
    Sylvan, Staffan
    Lennerstrand, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
    Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, article id 22251Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Epidemiology and transmission patterns of hepatitis C virus (HCV) are important subjects as we enter a new era of treatment with directly acting antivirals (DAAs). The highest prevalence of HCV in developed countries is found among intravenous drug users (IDUs), where unsafe needle sharing practices provide the main route of infection. Efforts to prohibit the continuous spread of HCV among these groups have been initiated by the community services and health care providers. Our goal was to understand how HCV was transmitted among IDUs within a limited population group. We provide a retrospective study (2005-2007) of the HCV transmission patterns in a population of IDUs in the Uppsala region of Sweden.

    METHOD: Eighty-two serum samples were collected from IDUs in Uppsala County. Our reverse transcription nested polymerase chain reaction (RT-nested PCR) and sequencing method enabled a comprehensive genetic analysis for a broad spectrum of genotypes of two relatively conserved regions, NS5B and NS3, that encodes for the viral polymerase and protease, respectively. HCV RNA in serum samples was amplified and sequenced with in-house primers. Sequence similarities between individuals and subgroups were analyzed with maximum likelihood (ML) phylogenetic trees. Published HCV reference sequences from other geographic regions and countries were also included for clarity.

    RESULTS: Phylogenetic analysis was possible for 59 NS5B (72%) and 29 NS3 (35%) sequences from Uppsala patients. Additionally, we also included 15 NS3 sequences from Örebro patients, making a total of 44 NS3 sequences for the analysis. By analyzing the NS3 sequences, two transmission sets were found between the IDUs (>98% sequence identity), with one set consisting of two individuals and another set consisting of three individuals. In addition, the phylogenetic analysis done with our serum samples displayed clusters that distinguished them from the reference sequences.

    CONCLUSION: Our method seems to enable us to trace the HCV transmission between IDUs. Furthermore, the method is fairly independent of the time of infection because the method uses relatively conserved HCV sequence regions (i.e. NS5B and NS3).

  • 6. Esson, Carol
    et al.
    Skerratt, Lee F
    Berger, Lee
    Malmsten, Jonas
    Strand, Tanja
    Lundkvist, Åke
    Järhult, Josef D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Michaux, Johan
    Mijiddorj, Tserennadmid Nadia
    Bayrakçısmith, Rana
    Mishra, Charudutt
    Johansson, Örjan
    Health and zoonotic Infections of snow leopards Panthera unica in the South Gobi desert of Mongolia.2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1604063Article in journal (Refereed)
    Abstract [en]

    Background: Snow leopards, Panthera uncia, are a threatened apex predator, scattered across the mountains of Central and South Asia. Disease threats to wild snow leopards have not been investigated.Methods and Results: Between 2008 and 2015, twenty snow leopards in the South Gobi desert of Mongolia were captured and immobilised for health screening and radio-collaring. Blood samples and external parasites were collected for pathogen analyses using enzyme-linked immunosorbent assay (ELISA), microscopic agglutination test (MAT), and next-generation sequencing (NGS) techniques. The animals showed no clinical signs of disease, however, serum antibodies to significant zoonotic pathogens were detected. These pathogens included, Coxiella burnetii, (25% prevalence), Leptospira spp., (20%), and Toxoplasma gondii (20%). Ticks collected from snow leopards contained potentially zoonotic bacteria from the genera Bacillus, Bacteroides, Campylobacter, Coxiella, Rickettsia, Staphylococcus and Streptococcus.Conclusions: The zoonotic pathogens identified in this study, in the short-term did not appear to cause illness in the snow leopards, but have caused illness in other wild felids. Therefore, surveillance for pathogens should be implemented to monitor for potential longer- term disease impacts on this snow leopard population.

  • 7. Fraenkel, Carl-Johan
    et al.
    Melhus, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Enterococcus faecium coisolated with Lactobacillus species can mimic vancomycin-resistant enterococci2011In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 1, p. 7335-Article in journal (Refereed)
  • 8. Griekspoor, Petra
    et al.
    Hansbro, Philip M
    Waldenström, Jonas
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Campylobacter jejuni sequence types show remarkable spatial and temporal stability in Blackbirds.2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The zoonotic bacterium Campylobacter jejuni has a broad host range but is especially associated with birds, both domestic and wild. Earlier studies have indicated thrushes of the genus Turdus in Europe to be frequently colonized with C. jejuni, and predominately with host-associated specific genotypes. The European Blackbird Turdus merula has a large distribution in Europe, including some oceanic islands, and was also introduced to Australia by European immigrants in the 1850s.

    METHODS: The host specificity and temporal stability of European Blackbird C. jejuni was investigated with multilocus sequence typing in a set of isolates collected from Sweden, Australia, and The Azores.

    RESULTS: Remarkably, we found that the Swedish, Australian, and Azorean isolates were genetically highly similar, despite extensive spatial and temporal isolation. This indicates adaptation, exquisite specificity, and stability in time for European Blackbirds, which is in sharp contrast with the high levels of recombination and mutation found in poultry-related C. jejuni genotypes.

    CONCLUSION: The maintenance of host-specific signals in spatially and temporally separated C. jejuni populations suggests the existence of strong purifying selection for this bacterium in European Blackbirds.

  • 9.
    Gullsby, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Centre for Research and Development, Gävleborg. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Bondeson, Kåre
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    No detection of macrolide-resistant Mycoplasma pneumoniae from Swedish patients, 1996-2013.2016In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Infection ecology & epidemiology, Vol. 6, no 1, article id 31374Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Mycoplasma pneumoniae is a common cause of respiratory infections which can cause life-threatening pneumonia and serious extrapulmonary manifestations. Since the year 2000, the emergence of macrolide-resistant M. pneumoniae strains has increased with varying incidences across countries. In China more than 90% of the strains are resistant. M. pneumoniae diagnostics is mostly done with molecular methods, and in Sweden antibiotic resistance surveillance is not routinely performed. The prevalence of macrolide-resistant M. pneumoniae has not previously been studied in Sweden.

    MATERIAL AND METHODS: A total of 563 M. pneumoniae-positive respiratory samples, collected from four counties in Sweden between 1996 and 2013, were screened for mutations associated with macrolide resistance using a duplex FRET real-time PCR method. The real-time PCR targets the 23S rRNA gene, and differentiation between wild-type and resistant strains was achieved with a melting curve analysis.

    RESULTS: Of the 563 samples included, 548 were analyzed for mutations associated with macrolide resistance. No mutations were found. The detection rate of macrolide-resistant M. pneumoniae in this study was 0% [0.00-0.84%].

    CONCLUSION: No macrolide-resistant M. pneumoniae has been detected in Sweden. However, the emergence and spread of macrolide-resistant M. pneumoniae strains in many countries commands continuous epidemiological surveillance.

  • 10.
    Hagman, Karl
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Barboutis, Christos
    Ehrenborg, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Fransson, Thord
    Jaenson, Thomas G T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Lindgren, Per-Eric
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Nyström, Fredrik
    Waldenström, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    On the potential roles of ticks and migrating birds in the ecology of West Nile virus2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, p. 20943-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Mosquitoes are the primary vectors of West Nile virus (WNV). Ticks have, however, been suggested to be potential reservoirs of WNV. In order to investigate their role in the spread of the virus, ticks, which had been collected from birds migrating northwards from Africa to Europe, were analyzed for the potential presence of WNV-RNA.

    METHODS: On the Mediterranean islands Capri and Antikythira a total of 14,824 birds were captured and investigated from which 747 ticks were collected.

    RESULTS AND CONCLUSION: Most of the identified ticks (93%) were nymphs and larvae of Hyalomma marginatum sensu lato, most of which were or appear to be Hyalomma rufipes. Of these ticks 729 were individually screened for WNV-RNA. None of the ticks was found to be WNV positive. Thus, there was no evidence that Hyalomma marginatum s.l. ticks play a role in the spread of WNV from Africa to Europe.

  • 11.
    Haxton, Eva
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Lindberg, Anna
    National Institute of Veterinary Medicine.
    Troell, Karin
    National Institute of Veterinary Medicine.
    Redican, Kerry J
    Virginia Maryland College of Veterinary Medicine Virginia Tech Blacksburg, Virginia.
    One Health education meets science2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5Article in journal (Other academic)
  • 12.
    Haxton, Eva
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Šinigoj, Špela
    Rivière-Cinnamond, Ana
    WHO.
    The Network for Evaluation of One Health: evidence-based added value of One Health.2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5Article in journal (Refereed)
  • 13.
    Hernández, Jorge
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Lindberg, Peter
    Waldenström, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Drobni, Mirva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    A novel Salmonella serovar isolated from Peregrine Falcon (Falco peregrinus) nestlings in Sweden: salmonella enterica enterica serovar Pajala (Salmonella Pajala)2012In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 2, p. 7373-Article in journal (Refereed)
    Abstract [en]

    A novel Salmonella serovar was isolated from Peregrine falcon (Falco peregrinus) nestlings in northern Sweden in 2006. Three isolates of the same clone was retrieved from three falcon siblings and characterized as Salmonella enterica sub-species enterica: O-phase 13, 23:-: e, n, z 15 and the H-phase was not present. We propose the geographical name Salmonella enterica, sub-species enterica serovar Pajala to this novel Salmonella.

  • 14.
    Holtenius, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Gillman, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    The Spanish flu in Uppsala, clinical and epidemiological impact of the influenza pandemic 1918-1919 on a Swedish county2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, p. 21528-Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION AND AIM: The Spanish flu reached Sweden in June 1918, and at least one-third of the population (then 5.8 million) became infected. Some 34,500 persons (5.9 per 1,000 people) died from influenza during the first year of the pandemic (when acute pneumonia is included, the number of deaths rose to 7.1 per 1,000 people). In this historical look back at the pandemic, our aim was to review the epidemiological impact on the Swedish county of Uppsala, the clinical outcomes and the economic impact on the regional hospital; a relevant backgound to consider the impact of a future virulent pandemic. We also focused on how the pandemic was perceived by the medical community and by health care authorities.

    METHODS: Health care reports, statistics, daily newspapers, medical journals, and records of patients treated for influenza at the Uppsala Academic Hospital from July 1918 to June 1919 were included in our review.

    RESULTS: An influenza related mortality rate of 693 persons (5.1 per 1,000 people) was reported in the Uppsala region from 1918-1919; from July 1918 to June 1919, 384 patients were treated for influenza at the Uppsala Academic Hospital. The first wave peaked in November 1918 with case fatality rates up to 30%; a second wave peaked in April 1919 with a lower rate of mortality. Of the patients treated, a total of 66 died. Of these, 60% were 20-29 years of age, and 85% were less than 40 years old. Autopsy reports revealed pneumonia in 89% of the cases; among these, 47% were hemorrhagic, 18% were bilateral, and 45% had additional extrapulmonary organ involvement. Signs of severe viral disease were documented, but secondary bacterial disease was the primary cause of death in the majority of cases.

    CONCLUSION: The epidemiologic and pathologic results were in accordance with other publications of this time period. The costs of running the hospital doubled from 1917 to 1920 and then reversed by 45%. Today, an influenza pandemic of the same virulence would paralyze health care systems and result in extremely high financial costs and rates of mortality.

  • 15. Jansson, Désirée S
    et al.
    Mushtaq, Memoona
    Johansson, Karl-Erik
    Bonnedahl, Jonas
    Waldenström, Jonas
    Andersson, Dan I
    Broman, Tina
    Berg, Charlotte
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Intestinal spirochaetes (genus Brachyspira) colonise wild birds in the southern Atlantic region and Antarctica.2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION: The genus Brachyspira contains well-known enteric pathogens of veterinary significance, suggested agents of colonic disease in humans, and one potentially zoonotic agent. There are recent studies showing that Brachyspira are more widespread in the wildlife community than previously thought. There are no records of this genus in wildlife from the southern Atlantic region and Antarctica. Our aim was therefore, to determine whether intestinal spirochaetes of genus Brachyspira colonise marine and coastal birds in this region.

    METHOD: Faecal samples were collected from marine and coastal birds in the southern Atlantic region, including sub-Antarctic islands and Antarctica, in 2002, 2009, and 2012, with the aim to isolate and characterise zoonotic agents. In total, 205 samples from 11 bird species were selectively cultured for intestinal spirochaetes of genus Brachyspira. To identify isolates to species level, they were subjected to phenotyping, species-specific polymerase chain reactions, sequencing of partial 16S rRNA, NADH oxidase (nox), and tlyA genes, and phylogenetic analysis. Antimicrobial susceptibility tests were performed.

    RESULTS: Fourteen unique strains were obtained from 10 birds of three species: four snowy sheathbills (Chionis albus), three kelp geese (Chloephaga hybrida subsp. malvinarum), and three brown skua (Stercorarius antarcticus subsp. lonnbergi) sampled on the Falkland Islands, Tierra del Fuego in Argentina, South Georgia, South Shetland Islands, and the Antarctic Peninsula. Five Brachyspira strains were closely related to potentially enteropathogenic Brachyspira sp. of chickens: B. intermedia (n=2, from snowy sheathbills), and B. alvinipulli (n=3, from a kelp goose and two snowy sheathbills). Three strains from kelp geese were most similar to the presumed non-pathogenic species 'B. pulli' and B. murdochii, whereas the remaining six strains could not be attributed to currently known species. No isolates related to human strains were found. None of the tested strains showed decreased susceptibility to tiamulin, valnemulin, doxycycline, tylvalosin, lincomycin, or tylosin.

    CONCLUSIONS: This is the first report of intestinal spirochaetes from this region. Despite limitations of current diagnostic methods, our results, together with earlier studies, show that Brachyspira spp., including potentially pathogenic strains, occur globally among free-living avian hosts, and that this genus encompasses a higher degree of biodiversity than previously recognised.

  • 16.
    Jonsson, Anna-Karin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Biochemial structure and function.
    Tängdén, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Melhus, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lannergård, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    A trial with IgY chicken antibodies to eradicate faecal carriage of Klebsiella pneumoniae and Escherichia coli producing extended-spectrum beta-lactamases2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, article id 28224Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae is an emerging therapeutic challenge, especially in the treatment of urinary tract infections. Following an outbreak of CTX-M-15 Klebsiella pneumoniae in Uppsala, Sweden, an orphan drug trial on IgY chicken antibodies was undertaken in an attempt to eradicate faecal carriage of ESBL-producing K. pneumoniae and Escherichia coli.

    METHODS: Hens were immunised with epitopes from freeze-dried, whole-cell bacteria (ESBL-producing K. pneumoniae and E. coli) and recombinant proteins of two K. pneumoniae fimbriae subunits (fimH and mrkD). The egg yolks were processed according to good manufacturing practice and the product was stored at-20°C until used. Using an internal database from the outbreak and the regular laboratory database, faecal carriers were identified and recruited from May 2005 to December 2013. The participants were randomised in a placebo-controlled 1:1 manner.

    RESULTS: From 749 eligible patients, 327 (44%) had deceased, and only 91 (12%) were recruited and signed the informed consent. In the initial screening performed using the polymerase chain reaction, 24 participants were ESBL positive and subsequently randomised and treated with either the study drug or a placebo. The study was powered for 124 participants. Because of a very high dropout rate, the study was prematurely terminated. From the outbreak cohort (n=247), only eight patients were screened, and only one was positive with the outbreak strain in faeces.

    CONCLUSIONS: The present study design, using IgY chicken antibodies for the eradication of ESBL-producing K. pneumonia and E. coli, was ineffective in reaching its goal due to high mortality and other factors resulting in a low inclusion rate. Spontaneous eradication of ESBL-producing bacteria was frequently observed in recruited participants, which is consistent with previous reports.

  • 17.
    Järhult, Josef D
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Stedt, Johan
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Zero prevalence of extended spectrum beta-lactamase-producing bacteria in 300 breeding Collared Flycatchers in Sweden2013In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 3Article in journal (Refereed)
    Abstract [en]

    Wild birds are important indicators and potential spreaders of antibiotic resistance. The order Passerines is scarcely studied apart from Corvus sp. but extended spectrum beta-lactamases (ESBLs) has been found in Blackbirds. We tested 300 fecal samples from a well-studied population of Collared Flycatchers (Ficedula albicollis) at the Island of Gotland in Sweden and found no ESBL-producing bacteria. These results support the idea of 'ecological guild' as Blackbirds are ground-foraging invertebrate feeders, whereas Collared Flycatchers are aerial insectivores not regularly coming into contact with fecal contaminations and therefore less prone to acquire pathogens spread by the fecal-oral route.

  • 18.
    Järhult, Josef D
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Wahlgren, John
    Hasan, Badrul
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mallard or chicken?: Comparing the isolation of avian influenza A viruses in embryonated Mallard and chicken eggs2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, article id 28458Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: To date, the most efficient and robust method for isolating avian influenza A viruses (IAVs) is using embryonated chicken eggs (ECEs). It is known that low-pathogenic avian IAVs undergo rapid genetic changes when introduced to poultry holdings, but the factors driving mutagenesis are not well understood. Despite this, there is limited data on the effects of the standard method of virus isolation of avian-derived viruses, that is, whether isolation in ECEs causes adaptive changes in avian IAVs. Eggs from a homologous species could potentially offer an isolation vessel less prone to induce adaptive changes.

    METHODS: We performed eight serial passages of two avian IAVs isolated from fecal samples of wild Mallards in both ECEs and embryonated Mallard eggs, and hemagglutination assay titers and hemagglutinin sequences were compared.

    RESULTS: There was no obvious difference in titers between ECEs and embryonated Mallard eggs. Sequence analyses of the isolates showed no apparent difference in the rate of introduction of amino acid substitutions in the hemagglutinin gene (three substitutions in total in embryonated Mallard eggs and two substitutions in ECEs).

    CONCLUSION: Embryonated Mallard eggs seem to be good isolation vessels for avian IAVs but carry some practical problems such as limited availability and short egg-laying season of Mallards. Our study finds isolation of Mallard-derived avian IAVs in ECEs non-inferior to isolation in embryonated Mallard eggs, but more research in the area may be warranted as this is a small-scale study.

  • 19. Kagera, Irene
    et al.
    Kahenya, Peter
    Mutua, Florence
    Anyango, Gladys
    Kyallo, Florence
    Grace, Delia
    Lindahl, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Status of aflatoxin contamination in cow milk produced in smallholder dairy farms in urban and peri-urban areas of Nairobi County: a case study of Kasarani sub county, Kenya.2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1547095Article in journal (Refereed)
    Abstract [en]

    Introduction: Milk consumption in Kenya supersedes other countries in East Africa. However, milk contamination with aflatoxin M1 (AFM1) is common, but the magnitude of this exposure and the health risks are poorly understood and need to be monitored routinely. This study aimed at assessing the awareness, knowledge and practices of urban and peri-urban farmers about aflatoxins and determining the levels of aflatoxin contamination in on-farm milk in a selected area within Nairobi County. Materials and methods: A cross-sectional study was undertaken to assess aflatoxin contamination levels of milk in Kasarani sub-county. A total of 84 milk samples were collected from small-holder dairy farms and analyzed for AFM1 using Enzyme-Linked Immunosorbent Assay (ELISA). Results and Discussion: Ninety nine percent of the samples (83/84) analysed were contaminated with AFM1. The mean aflatoxin level was 84 ng/kg with 64% of the samples exceeding the EU legal limit of 50 ng/kg. Whereas 80% of the farmers were aware of aflatoxin, there was no correlation between farmers' knowledge and gender with AFM1 prevalence. Conclusion: This study concludes that AFM1 is a frequent contaminant in milk and there is need to enhance farmers awareness on mitigation.

  • 20. Kuboka, Maureen M
    et al.
    Imungi, Jasper K
    Njue, Lucy
    Mutua, Florence
    Grace, Delia
    Lindahl, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Occurrence of aflatoxin M1 in raw milk traded in peri-urban Nairobi, and the effect of boiling and fermentation.2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1625703Article in journal (Refereed)
    Abstract [en]

    Background: Dairy production in Kenya is important and dominated by small-holder farmers who market their produce through small-scale traders in the informal sector. Method: This study aimed to determine the prevalence of aflatoxin (AFM1) in informally marketed milk in peri-urban Nairobi, Kenya, and to assess knowledge of milk traders on aflatoxins using questionnaires. A total of 96 samples were analyzed for AFM1 using enzyme-linked immunosorbent assay. In addition, boiling and fermentation experiments were carried out in the laboratory. Results: All samples had AFM1 above the limit of detection (5 ng/kg) (mean of 290.3 ± 663.4 ng/kg). Two-thirds of the samples had AFM1 levels above 50 ng/kg and 7.5% of the samples exceeded 500 ng/kg. Most of the traders had low (69.8%) or medium (30.2%) knowledge. Educated (p = 0.01) and female traders (p= 0.04) were more knowledgeable. Experimentally, fermenting milk to lala (a traditional fermented drink) and yogurt significantly reduced AFM1 levels (p< 0.01) (71.8% reduction in lala after incubation at room temperature for 15 h, and 73.6% reduction in yogurt after incubation at 45ºC for 4h). Boiling had no effect. Conclusion: The study concluded that the prevalence of raw milk with AFM1 was high, while knowledge was low. Fermentation reduced the AFM1 levels.

  • 21. Lohmus, Mare
    et al.
    Lindström, Anders
    Björklund, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    HOW OFTEN DO THEY MEET? GENETIC SIMILARITY BETWEEN EUROPEAN POPULATIONS OF A POTENTIAL DISEASE VECTOR CULEX PIPIENS2012In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 2Article in journal (Refereed)
  • 22. Naguib, Mahmoud M
    et al.
    Verhagen, Josanne H
    Samy, Ahmed
    Eriksson, Per
    Fife, Mark
    Lundkvist, Åke
    Ellström, Patrik
    Järhult, Josef D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Avian influenza viruses at the wild-domestic bird interface in Egypt2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1575687Article in journal (Refereed)
    Abstract [en]

    Wild birds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) constitute the natural reservoir for low pathogenic avian influenza (LPAI) viruses. In Egypt, highly pathogenic avian influenza (HPAI) H5N1 and LPAI H9N2 viruses are endemic in domestic poultry, forming a threat to animal and human health and raising questions about the routes of introduction and mechanisms of persistence. Recently, HPAI H5N8 virus was also introduced into Egyptian domestic birds. Here we review the literature on the role of wild birds in the introduction and endemicity of avian influenza viruses in Egypt. Dabbling ducks in Egypt harbor an extensive LPAI virus diversity and may constitute the route of introduction for HPAI H5N1 and HPAI H5N8 viruses into Egypt through migration, however their role in the endemicity of HPAI H5N1, LPAI H9N2 and potentially other avian influenza virus (AIV) strains - by means of reassortment of viral genes - is less clear. Strengthened surveillance programs, in both domestic and wild birds, that include all LPAI virus subtypes and full genome sequencing are needed to better assess the wild-domestic bird interface and form a basis for evidence-based measures to limit and prevent AIV transmission between wild and domestic birds.

  • 23. Nguyen-Tien, Thang
    et al.
    Lundkvist, Åke
    Lindahl, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Urban transmission of mosquito-borne flaviviruses - a review of the risk for humans in Vietnam.2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1660129Article in journal (Refereed)
    Abstract [en]

    Vietnam is a tropical country where mosquito-borne diseases are common. This review explores the transmission of mosquito-borne flaviviruses in urban areas of Vietnam. It concludes that urban transmission has mainly been studied for Dengue virus, and so far, much less for Japanese encephalitis virus. Dengue is the most common flavivirus in Vietnam. Due to fast urbanization and favorable climatic conditions, the viral transmission concentrates mainly to large cities with high population density including Ha Noi, Nha Trang and Ho Chi Minh. Human cases of Japanese encephalitis have been controlled by an expanded immunization program. However, this virus is still circulating throughout the country, also in cities due to the pig rearing practices in urban and peri-urban areas. Zika virus is an additional major concern because it has long circulated in the Northern area and is now increasingly diagnosed in urban areas of the Central, Central Highlands and Southern regions using the same mosquito vectors as Dengue virus. There was alarge outbreak of Zika disease from 2016 to early 2017, with most infections observed in Ho Chi Minh city, the largest town in Vietnam. Other flaviviruses circulate in Vietnam but have not been investigated in terms of urban transmission.

  • 24.
    Nilsson, Kenneth
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Center for Clinical Research Dalarna. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Wallménius, Katarina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    Rundlöf-Nygren, Pernilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Strömdahl, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Påhlson, Carl
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.
    African tick bite fever in returning Swedish travellers: Report of two cases and aspects of diagnostics2017In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 7, no 1, article id 1343081Article in journal (Refereed)
    Abstract [en]

    Introduction: African tick-bite fever, caused by Rickettsia africae, is endemic in rural areas of sub-Saharan Africa and a possible cause of fever in returning Swedish travellers. Two patients are presented, and the advantages and disadvantages of different diagnostic methods are discussed.

    Patients and methods: Two middle-aged men fell ill with fever after returning home from South Africa. Both had single eschars and one also presented with a lymph node swelling. Samples were taken for serology, general bacterial culture from the wound (Patient 1) using a swab and additionally for Patient 2 PCR of a skin biopsy from the eschar.

    Results and discussion: Both patients seroconverted one month after onset. Real-time PCR of the biopsy was positive, where sequencing of the gltA gene was 99–100% consistent with R. africae. A drop of fluid from the biopsy contained a sufficient number of bacteria to also allow for isolation of rickettsiae in Vero cell culture. Direct molecular detection by PCR from a swab used for bacteria culture from the eschar from Patient 1 also yielded a positive result. In conclusion, the findings highlight the usefulness of swabs for early non-invasive diagnosis of African tick-bite fever in febrile travellers.

  • 25.
    Pauksens, Karlis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Long-term follow-up in patients with HIV vaccinated with pandemic influenza A(H1N1)/09 AS03-adjuvanted split virion vaccine and seasonal trivalent influenza split virion vaccine2013In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 3, p. 20766-Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION:

    In Sweden in 2009, two doses of the pandemic influenza A(H1N1)/09 AS03-adjuvanted split virion vaccine were recommended for those with HIV infection along with one dose of seasonal trivalent influenza vaccine (TIV). At that time, no data for HIV patients and their response to the adjuvanted vaccine were available.

    METHODS:

    Forty-two HIV-infected individuals were vaccinated with the pandemic vaccine on study days 0 and 28. Twenty-one of them received TIV on day 56 and 21 did not. Serum samples were taken at these time points, and also on day 86 and after 1 year for serologic analyses.

    RESULTS:

    Before vaccination, none of the 42 patients had putatively protective levels of antibodies (haemagglutination inhibition [HI] titres ≥1:40) to the pandemic-like strain A/California/7/2009 H1N1. After dose 1, the seroprotection rate (SPR) and seroconversion rate (SCR) were both 69% (29 of 42). After dose 2, the SPR and SCR were 89 and 86%, respectively. At 1 year, 10 (34%) of 29 had protective antibodies and 16 (62%) of 26 who had had protective antibody levels had lost them. There was a retained factor increase of the geometric mean titre (GMT) of 3.9. Serological analyses could be performed in 19 subjects who were vaccinated with TIV and in 21 who were not. Protective antibodies to the three strains before vaccination were 20-37%. The SCR was 26% to A/Brisbane/59/2007 H1N1, 47% to A/Uruguay/10/2007/ H3N2 and 42% to B/Brisbane/60/2008. At 1 year, the factor increase of GMT was 1.8 to the two influenza A strains.

    CONCLUSION:

    Two doses of adjuvanted influenza vaccine improved the SCR and the SPR among HIV-infected subjects. Long-term follow-up indicates revaccination in the next influenza season whether they received an adjuvanted or non-adjuvanted influenza vaccine.

  • 26.
    Rashid, Mahmudur
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. 1984.
    Rakib, Mufti Mahmud
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Badrul, Hasan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Antimicrobial-resistant and ESBL-producing Escherichia coli in different ecological niches in Bangladesh2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, article id 26712Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION:

    The rapid and wide-scale environmental spread of multidrug-resistant bacteria in different ecosystems has become a serious issue in recent years.

    OBJECTIVES:

    To investigate the epidemiology of antimicrobial resistance and extended spectrum beta-lactamase (ESBL) in Bangladeshi wild birds and aquatic environments, samples were taken from Open Bill Stork (Anastomus oscitans) (OBS) and the nearby water sources.

    METHODS:

    Water and fresh fecal samples were collected from several locations. All samples were processed and cultured for Escherichia coli and tested for antibiotic susceptibility against commonly used antibiotics. ESBL producers were characterized at genotypic level using polymerase chain reaction (PCR), sequencing, multilocus sequence typing, and rep-PCR.

    RESULTS AND DISCUSSION:

    A total of 76 E. coli isolates from the 170 OBS and 8 E. coli isolates from three river sources were isolated. In total, 29% of E. coli isolated from OBS and all of the E. coli isolated from water sources were resistant to at least one of the tested antimicrobials. Resistant phenotypes were observed with all antimicrobials except tigecycline, gentamicin, imipenem, and chloramphenicol. Multidrug resistance was observed in 2.6% of OBS and 37.5% of the water isolates. Also, 1.2% of the ESBL-producing E. coli were isolated from OBS, whereas 50% of the E. coli isolated from water sources were ESBL producers possessing the CTX-M-15 gene. The most concerning aspect of our findings was the presence of human-associated E. coli sequence types in the water samples, for example, ST156-complex156, ST10-complex10 and ST46.

    CONCLUSION:

    This study reports the presence of multidrug-resistant ESBL-producing E. coli in OBSs and nearby aquatic sources in Bangladesh

  • 27. Shome, Rajeswari
    et al.
    Deka, Ram Pratim
    Sahay, Swati
    Grace, Delia
    Lindahl, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Seroprevalence of hemorrhagic septicemia in dairy cows in Assam, India.2019In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 9, no 1, article id 1604064Article in journal (Refereed)
    Abstract [en]

    Hemorrhagic septicemia (HS) is a highly fatal disease caused by Pasteurella multocida that often cause outbreaks in buffalo and cattle in India, and thus is a major cause of production losses. It is one of the livestock diseases with the highest mortality, and despite available vaccines, outbreaks still occur. To assess the seroprevalence in the state of Assam, Northeast India, 346 serum samples from cows from 224 randomly selected households, from both urban and rural areas of three districts, were tested with a commercial ELISA. In total 88 cows were seropositive (25.4%), and indigenous cattle were significantly more seropositive (33.5%) compared to the crossbred cattle (18.5%) (p = 0.002). Herd prevalence was 35.7%, and more rural farms (47.4%) were positive compared to the urban farms (23.6%) (p < 0.001). No other risk factors were identified in this study. Only one farm had vaccinated against HS, but there were no seropositive animals detected in that herd. This study shows that HS is highly prevalent in Assam. Considering the importance of dairy production in India, and the dependence of the rural Assam population on farming and livestock keeping, more extensive vaccination campaigns would be important.

  • 28.
    Starlander, Gustaf
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Wirén, Marcus
    Melhus, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    First documented case of a Staphylococcus lugdunensis strain carrying the mecA gene in Northern Europe2011In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 1, p. 8410-Article in journal (Refereed)
    Abstract [en]

    Staphylococcus lugdunensis is a clinically common wound pathogen belonging to coagulase-negative staphylococci. We herein report the first case of a S. lugdunensis isolate carrying the mecA gene in Northern Europe.

  • 29. Stedt, Johan
    et al.
    Bonnedahl, Jonas
    Hernandez, Jorge
    McMahon, Barry J
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Hasan, Badrul
    UCD School of Agriculture & Food Science, University College Dublin, Belfield, Dublin, Ireland.
    Olsen, Björn
    UCD School of Agriculture & Food Science, University College Dublin, Belfield, Dublin, Ireland.
    Drobni, Mirva
    UCD School of Agriculture & Food Science, University College Dublin, Belfield, Dublin, Ireland.
    Waldenström, Jonas
    Antibiotic resistance patterns in Escherichia coli from gulls in nine European countries2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, p. 21565-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The prevalence of antibiotic resistant faecal indicator bacteria from humans and food production animals has increased over the last decades. In Europe, resistance levels in Escherichia coli from these sources show a south-to-north gradient, with more widespread resistance in the Mediterranean region compared to northern Europe. Recent studies show that resistance levels can be high also in wildlife, but it is unknown to what extent resistance levels in nature conform to the patterns observed in human-associated bacteria.

    METHODS: To test this, we collected 3,158 faecal samples from breeding gulls (Larus sp.) from nine European countries and tested 2,210 randomly isolated E. coli for resistance against 10 antibiotics commonly used in human and veterinary medicine.

    RESULTS: Overall, 31.5% of the gull E. coli isolates were resistant to ≥1 antibiotic, but with considerable variation between countries: highest levels of isolates resistant to ≥1 antibiotic were observed in Spain (61.2%) and lowest levels in Denmark (8.3%). For each tested antibiotic, the Iberian countries were either the countries with the highest levels or in the upper range in between-country comparisons, while northern countries generally had a lower proportion of resistant E. coli isolates, thereby resembling the gradient of resistance seen in human and food animal sources.

    CONCLUSION: We propose that gulls may serve as a sentinel of environmental levels of antibiotic resistant E. coli to complement studies of human-associated microbiota.

  • 30.
    Storberg, Viktor
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, International Maternal and Child Health (IMCH).
    ESBL-producing Enterobacteriaceae in Africa: a non-systematic literature review of research published 2008-20122014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, p. 20342-Article in journal (Refereed)
    Abstract [en]

    Introduction: Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBL) has been found all over the world, and risk factors for acquiring these bacteria involve hospital care and antibiotic treatment. Surveillance studies are present in Europe, North America, and Asia, but there is no summarizing research published on the situation in Africa.

    Aim: This review aims to describe the prevalence of ESBL-producing Enterobacteriaceae in hospital and community settings in Africa and the ESBL genes involved. Method: A non-systematic literature search was performed in PubMed. All articles published between 2008 and 2012 were screened and read in full text. Relevant articles were assessed for quality of evidence and included in the review. Articles were divided into regional areas in Africa and tabulated.

    Results: ESBL-producing Enterobacteriaceae in hospitalized patients and in communities varies largely between countries and specimens but is common in Africa. ESBLs (class A and D) and plasmid-encoded AmpC (pAmpC) were regularly found, but carbapenemases were also present.

    Conclusion: ESBL-producing Enterobacteriaceae in hospital and community settings in Africa is common. Surveillance of antimicrobial resistance needs to be implemented in Africa to tailor interventions targeted at stopping the dissemination of ESBL-producing Enterobacteriaceae.

  • 31. Svebrant, Sofia
    et al.
    Olsen, Therese
    Larsson, Jim
    Öhagen, Patrik
    Söderström, Hanna
    Järhult, Josef D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    The enzyme toilet rim block “pCure” does not efficiently remove drug residues in a hospital setting - exemplifying the importance of on-site implementation testing2018In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 8, no 1Article in journal (Refereed)
  • 32.
    Söderqvist, Karin
    et al.
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ahmed Osman, Omneya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wolff, Cecilia
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vågsholm, Ivar
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Boqvist, Sofia
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad​2017In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 7, no 1, article id 1328963Article in journal (Refereed)
    Abstract [en]

    Introduction: Ready-to-eat (RTE) leafy vegetables have a natural leaf microbiota that changes during different processing and handling steps from farm to fork. The objectives of this study were (i) to compare the microbiota of RTE baby spinach and mixed-ingredient salad before and after seven days of storage at 8°C or 15°C; (ii) to explore associations between bacterial communities and the foodborne pathogens Listeria monocytogenes, pathogenic Yersinia enterocolitica, and pathogen model organism Escherichia coli O157:H7 gfp+ when experimentally inoculated into the salads before storage; and (iii) to investigate if bacterial pathogens may be detected in the 16S rRNA amplicon dataset. Material and methods: The microbiota was studied by means of Illumina 16S rRNA amplicon sequencing. Subsets of samples were inoculated with low numbers (50-100 CFU g(-1)) of E. coli O157:H7 gfp+, pathogenic Y. enterocolitica or L. monocytogenes before storage. Results and discussion: The composition of bacterial communities changed during storage of RTE baby spinach and mixed-ingredient salad, with Pseudomonadales as the most abundant order across all samples. Although pathogens were present at high viable counts in some samples, they were only detected in the community-wide dataset in samples where they represented approximately 10% of total viable counts. Positive correlations were identified between viable counts of inoculated strains and the abundance of Lactobacillales, Enterobacteriales, and Bacillales, pointing to positive interactions or similar environmental driver variables that may make it feasible to use such bacterial lineages as indicators of microbial health hazards in leafy vegetables. The data from this study contribute to a better understanding of the bacteria present in RTE salads and may help when developing new types of biocontrol agents.​.

  • 33.
    Tano, Eva
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Melhus, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Level of decontamination after washing textiles at 60°C or 70°C followed by tumble drying2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, article id 24314Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Several major outbreaks in healthcare facilities have occurred with the emergence of multi-resistant bacteria. A possible route for dissemination is the hospital textiles and inadequate laundering of them. The aim of this study was to develop an easy-to-use method for simulating the laundering process of hospital textiles, and thereafter apply the method when evaluating the decontaminating efficacy of two different washing temperatures.

    METHODS: The laundering process, including tumble drying, took place at two professional laundries. Enterococcus faecium was used as bioindicator.

    RESULTS: The results showed that a lowering of the washing temperature from 70°C to 60°C did not affect the decontamination efficacy; the washing cycle alone reduced the number of bacteria with 3-5 log10 CFU, whereas the following tumble drying reduced the bacterial numbers with another 3-4 log10 CFU, yielding the same final result independent of washing temperature. Without tumble drying, there was an obvious risk of adding non-fermenting gram-negative bacteria to the fabric. These bacteria originated from the washing cycle.

    CONCLUSION: A simple method to simulate hospital laundering was developed. To save energy, it is possible to use a washing temperature of 60°C, but the washing cycle should be followed by tumble drying, and the whole laundering process needs to be monitored to maintain sufficient textile hygiene.

  • 34.
    Verner-Carlsson, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lõhmus, Mare
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sundström, Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Strand, Tanja M
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Verkerk, Monique
    Reusken, Chantal
    Yoshimatsu, Kumiko
    Arikawa, Jiro
    van de Goot, Frank
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    First evidence of Seoul hantavirus in the wild rat population in the Netherlands2015In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 5, p. 27215-Article in journal (Refereed)
    Abstract [en]

    We report the first detection of Seoul hantavirus (SEOV)-specific antibodies in the wild brown rat population in the Netherlands. SEOV-reactive antibodies were found in three rats out of 16 in a repeated series of tests including immunofluorescence assay, immunoblot, and enzyme-linked immunosorbent assay. Focus reduction neutralization test confirmed the presence of SEOV-specific antibodies, and reverse-transcription polymerase chain reaction (RT-PCR) confirmed the presence of hantaviral RNA. This discovery follows the recent findings of SEOV infections in wild and pet brown rats and humans in England, Wales, France, Belgium, and Sweden, indicating an even higher importance of this hantavirus for public health in large areas of Europe.

  • 35. Wallerström, Sofie
    et al.
    Lagerqvist, Nina
    Temperton, Nigel J
    Cassmer, Michaela
    Moreno, Ana
    Karlsson, Malin
    Leijon, Mikael
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Falk, Kerstin I
    Detection of antibodies against H5 and H7 strains in birds: evaluation of influenza pseudovirus particle neutralization tests2014In: Infection Ecology & Epidemiology, ISSN 2000-8686, E-ISSN 2000-8686, Vol. 4, article id 23011Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION: Avian influenza viruses circulate in bird populations, and it is important to maintain and uphold our knowledge of the viral strains that are currently of interest in this context. Here, we describe the use of hemagglutinin-pseudotype retroviruses based on highly pathogenic influenza viruses for the screening of avian sera for influenza A antibodies. Our aim was also to determine whether the pseudovirus neutralization tests that we assessed were sensitive and simple to use compared to the traditional methods, including hemagglutination inhibition assays and microneutralization tests.

    MATERIAL AND METHODS: H5 and H7 pseudovirus neutralization tests were evaluated by using serum from infected rabbits. Subsequently, the assays were further investigated using a panel of serum samples from avian species. The panel contained samples that were seropositive for five different hemagglutinin subtypes as well as influenza A seronegative samples.

    RESULTS AND DISCUSSION: The results suggest that the pseudovirus neutralization test is an alternative to hemagglutination inhibition assays, as we observed comparable titers to those of both standard microneutralizations assays as well as hemagglutinin inhibition assays. When evaluated by a panel of avian sera, the method also showed its capability to recognize antibodies directed toward low-pathogenic H5 and H7. Hence, we conclude that it is possible to use pseudoviruses based on highly pathogenic avian influenza viruses to screen avian sera for antibodies directed against influenza A subtypes H5 and H7.

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