1. |
- Mueller, Ralf C., et al.
(author)
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A high-quality genome and comparison of short-versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
- 2021
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In: GigaScience. - : Oxford University Press. - 2047-217X. ; 10:12
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Journal article (peer-reviewed)abstract
- Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long -read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.
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2. |
- Atterby, Clara, et al.
(author)
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The Potential of Isolation Source to Predict Colonization in Avian Hosts : A Case Study in Campylobacter jejuni Strains From Three Bird Species
- 2018
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
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Journal article (peer-reviewed)abstract
- Campylobacter jejuni is the primary cause of bacterial gastroenteritis worldwide, infecting humans mostly through consumption of contaminated poultry. C. jejuni is common in the gut of wild birds, and shows distinct strain-specific association to particular bird species. This contrasts with farm animals, in which several genotypes co-exist. It is unclear if the barriers restricting transmission between host species of such specialist strains are related to environmental factors such as contact between host species, bacterial survival in the environment, etc., or rather to strain specific adaptation to the intestinal environment of specific hosts. We compared colonization dynamics in vivo between two host-specific C. jejuni from a song thrush (ST-1304 complex) and a mallard (ST-995), and a generalist strain from chicken (ST-21 complex) in a wild host, the mallard (Anas platyrhynchos). In 18-days infection experiments, the song thrush strain showed only weak colonization and was cleared from all birds after 10 days, whereas both mallard and chicken strains remained stable. When the chicken strain was given 4 days prior to co-infection of the same birds with a mallard strain, it was rapidly outcompeted by the latter. In contrast, when the mallard strain was given 4 days prior to co-infection with the chicken strain, the mallard strain remained and expansion of the chicken strain was delayed. Our results suggest strain-specific differences in the ability of C. jejuni to colonize mallards, likely associated with host origin. This difference might explain observed host association patterns in C. jejuni from wild birds.
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3. |
- Eriksson, Per, et al.
(author)
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Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species - Support for the Community Concept
- 2019
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 10
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Journal article (peer-reviewed)abstract
- Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.
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4. |
- Helin, Anu S., et al.
(author)
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A rapid and transient innate immune response to avian influenza infection in mallards
- 2018
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In: Molecular Immunology. - : Elsevier. - 0161-5890 .- 1872-9142. ; 95, s. 64-72
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Journal article (peer-reviewed)abstract
- The vertebrate innate immune system provides hosts with a rapid, non-specific response to a wide range of invading pathogens. However, the speed and duration of innate responses will be influenced by the co-evolutionary dynamics of specific host-pathogen combinations. Here, we show that low pathogenic avian influenza virus (LPAI) subtype H1N1 elicits a strong but extremely transient innate immune response in its main wildlife reservoir, the mallard (Anas platyrhynchos). Using a series of experimental and methodological improvements over previous studies, we followed the expression of retinoic acid inducible gene 1 (RIG-I) and myxovirus resistance gene (Mx) in mallards semi-naturally infected with low pathogenic H1N1. One day post infection, both RIG-I and Mx were significantly upregulated in all investigated tissues. By two days post infection, the expression of both genes had generally returned to basal levels, and remained so for the remainder of the experiment. This is despite the fact that birds continued to actively shed viral particles throughout the study period. We additionally show that the spleen plays a particularly active role in the innate immune response to LPAI. Waterfowl and avian influenza viruses have a long co-evolutionary history, suggesting that the mallard innate immune response has evolved to provide a minimum effective response to LPAIs such that the viral infection is brought under control while minimising the damaging effects of a sustained immune response.
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5. |
- Helin, Anu S., et al.
(author)
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Expression of immune genes RIG-I and Mx in mallard ducks infected with low pathogenic avian influenza (LPAI) : A dataset
- 2018
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In: Data in Brief. - : Elsevier. - 2352-3409. ; 18, s. 1562-1566
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Journal article (peer-reviewed)abstract
- This article provides data on primer sequences used to amplify the innate immune genes RIG-I and Mx and a set of normalizing reference genes in mallards (Anal platyrhynchos), and shows which reference genes are stable, per tissue, for our experimental settings. Data on the expressional changes of these two genes over a time-course of infection with low pathogenic avian influenza virus (LPAI) are provided. Individual-level data are also presented, including LPAI infection load, and per tissue gene expression of RIG-I and Mx. Gene expression in two outlier individuals is explored in more depth. (C) 2018 The Authors. Published by Elsevier Inc.
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6. |
- Naguib, Mahmoud, et al.
(author)
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A Comparison of Host Responses to Infection with Wild-Type Avian Influenza Viruses in Chickens and Tufted Ducks
- 2023
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In: Microbiology Spectrum. - : American Society for Microbiology. - 2165-0497. ; 11:4
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Journal article (peer-reviewed)abstract
- Cross-species transmission of influenza A virus (IAV) from wild waterfowl to poultry is the first step in a chain of events that can ultimately lead to exposure and infection of humans. Herein, we study the outcome of infection with eight different mallard-origin IAV subtypes in two different avian hosts: tufted ducks and chickens. We found that infection and shedding patterns as well as innate immune responses were highly dependent on viral subtypes, host species, and inoculation routes. For example, intraoesophageal inoculation, commonly used in mallard infection experiments, resulted in no infections in contrast to oculonasal inoculation, suggesting a difference in transmission routes. Despite H9N2 being endemic in chickens, inoculation of mallard-origin H9N2 failed to cause viable infection beyond 1 day postinfection in our study design. The innate immune responses were markedly different in chickens and tufted ducks, and despite the presence of retinoic acid-inducible gene-I (RIG-I) in tufted duck transcriptomes, it was neither up nor downregulated in response to infection. Overall, we have revealed the heterogeneity of infection patterns and responses in two markedly different avian hosts following a challenge with mallard-origin IAV. These virus-host interactions provide new insights into important aspects of interspecies transmission of IAV.IMPORTANCE Our current findings highlight important aspects of IAV infection in birds that have implications for our understanding of its zoonotic ecology. In contrast to mallards where the intestinal tract is the main site of IAV replication, chickens and tufted ducks show limited or no signs of intestinal infection suggesting that the fecal-oral transmission route might not apply to all bird IAV host species. Our results indicate that mallard-origin IAVs undergo genetic changes upon introduction into new hosts, suggesting rapid adaptation to a new environment. However, similar to the mallard, chickens and tufted ducks show a limited immune response to infection with low pathogenic avian influenza viruses. These findings and future studies in different IAV hosts are important for our understanding of barriers to IAV transmission between species and ultimately from the wild reservoir to humans. Our current findings highlight important aspects of IAV infection in birds that have implications for our understanding of its zoonotic ecology. In contrast to mallards where the intestinal tract is the main site of IAV replication, chickens and tufted ducks show limited or no signs of intestinal infection suggesting that the fecal-oral transmission route might not apply to all bird IAV host species.
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7. |
- Ramey, Andrew M., et al.
(author)
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Antibiotic-Resistant Escherichia coli in Migratory Birds Inhabiting Remote Alaska
- 2018
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In: EcoHealth. - : Springer. - 1612-9202 .- 1612-9210. ; 15:1, s. 72-81
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Journal article (peer-reviewed)abstract
- We explored the abundance of antibiotic-resistant Escherichia coli among migratory birds at remote sites in Alaska and used a comparative approach to speculate on plausible explanations for differences in detection among species. At a remote island site, we detected antibiotic-resistant E. coli phenotypes in samples collected from glaucous-winged gulls (Larus glaucescens), a species often associated with foraging at landfills, but not in samples collected from black-legged kittiwakes (Rissa tridactyla), a more pelagic gull that typically inhabits remote areas year-round. We did not find evidence for antibiotic-resistant E. coli among 347 samples collected primarily from waterfowl at a second remote site in western Alaska. Our results provide evidence that glaucous-winged gulls may be more likely to be infected with antibiotic-resistant E. coli at remote breeding sites as compared to sympatric black-legged kittiwakes. This could be a function of the tendency of glaucous-winged gulls to forage at landfills where antibiotic-resistant bacterial infections may be acquired and subsequently dispersed. The low overall detection of antibiotic-resistant E. coli in migratory birds sampled at remote sites in Alaska is consistent with the premise that anthropogenic inputs into the local environment or the relative lack thereof influences the prevalence of antibiotic-resistant bacteria among birds inhabiting the area.
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8. |
- van Dijk, Jacintha G. B., et al.
(author)
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A Comparative Study of the Innate Humoral Immune Response to Avian Influenza Virus in Wild and Domestic Mallards
- 2020
-
In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 11, s. 1-13
-
Journal article (peer-reviewed)abstract
- Domestic mallards (Anas platyrhynchos domesticus) are traditionally used as a model to investigate infection dynamics and immune responses to low pathogenic avian influenza viruses (LPAIVs) in free-living mallards. However, it is unclear whether the immune response of domestic birds reflects the response of their free-living counterparts naturally exposed to these viruses. We investigated the extent to which the innate humoral immune response was similar among (i) wild-type domestic mallards in primary and secondary infection with LPAIV H4N6 in a laboratory setting (laboratory mallards), (ii) wild-type domestic mallards naturally exposed to LPAIVs in a semi-natural setting (sentinel mallards), and (iii) free-living mallards naturally exposed to LPAIVs. We quantified innate humoral immune function by measuring non-specific natural antibodies (agglutination), complement activity (lysis), and the acute phase protein haptoglobin. We demonstrate that complement activity in the first 3 days after LPAIV exposure was higher in primary-exposed laboratory mallards than in sentinel and free-living mallards. LPAIV H4N6 likely activated the complement system and the acute phase response in primary-exposed laboratory mallards, as lysis was higher and haptoglobin lower at day 3 and 7 post-exposure compared to baseline immune function measured prior to exposure. There were no differences observed in natural antibody and haptoglobin concentrations among laboratory, sentinel, and free-living mallards in the first 3 days after LPAIV exposure. Our study demonstrates that, based on the three innate humoral immune parameters measured, domestic mallards seem an appropriate model to investigate innate immunology of their free-living counterparts, albeit the innate immune response of secondary-LPAIV exposed mallards is a better proxy for the innate immune response in pre-exposed free-living mallards than that of immunologically naive mallards.
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9. |
- Akaberi, Dario, 1989-
(author)
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Identification of protease inhibitors against Flaviviruses and Coronaviruses
- 2023
-
Doctoral thesis (other academic/artistic)abstract
- Vector-borne flaviviruses and coronaviruses of zoonotic origins are important human pathogens and represent a serious threat to public health worldwide. Flaviviruses can be found on all continents, apart from Antarctica, where they are transmitted by arthropod vectors causing millions of infections every year. While most of the infections are mild or asymptomatic, flaviviruses like dengue and yellow fever viruses can cause potentially lethal hemorrhagic fever and shock syndrome. Neurotropic flaviviruses like West Nile, Japanese encephalitis, and Tick-borne encephalitis (TBEV) can cause meningoencephalitis with long-term symptoms. Coronaviruses, and in particular betacoronaviruses of zoonotic origin like SARS (2003) and MERS (2012), have been periodically emerging since the early 2000s causing outbreaks of severe respiratory syndrome. The latest example is SARS-CoV-2 that after causing a cluster of infection in the Chinese city of Wuhan, spread all over the world causing at present over 6.9 million deaths. Although vaccines are essential in preventing infections or severe disease and hospitalization in the case of SARS-CoV-2, antivirals represent an extremely valuable tool for treatment and prevention of current and future flavivirus and coronavirus infections. In the work presented in this thesis we have used a combination of in silico and in vitro techniques to identify and test the activity of potential inhibitors of viral proteases. In our first study (paper 1) we unexpectedly identified an HIV protease inhibitor with in vitro activity against ZIKV NS2B-NS3 protease. The inhibitor was identified by virtual screening of a library of known protease inhibitors, evaluated by molecular dynamics simulation and finally tested against recombinant ZIKV protease using a FRET-based enzymatic assay. The same combination of molecular docking and molecular dynamics simulations were also used to correctly predict the activity of a known pan-Flavivirus protease inhibitor against TBEV protease (paper 2). As a result, we were the first to report peptide-based compounds with in vitro activity against TBEV. After the outbreak of the COVID-19 we switched our attention to SARS-CoV-2. We first tested the inhibitory effect of the broad-spectrum antiviral nitric oxide (NO) and found that the NO-releasing compound SNAP had a dose dependent inhibitory effect on SARS-CoV-2 replication in cell-based assays (paper 3). We speculated that SNAP could inhibit SARS-COV-2 protease by trans-nitration of the catalytic Cys145 of SARS-CoV-2 main protease and found that SNAP had a dose dependent inhibitory effect on recombinant SARS-CoV-2 Mpro protease activity in an in vitro enzymatic assay. In our last study (paper 4) we identified a new class of potent SARS-CoV-2 protease inhibitors through the affinity screening of DNA-encoded-chemical libraries containing 4.2 billion compounds. The identified compounds inhibited recombinant SARS-CoV-2 protease with IC50 as low as 25 nM and had a dose dependent antiviral effect in the low micromolar range in infected Calu-3 and Caco-2 cell lines.
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10. |
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11. |
- Akaberi, Dario, 1989-, et al.
(author)
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Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro
- 2020
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In: Redox Biology. - : Elsevier. - 2213-2317. ; 37
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Journal article (peer-reviewed)abstract
- The ongoing SARS-CoV-2 pandemic is a global public health emergency posing a high burden on nations' health care systems and economies. Despite the great effort put in the development of vaccines and specific treatments, no prophylaxis or effective therapeutics are currently available. Nitric oxide (NO) is a broad-spectrum antimicrobial and a potent vasodilator that has proved to be effective in reducing SARS-CoV replication and hypoxia in patients with severe acute respiratory syndrome. Given the potential of NO as treatment for SARS-CoV-2 infection, we have evaluated the in vitro antiviral effect of NO on SARS-CoV-2 replication. The NO-donor S-nitroso-N-acetylpenicillamine (SNAP) had a dose dependent inhibitory effect on SARS-CoV-2 replication, while the non S-nitrosated NAP was not active, as expected. Although the viral replication was not completely abolished (at 200 μM and 400 μM), SNAP delayed or completely prevented the development of viral cytopathic effect in treated cells, and the observed protective effect correlated with the level of inhibition of the viral replication. The capacity of the NO released from SNAP to covalently bind and inhibit SARS-CoV-2 3CL recombinant protease in vitro was also tested. The observed reduction in SARS-CoV-2 protease activity was consistent with S-nitrosation of the enzyme active site cysteine.
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12. |
- Akaberi, Dario, et al.
(author)
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Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors
- 2021
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In: Antiviral Research. - : Elsevier. - 0166-3542 .- 1872-9096. ; 190
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Journal article (peer-reviewed)abstract
- Tick-borne encephalitis (TBE) is a severe neurological disorder caused by tick-borne encephalitis virus (TBEV), a member of the Flavivirus genus. Currently, two vaccines are available in Europe against TBEV. However, TBE cases have been rising in Sweden for the past twenty years, and thousands of cases are reported in Europe, emphasizing the need for antiviral treatments against this virus. The NS2B-NS3 protease is essential for flaviviral life cycle and has been studied as a target for the design of inhibitors against several well-known flaviviruses, but not TBEV. In the present study, Compound 86, a known tripeptidic inhibitor of dengue (DENV), West Nile (WNV) and Zika (ZIKV) proteases, was predicted to be active against TBEV protease using a combination of in silico techniques. Further, Compound 86 was found to inhibit recombinant TBEV protease with an IC50 = 0.92 mu M in the in vitro enzymatic assay. Additionally, two more peptidic analogues were synthetized and they displayed inhibitory activities against both TBEV and ZIKV proteases. In particular, Compound 104 inhibited ZIKV protease with an IC50 = 0.25 mu M. These compounds represent the first reported inhibitors of TBEV protease to date and provides valuable information for the further development of TBEV as well as pan-flavivirus protease inhibitors.
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13. |
- Albinsson, Bo, et al.
(author)
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Multi laboratory evaluation of ReaScan TBE IgM rapid test, 2016 to 2017
- 2020
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In: Eurosurveillance. - : EUR CENTRE DIS PREVENTION & CONTROL. - 1025-496X .- 1560-7917. ; 25:12, s. 27-36
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Journal article (peer-reviewed)abstract
- Tick-borne encephalitis (TBE) is a potentially severe neurological disease caused by TBE virus (TBEV). In Europe and Asia, TBEV infection has become a growing public health concern and requires fast and specific detection. Aim: In this observational study, we evaluated a rapid TBE IgM test, ReaScan TBE, for usage in a clinical laboratory setting. Methods: Patient sera found negative or positive for TBEV by serological and/or molecular methods in diagnostic laboratories of five European countries endemic for TBEV (Estonia, Finland, Slovenia, the Netherlands and Sweden) were used to assess the sensitivity and specificity of the test. The patients' diagnoses were based on other commercial or quality assured in-house assays, i.e. each laboratory's conventional routine methods. For specificity analysis, serum samples from patients with infections known to cause problems in serology were employed. These samples tested positive for e.g. Epstein-Barr virus, cytomegalovirus and Anaplasma phagocytophilum, or for flaviviruses other than TBEV, i.e. dengue, Japanese encephalitis, West Nile and Zika viruses. Samples from individuals vaccinated against flaviviruses other than TBEV were also included. Altogether, 172 serum samples from patients with acute TBE and 306 TBE IgM negative samples were analysed. Results: Compared with each laboratory's conventional methods, the tested assay had similar sensitivity and specificity (99.4% and 97.7%, respectively). Samples containing potentially interfering antibodies did not cause specificity problems. Conclusion: Regarding diagnosis of acute TBEV infections, ReaScan TBE offers rapid and convenient complementary IgM detection. If used as a stand-alone, it can provide preliminary results in a laboratory or point of care setting.
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14. |
- Atterby, Clara
(author)
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Antibiotic resistance gone wild : A One Health perspective on carriage, selection and transmission of Extended-Spectrum Cephalosporinase- and Carbapenemase-producing Enterobacteriaceae
- 2019
-
Doctoral thesis (other academic/artistic)abstract
- Antibiotics have saved millions of lives since they came into clinical use during the Second World War in the 1940s. Today, our effective use of antibiotics is under great threat due to emerging antibiotic resistance in bacteria. This thesis addresses the problems of antibiotic resistance from a ”One Health” perspective. The focus is on antibiotic resistant Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) in the environment and wildlife, and also considering the situation in healthy humans and livestock. In Paper I-III, high occurrence of Extended-Spectrum Beta-Lactamase (ESBL) -producing E. coli and/or K. pneumoniae was detected in fecal samples from wild birds, and the bacteria had genetic similarities to bacteria that cause disease in humans. Proximity to humans was associated with higher occurrence of cephalosporinase (ESBL and pAmpC)-producing E. coli in wild gulls. In Paper IV, ciprofloxacin resistant E. coli was enriched in the gut of mallards exposed to low concentrations of ciprofloxacin, and plasmid conjugation between E. coli bacteria readily took place. In Paper V, carbapenem resistant and blaOXA-48 harbouring- E. coli/K. pneumoniae was rare, but present in healthy humans in rural Cambodia, while cephalosporinase-producing E. coli/K. pneumoniae was common in both humans and livestock. The same ESBL/pAmpC genes were detected in humans and livestock, and exposure to animal manure and slaughter products were risk factors for fecal carriage in humans.In conclusion, wild birds can function as potential resistance reservoirs and sentinels for antibiotic resistant E. coli. Environmental pollution from humans is the primary source for antibiotic resistant Enterobacteriaceae found in wildlife, but selection for antibiotic resistant bacteria may also occur in wild birds. The results indicate that transmission of cephalosporinase-producing E. coli/K. pneumoniae occur between wildlife, humans and livestock, but more in-depth molecular work is needed to determine the mechanisms of dissemination. The high community carriage of multidrug-resistant bacteria in rural Cambodia is worrying and highlights Southeast Asia as a hotspot for antibiotic resistance. Antibiotic resistance surveillance is biased towards high-income countries and research should be focused more on low- and middle-income countries, and also include the important “One Health” perspective.
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15. |
- Atterby, Clara, et al.
(author)
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ESBL-producing Escherichia coli in Swedish gulls : A case of environmental pollution from humans?
- 2017
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In: PLOS ONE. - San Francisco, CA, United States : PLOS. - 1932-6203. ; 12:12
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Journal article (peer-reviewed)abstract
- ESBL-producing bacteria are present in wildlife and the environment might serve as a resistance reservoir. Wild gulls have been described as frequent carriers of ESBL-producing E. coli strains with genotypic characteristics similar to strains found in humans. Therefore, potential dissemination of antibiotic resistance genes and bacteria between the human population and wildlife need to be further investigated. Occurrence and characterization of ESBL-producing E. coli in Swedish wild gulls were assessed and compared to isolates from humans, livestock and surface water collected in the same country and similar time-period. Occurrence of ESBL-producing E. coli in Swedish gulls is about three times higher in gulls compared to Swedish community carriers (17% versus 5%) and the genetic characteristics of the ESBL-producing E. coli population in Swedish wild gulls and Swedish human are similar. ESBL-plasmids IncF-and IncI1-type carrying ESBL-genes blaCTX-M-15 or blaCTX-M-14 were most common in isolates from both gulls and humans, but there was limited evidence of clonal transmission. Isolates from Swedish surface water harbored similar genetic characteristics, which highlights surface waters as potential dissemination routes between wildlife and the human population. Even in a low-prevalence country such as Sweden, the occurrence of ESBL producing E. coli in wild gulls and the human population appears to be connected and the occurrence of ESBL-producing E. coli in Swedish gulls is likely a case of environmental pollution.
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16. |
- Atterby, Clara, et al.
(author)
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Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment
- 2021
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In: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 65:3
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Journal article (peer-reviewed)abstract
- Emergence and selection of antibiotic resistance following exposure to high antibiotic concentrations have been repeatedly shown in clinical and agricultural settings, whereas the role of the weak selective pressures exerted by antibiotic levels below the MIC (sub-MIC) in aquatic environments due to anthropogenic contamination remains unclear. Here, we studied how exposure to sub-MIC levels of ciprofloxacin enriches for Escherichia coli with reduced susceptibility to ciprofloxacin using a mallard colonization model. Mallards were inoculated with two isogenic extended-spectrum-beta-lactamase (ESBL)-encoding E. coli strains, differing only by a gyrA mutation that results in increased MICs of ciprofloxacin, and exposed to different levels of ciprofloxacin in their swimming water. Changes in the ratios of mutant to parental strains excreted in feces over time and ESBL plasmid spread within the gut microbiota from individual birds were investigated. Results show that in vivo selection of gyrA mutants occurred in mallards during exposure to ciprofloxacin at concentrations previously found in aquatic environments. During colonization, resistance plasmids were readily transferred between strains in the intestines of the mallards, but conjugation frequencies were not affected by ciprofloxacin exposure. Our results highlight the potential for enrichment of resistant bacteria in wildlife and underline the importance of reducing antibiotic pollution in the environment.
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17. |
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18. |
- Blum, Kristin M., et al.
(author)
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Removal of 30 active pharmaceutical ingredients in surface water under long-term artificial UV irradiation
- 2017
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In: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 176, s. 175-182
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Journal article (peer-reviewed)abstract
- This study investigated the i) kinetics, and ii) proportion of photolysis of 30 relatively stable active pharmaceutical ingredients (APIs) during artificial UV irradiation for 28 d in ammonium acetate buffer, filtered and unfiltered river water. Buffer was included to control removal kinetics under stable pH conditions and without particulate matter. Dark controls were used to determine removal due to other processes than photolysis and calculate the proportion of photolysis of the total removal. The removal of each API in each matrix was determined using online solid phase extraction/liquid chromatography tandem mass spectrometry (online SPE/LC-MS/MS). Most APIs transformed during the 28 d of UV irradiation and the dark controls showed that photolysis was the major removal process for the majority of the APIs studied. The half-lives ranged from 6 h (amitriptyline) in unfiltered river water to 884 h (37 d, carbamazepine) in buffer. In unfiltered river water, the proportion of APIs with short half-lives (<48 h) was much higher (29%) than in the other matrices (4%), probably due to additional organic carbon, which could have promoted indirect photolysis. Furthermore, two APIs, memantine and fluconazole, were stable in all three matrices, while alprazolam was stable in buffer and unfiltered river water and four additional APIs were stable in buffer. Considering the relatively long-term UV-exposure, this study enabled the investigation of environmentally relevant half-lives in natural waters. Many APIs showed high persistence, which is environmentally concerning and emphasizes the importance of further studies on their environmental fate and effects.
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19. |
- Bruhn-Olszewska, Bozena, et al.
(author)
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Loss of Y in leukocytes as a risk factor for critical COVID-19 in men.
- 2022
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In: Genome medicine. - : Springer Science and Business Media LLC. - 1756-994X. ; 14:1
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Journal article (peer-reviewed)abstract
- The COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk factor candidate in COVID-19 due to its prior association with many chronic age-related diseases, and its impact on immune gene transcription.Publicly available scRNA-seq data of PBMC samples derived from male patients critically ill with COVID-19 were reanalyzed, and LOY status was added to the annotated cells. We further studied LOY in whole blood for 211 COVID-19 patients treated at intensive care units (ICU) from the first and second waves of the pandemic. Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs.Reanalysis of available scRNA-seq data revealed LDNs and monocytes as the cell types most affected by LOY. Subsequently, DNA analysis indicated that 46%, 32%, and 29% of critically ill patients showed LOY above 5% cut-off in LDNs, granulocytes, and monocytes, respectively. Hence, the myeloid lineage that is crucial for the development of severe COVID-19 phenotype is affected by LOY. Moreover, LOY correlated with increasing WHO score (median difference 1.59%, 95% HDI 0.46% to 2.71%, p=0.025), death during ICU treatment (median difference 1.46%, 95% HDI 0.47% to 2.43%, p=0.0036), and history of vessel disease (median difference 2.16%, 95% HDI 0.74% to 3.7%, p=0.004), among other variables. In 16 recovered patients, sampled during ICU stay and 93-143 days later, LOY decreased significantly in whole blood and PBMCs. Furthermore, the number of LDNs at the recovery stage decreased dramatically (median difference 76.4 per 10,000 cell sorting events, 95% HDI 55.5 to 104, p=6e-11).We present a link between LOY and an acute, life-threatening infectious disease. Furthermore, this study highlights LOY as the most prominent clonal mutation affecting the myeloid cell lineage during emergency myelopoiesis. The correlation between LOY level and COVID-19 severity might suggest that this mutation affects the functions of monocytes and neutrophils, which could have consequences for male innate immunity.
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20. |
- Bröjer, Caroline, et al.
(author)
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Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir
- 2013
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In: Journal of Wildlife Diseases. - : Wildlife Disease Association. - 0090-3558 .- 1943-3700. ; 49:1, s. 103-113
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Journal article (peer-reviewed)abstract
- Low-pathogenic avian influenza (LPAI) viruses in wild birds are important as they can constitute the basis for the development of highly pathogenic avian influenza viruses or form part of human-adapted strains with pandemic potential. However, the pathogenesis of LPAI viruses is not well characterized in dabbling ducks, one of the natural reservoirs of LPAI viruses. Between 21 September 2009 and 21 December 2009, we used real-time reverse transcriptase polymerase chain reaction (q-PCR), histopathology, and immunohistochemistry (IHC) to study Mallards (Anas platyrhynchos) infected with an influenza A/H1N1 virus isolated from a wild Mallard in Sweden. The ducks were either inoculated intraesophageally ("artificial infection") or infected by virus shed by other ducks in the experiment ("contact infection"). The ducks were subjected to three low concentrations (80 ng/L, 1 mu g/L, and 80 mu g/L) of the active metabolite of oseltamivir (Tamiflu (R)), oseltamivir carboxylate (OC), which resulted in the development of the viral resistance mutation H274Y at 1 and 80 mu g/L. The LPAI virus infection was localized to the intestinal tract and cloacal bursa except in one Mallard. The exception was a duck euthanized 1 day postinoculation, whose infection was located solely in the lung, possibly due to intratracheal deposition of virus. The intestinal infection was characterized by occasional degenerating cells in the lamina propria and presence of viral antigen as detected by IHC, as well as positive q-PCR performed on samples from feces and intestinal contents. Histopathologic changes, IHC positivity, and viral shedding all indicated that the infection peaked early, around 2 days postinfection. Furthermore, more viral antigen and viral RNA were detected with IHC and q-PCR in the proximal parts early in the infection. There was no obvious difference in the course of the infection in artificial versus contact infection, when the level of OC was increased from 80 ng/L to 1 mu g/L (based on IHC and q-PCR), when the level of OC was increased to 80 mu/L, or when the resistance mutation H274Y developed (based on q-PCR).
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21. |
- Cabrera-Pardo, Jaime R., et al.
(author)
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A One Health - One World initiative to control antibiotic resistance : A Chile - Sweden collaboration
- 2019
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In: One Health. - : Elsevier BV. - 2352-7714. ; 8
-
Journal article (peer-reviewed)abstract
- Controlling antibiotic resistance is a global concern. The One Health initiative has provided a strategy to deal with this problem efficiently within a country. However, due to the global nature of the problem it is paramount not only to focus on specific countries, but to establish ways to avoid the development of antibiotic resistance in different geographical regions. In this letter, we propose a One Health - One World approach that would enable different countries to connect by sharing information about infections, outbreaks and surveillance. We believe such a strategy should be implemented worldwide in order to mitigate the development and dissemination of antibiotic resistance.
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22. |
- Chapman, Joanne R., et al.
(author)
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A Panel of Stably Expressed Reference Genes for Real-Time qPCR Gene Expression Studies of Mallards (Anas platyrhynchos)
- 2016
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:2
-
Journal article (peer-reviewed)abstract
- Determining which reference genes have the highest stability, and are therefore appropriate for normalising data, is a crucial step in the design of real-time quantitative PCR (qPCR) gene expression studies. This is particularly warranted in non-model and ecologically important species for which appropriate reference genes are lacking, such as the mallard-a key reservoir of many diseases with relevance for human and livestock health. Previous studies assessing gene expression changes as a consequence of infection in mallards have nearly universally used beta-actin and/or GAPDH as reference genes without confirming their suitability as normalisers. The use of reference genes at random, without regard for stability of expression across treatment groups, can result in erroneous interpretation of data. Here, eleven putative reference genes for use in gene expression studies of the mallard were evaluated, across six different tissues, using a low pathogenic avian influenza A virus infection model. Tissue type influenced the selection of reference genes, whereby different genes were stable in blood, spleen, lung, gastrointestinal tract and colon. beta-actin and GAPDH generally displayed low stability and are therefore inappropriate reference genes in many cases. The use of different algorithms (GeNorm and NormFinder) affected stability rankings, but for both algorithms it was possible to find a combination of two stable reference genes with which to normalise qPCR data in mallards. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies in ducks. The fact that nearly all previous studies of the influence of pathogen infection on mallard gene expression have used a single, non-validated reference gene is problematic. The toolkit of putative reference genes provided here offers a solid foundation for future studies of gene expression in mallards and other waterfowl.
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23. |
- Diez-Escudero, Anna, et al.
(author)
-
3D-printed porous Ti6Al4V alloys with silver coating combine osteocompatibility and antimicrobial properties
- 2022
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In: Biomaterials Advances. - : Elsevier. - 2772-9516 .- 2772-9508. ; 133
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Journal article (peer-reviewed)abstract
- Additive manufacturing allows for the production of porous metallic implants for use in orthopaedics, providing excellent mechanical stability and osseointegration. However, the increased surface area of such porous implants also renders them susceptible to bacterial colonization. In this work, two trabecular porous Ti6Al4V alloys produced by electron beam melting were investigated for their osteocompatibility and antimicrobial effects, comparing samples with a silver-coated surface to uncoated samples. Dense grit-blasted Ti samples were used for comparison. The porous samples had pore sizes of 500-600 mu m and 5 to 10 mu m surface roughness, the silver-coated samples contained 7 at.% Ag, resulting in a cumulative Ag release of 3.5 ppm up to 28 days. Silver reduced the adhesion of Staphylococcus aureus to porous samples and inhibited 72 h biofilm formation by Staphylococcus epidermidis but not that of S. aureus. Primary human osteoblast adhesion, proliferation and differentiation were not impaired in the presence of silver, and expression of osteogenic genes as well as production of mineralized matrix were similar on silver-coated and uncoated samples. Our findings indicate that silver coating of porous titanium implants can achieve antimicrobial effects without compromising osteocompatibility, but higher silver contents may be needed to yield a sustained protection against fast-growing bacteria.
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24. |
- Diez-Escudero, Anna, et al.
(author)
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Trabecular Titanium for Orthopedic Applications : Balancing Antimicrobial with Osteoconductive Properties by Varying Silver Contents
- 2022
-
In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 14:37, s. 41751-41763
-
Journal article (peer-reviewed)abstract
- Periprosthetic joint infection (PJI) and implant loosening are the most common complications after joint replacement surgery. Due to their increased surface area, additively manufactured porous metallic implants provide optimal osseointegration but they are also highly susceptible to bacterial colonization. Antibacterial surface coatings of porous metals that do not inhibit osseointegration are therefore highly desirable. The potential of silver coatings on arthroplasty implants to inhibit PJI has been demonstrated, but the optimal silver content and release kinetics have not yet been defined. A tight control over the silver deposition coatings can help overcome bacterial infections while reducing cytotoxicity to human cells. In this regard, porous titanium sputtered with silver and titanium nitride with increasing silver contents enabled controlling the antibacterial effect against common PJI pathogens while maintaining the metabolic activity of human primary cells. Electron beam melting additively manufactured titanium alloys, coated with increasing silver contents, were physico-chemically characterized and investigated for effects against common PJI pathogens. Silver contents from 7 at % to 18 at % of silver were effective in reducing bacterial growth and biofilm formation. Staphylococcus epidermidis was more susceptible to silver ions than Staphylococcus aureus. Importantly, all silver-coated titanium scaffolds supported primary human osteoblasts proliferation, differentiation, and mineralization up to 28 days. A slight reduction of cell metabolic activity was observed at earlier time points, but no detrimental effects were found at the end of the culture period. Silver release from the silver-coated scaffolds also had no measurable effects on primary osteoblast gene expression since similar expression of genes related to osteogenesis was observed regardless the presence of silver. The investigated silver-coated porous titanium scaffolds may thus enhance osseointegration while reducing the risk of biofilm formation by the most common clinically encountered pathogens.
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25. |
- El Zowalaty, Mohamed E., et al.
(author)
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From SARS to COVID-19 : A previously unknown SARS- related coronavirus (SARS-CoV-2) of pandemic potential infecting humans ? Call for a One Health approach
- 2020
-
In: One Health. - : ELSEVIER. - 2352-7714. ; 9
-
Journal article (peer-reviewed)abstract
- Human coronaviruses continue to pose a threat to human health. The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 which causes coronavirus disease-2019 (COVID-19), an acute respiratory disease marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. This recent emergence of a previously unknown coronavirus in China leads to huge impacts on humans globally. Covid-19 is a challenge to global public health. Here, we discuss the COVID-19 outbreak in a one health context, highlighting the need for the implementation of one health measures and practices to improve human health and reduce the emergence of pandemic viruses.
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26. |
- El Zowalaty, Mohamed E., et al.
(author)
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Genome Sequence of Listeria innocua Strain MEZLIS26, Isolated from a Goat in South Africa
- 2019
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In: Microbiology Resource Announcements. - 2576-098X. ; 8:44
-
Journal article (peer-reviewed)abstract
- Here, we report the draft genome sequence of Listeria innocua strain MEZLIS26, isolated from a healthy goat in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,800,777 bp, with a G+C content of 37.4%, 2,755 coding DNA sequences (CDSs), 49 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).
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27. |
- El Zowalaty, Mohamed E., et al.
(author)
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Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa
- 2020
-
In: Journal of Global Antimicrobial Resistance. - OXFORD ENGLAND : Elsevier BV. - 2213-7165 .- 2213-7173. ; 23, s. 445-449
-
Journal article (peer-reviewed)abstract
- Objectives: The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa. Methods: Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree. Results: Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844. Conclusion: The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli. (C) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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28. |
- El Zowalaty, Mohamed E., et al.
(author)
-
Genome sequences of two Salmonella enterica strains (MEZSAL74 and MEZSAL81) harbouring multiple antimicrobial resistance genes isolated from livestock in South Africa
- 2020
-
In: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 21, s. 396-398
-
Journal article (other academic/artistic)abstract
- Objectives: Antimicrobial-resistant livestock-associated Salmonella enterica infections pose a significant public-health threat worldwide. Here we report for the first time the draft genome sequences of two multidrug-resistant livestock-associated S. enterica strains isolated from a chicken and a cow in South Africa. Methods: Genomic DNA of S. enterica strains MEZSAL74 and MEZSAL81 was sequenced using an Illumina MiSeq platform. The generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids. Multilocus sequence typing (MLST) was also performed. In order to compare isolates MEZSAL74 and MEZSAL81 with other previously sequenced S. enterica isolates, raw read sequences were downloaded and all sequence files were treated identically to generate a bootstrapped maximum likelihood phylogenetic tree. Results: Extrachromosomal plasmids and genetic determinants of antimicrobial resistance were detected in both sequenced bacterial isolates to aminoglycosides and fluoroquinolones. By MLST, strain MEZSAL74 belonged to an unknown sequence type (ST) and strain MEZSAL81 belonged to ST33. Conclusion: The genome sequences of strains MEZSAL74 and MEZSAL81 reported here will serve as a reference for molecular epidemiological studies of antimicrobial-resistant livestock-associated S. enterica in Africa. (c) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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29. |
- Eriksson, Hannah K., MD, et al.
(author)
-
Early Staphylococcal Periprosthetic joint infection (PJI) caused by Staphylocci resistant to rifampicin : Inferior outcomes after Debridement, Antibiotics and Implant retention (DAIR)
-
Other publication (other academic/artistic)abstract
- Objectives: The purpose of this retrospective cohort study was to investigate whether rifampicin resistance in early periprosthetic joint infection (PJI) caused by Staphylococci (Coagulase negative staphylococci (CoNS) or Staphyloccocus aureus (SA)) affects the treatment outcome after debridement, antibiotics and implant retention (DAIR).Patients and methods: 81 patients (42 women) with a mean age of 72 (41-93) years affected by early PJI (30 knees, 51 hips) were included. Early PJI was defined as infection diagnosed within 6 weeks after the index surgical procedure, where index procedures could be either primary or revision surgeries. The diagnosis of PJI was based on MSIS (Musculoskeletal Infection Society) criteria and all patients were treated surgically by DAIR, repeated if needed. Infection-free survival was estimated using the Kaplan Meier method, and Cox regression models were fitted to assess the risk of unsuccessful treatment outcome, adjusted for the potential confounders sex, joint (hip or knee), type of index surgery (primary or revision) and age (dichotomised into age ˂ 70 or ≥ 70). Outcome measures: The primary endpoint was to compare treatment outcome in patients with PJI caused by rifampicin-resistant or rifampicin-sensitive Staphylococci after one DAIR procedure and secondary endpoint to compare outcome after two DAIR procedures. Results: The treatment was unsuccessful in 58% of patients after one DAIR procedure and in 42% after two DAIR procedures. In the group of patients with rifampicin-resistant Staphylococci, treatment was unsuccessful in 80% after one DAIR and 70% after two DAIR procedures. In patients with rifampicin-sensitive bacteria, 49% of the patients had an unsuccessful treatment after one DAIR and 33% after two DAIR. Patients with rifampicin-resistant staphylococcal PJI had a risk of infection relapse of 1.9 (95% CI: 1.1-3.6, p=0.04) after one DAIR when compared with patients with rifampicin-sensitive bacteria, and a 4.1 (95% CI: 1.2-14.1, p=0.03) -fold risk of treatment failure after two DAIR procedures.Conclusion: Staphylococcal resistance to rifampicin is associated with inferior outcomes in early PJI treated by DAIR. These findings are suggestive of a change in practice since DAIR may not be a useful strategy under these circumstances.
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30. |
- Eriksson, Hannah K., MD, et al.
(author)
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Early Staphylococcal Periprosthetic Joint Infection (PJI) Treated with Debridement, Antibiotics, and Implant Retention (DAIR) : Inferior Outcomes in Patients with Staphylococci Resistant to Rifampicin
- 2023
-
In: Antibiotics. - : MDPI. - 2079-6382. ; 12:11
-
Journal article (peer-reviewed)abstract
- It is unknown how rifampicin resistance in staphylococci causing a periprosthetic joint infection (PJI) affects outcomes after debridement, antibiotics, and implant retention (DAIR). We thus aimed to compare the risk of relapse in DAIR-treated early PJI caused by staphylococci with or without rifampicin resistance. In total, 81 patients affected by early PJI were included, and all patients were treated surgically with DAIR. This was repeated if needed. The endpoint of relapse-free survival was estimated using the Kaplan–Meier method, and Cox regression models were fitted to assess the risk of infection relapse for patients infected with rifampicin-resistant bacteria, adjusted for age, sex, type of joint, and type of index surgery. In patients with rifampicin-resistant staphylococci, relapse was seen in 80% after one DAIR procedure and in 70% after two DAIR procedures. In patients with rifampicin-sensitive bacteria, 51% had an infection relapse after one DAIR procedure and 33% had an infection relapse after two DAIR procedures. Patients with rifampicin-resistant staphylococcal PJI thus had an increased adjusted risk of infection relapse of 1.9 (95% CI: 1.1–3.6, p = 0.04) after one DAIR procedure compared to patients with rifampicin-sensitive bacteria and a 4.1-fold (95% CI: 1.2–14.1, p = 0.03) increase in risk of infection relapse after two DAIR procedures. Staphylococcal resistance to rifampicin is associated with inferior outcomes after DAIR. These findings suggest that DAIR may not be a useful strategy in early PJI caused by rifampicin-resistant staphylococci.
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31. |
- Eriksson, Hannah K., et al.
(author)
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Linezolid in the treatment of periprosthetic joint infection caused by coagulase-negative staphylococci
- 2019
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In: Infectious Diseases. - : TAYLOR & FRANCIS LTD. - 2374-4235 .- 2374-4243. ; 51:9, s. 683-690
-
Journal article (peer-reviewed)abstract
- Background: Periprosthetic joint infection (PJI) caused by coagulase-negative staphylococci (CoNS) is increasingly common and is sometimes treated with off-label use of linezolid.Methods: We conducted a retrospective study of patients with PJI caused by CoNS treated with surgical intervention and orally administrated linezolid during the period 1995-2014 (n = 28). Clinical outcomes and adverse events related to linezolid administration were evaluated. Mean time to follow-up was 4.3 years (range: 0.2-12).Results: Twenty-two of 28 patients were infection-free at follow-up. No CoNS strain was resistant to vancomycin, but 16 of 28 were resistant to rifampicin, 23 of 28 to clindamycin and 20 of 27 to quinolones. The mean duration of linezolid treatment was 4.2 weeks (range: 1-12). Eleven of 28 patients had an adverse event related to the antimicrobial treatment, and four had to discontinue linezolid, but all adverse events were reversible within 2 months after discontinuation.Conclusions: Oral linezolid administration combined with adequate surgical treatment may be useful for the treatment of PJIs caused by CoNS.
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32. |
- Esson, Carol, et al.
(author)
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Health and zoonotic Infections of snow leopards Panthera unica in the South Gobi desert of Mongolia.
- 2019
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In: Infection Ecology & Epidemiology. - : Informa UK Limited. - 2000-8686. ; 9:1
-
Journal article (peer-reviewed)abstract
- 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.
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33. |
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34. |
- Hassan, Mohammad M., et al.
(author)
-
Prevalence and Diversity of Avian Influenza Virus Hemagglutinin Sero-Subtypes in Poultry and Wild Birds in Bangladesh
- 2020
-
In: Veterinary Sciences. - : MDPI. - 2306-7381. ; 7:2
-
Journal article (peer-reviewed)abstract
- Highly pathogenic avian influenza H5 viruses have pandemic potential, cause significant economic losses and are of veterinary and public health concerns. This study aimed to investigate the distribution and diversity of hemagglutinin (HA) subtypes of avian influenza virus (AIV) in poultry and wild birds in Bangladesh. We conducted an avian influenza sero-surveillance in wild and domestic birds in wetlands of Chattogram and Sylhet in the winter seasons 2012-2014. We tested serum samples using a competitive enzyme-linked immunosorbent assay (c-ELISA), and randomly selected positive serum samples (170 of 942) were tested using hemagglutination inhibition (HI) to detect antibodies against the 16 different HA sero-subtypes. All AIV sero-subtypes except H7, H11, H14 and H15 were identified in the present study, with H5 and H9 dominating over other subtypes, regardless of the bird species. The diversity of HA sero-subtypes within groups ranged from 3 (in household chickens) to 10 (in migratory birds). The prevalence of the H5 sero-subtype was 76.3% (29/38) in nomadic ducks, 71.4% (5/7) in household chicken, 66.7% (24/36) in resident wild birds, 65.9% (27/41) in migratory birds and 61.7% (29/47) in household ducks. Moreover, the H9 sero-subtype was common in migratory birds (56%; 23/41), followed by 38.3% (18/47) in household ducks, 36.8% (14/38) in nomadic ducks, 30.6% (11/66) in resident wild birds and 28.5% (2/7) in household chickens. H1, H4 and H6 sero-subtypes were the most common sero-subtypes (80%; 8/10, 70%; 7/10 and 70%; 7/10, respectively) in migratory birds in 2012, H9 in resident wild birds (83.3%; 5/6) and H2 in nomadic ducks (73.9%; 17/23) in 2013, and the H5 sero-subtype in all types of birds (50% to 100%) in 2014. The present study demonstrates that a high diversity of HA subtypes circulated in diverse bird species in Bangladesh, and this broad range of AIV hosts may increase the probability of AIVs' reassortment and may enhance the emergence of novel AIV strains. A continued surveillance for AIV at targeted domestic-wild bird interfaces is recommended to understand the ecology and evolution of AIVs.
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35. |
- Hassan, Mohammad Mahmudul, et al.
(author)
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Residual antimicrobial agents in food originating from animals
- 2021
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In: Trends in Food Science & Technology. - : Elsevier. - 0924-2244 .- 1879-3053. ; 111, s. 141-150
-
Journal article (peer-reviewed)abstract
- Background: The agricultural food products industry in Bangladesh depends on utilizing antimicrobials indiscriminately as growth promoters and for controlling infectious diseases. Thus, there is always a risk of antimicrobial agent accumulation in food sources that originate from agricultural production.Methods: In the present study, we collected data from published articles between January, 2013 and December, 2019 on antimicrobial residues in human food sources such as meat, milk, eggs, and fishes.Results: Liver contained the highest percentage of antimicrobial residues (74%; 95% CI: 59.66?85.37) against the in vitro enteric pathogen Escherichia coli in layer chickens. Similar results were demonstrated in liver (68%; 95% CI: 53.30?80.48) and kidney (66%, 95% CI: 51.23?78.79) of layer chickens against Bacillus cereus and Bacillus subtilis. Amongst all antibiotics, the highest concentrations of ciprofloxacin were detected in kidney (48.57%; 95% CI: 31.38?66.01), followed by liver (47.56; 95% CI: 40.88?54.30) of broiler chickens. Ciprofloxacin was also present in liver (46.15%; 95% CI: 33.70?58.96) of layer chickens. The percentage of ciprofloxacin in thigh and breast meat in broiler bird were 41.54% (95% CI: 34.54?48.79) and 37.95% (95% CI: 31.11?45.15) respectively. Enrofloxacin was the second most dominant antimicrobial agent and was present in the liver of both types of poultry (Broiler and Layer chickens: 41.54%; 95% CI: 29.44?54.4 and 437.33%; 95% CI: 30.99?44.01). The prevalence rates of enrofloxacin in thigh and breast meat of broiler chickens were 24.10% (95% CI: 18.28?30.73) and 20.51% (95% CI: 15.08?26.87), respectively. Tetracycline, a commonly used antibiotic in livestock, was present in the liver (49.23%; 95% CI: 36.60?61.93) of layer chickens. In case of aquaculture food products, the highest amount of amoxicillin (683.2 mg/kg) was detected in Tilapia fish (Oreochromis niloticus), followed by 584.4 mg/kg in climbing perch (Anabas testudineus) and 555.6 mg/kg in Rui fish (Labeo rohita). Among the five types of fishes, Rui fish (0.000515 mg/kg) contained the highest concentrations of chloramphenicol antibiotic residues.Conclusions: The presence of antimicrobial residues in meat, milk, egg, and fish is a serious public health threat due to the potential induction of antimicrobial resistance. It can negatively impact the food supply chain, especially with the current strain that it is already facing with the current COVID-19 pandemic. The findings of the present study highlight the ongoing risk of residual antimicrobial agents in food of animal origin in Bangladesh and countries with similar practices. This can draw the attention of public health officials to propose plans to mitigate or stop this practice.
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36. |
- Hassan, Mohammad M., et al.
(author)
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Serological Evidence of Avian Influenza in Captive Wild Birds in a Zoo and Two Safari Parks in Bangladesh
- 2020
-
In: Veterinary Sciences. - : MDPI AG. - 2306-7381. ; 7:3
-
Journal article (peer-reviewed)abstract
- Avian influenza (AI) is endemic and frequently causes seasonal outbreaks in winter in Bangladesh due to high pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2. Among avian influenza A viruses (AIV), H5, H7, and H9 subtypes have the most zoonotic potential. Captive birds in zoos and safari parks are used for educational, recreational, breeding, and conservational purposes in Bangladesh. To screen for AIV in captive birds to assess potential public health threats, we conducted a cross-sectional study in two safari parks and one zoo in Bangladesh for four months, from November to December 2013 and from January to February 2014. We collected blood samples, oropharyngeal, and cloacal swabs from 228 birds. We tested serum samples for AIV antibodies using competitive enzyme-linked immunosorbent assay (c-ELISA) and AIV sero-subtype H5, H7, and H9 using hemagglutination inhibition (HI) test. Swab samples were tested for the presence of avian influenza viral RNA using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Across all the samples, AIV antibody prevalence was 9.7% (95% CI: 6.1-14.2, n = 228) and AIV HA subtype H5, H7 and H9 sero-prevalence was 0% (95% CI: 0-1.6, n = 228), 0% (95% CI: 0-1.6, n = 228) and 6.6% (95% CI: 3.72-10.6, n = 228), respectively. No AI viral RNA (M-gene) was detected in any swab sample (0%, 95% CI: 0-1.6, n = 228). Birds in the Safari park at Cox's Bazar had a higher prevalence in both AIV antibody prevalence (13.5%) and AIV H9 sero-prevalence (9.6%) than any of the other sites, although the difference was not statistically significant. Among eight species of birds, Emu (Dromaius novaehollandiae) had the highest sero-positivity for both AIV antibody prevalence (26.1%) and AIV H9 prevalence (17.4%) followed by Golden pheasant (Chrysolophus pictus) with AIV antibody prevalence of 18.2% and AIV H9 prevalence of 11.4%. Our results highlight the presence of AI antibodies indicating low pathogenic AIV mingling in captive birds in zoos and safari parks in Bangladesh. Continuous programmed surveillance is therefore recommended to help better understand the diversity of AIVs and provide a clear picture of AI in captive wild birds, enabling interventions to reduce the risk of AIV transmission to humans.
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37. |
- Hessman, Jon, et al.
(author)
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High Prevalence and Temporal Variation of Extended Spectrum β-Lactamase–Producing Bacteria in Urban Swedish Mallards
- 2018
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In: Microbial Drug Resistance. - : Mary Ann Liebert Inc. - 1076-6294 .- 1931-8448.
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Journal article (peer-reviewed)abstract
- Antibiotic resistant bacteria present a growing global healthcare challenge. Previous research demonstrates that wild birds harbor extended spectrum -lactamase (ESBL)-producing Enterobacteriaceae and may contribute to their dissemination. We aimed to assess prevalence and temporal variation in the detection rate of ESBL-producing bacteria in urban wild birds and to evaluate methods regarding sample handling. Monthly fecal sampling was performed in 2013 at an urban pond in Sweden. ESBL-producing Escherichia coli and Klebsiella pneumoniae were analyzed by polymerase chain reaction targeting bla(CTX-M). Subsets of samples were analyzed in multiple replicates and without previous freezing. Pond water samples were screened for 12 antibiotics. Out of 813 fecal samples, 47% grew ESBL-producing E. coli, a higher prevalence than in similar studies. Detection rate varied considerably between months, ranging from 4.2% in May to 84% in July, and was significantly higher during warm months. A majority of isolates harbored CTX-M-15 type ESBL. Detection rates were increased by duplicating samples and by avoiding freezing. No antibiotics were detected in pond water. This study demonstrates high prevalence and a previously undescribed temporal variation in detection rate of ESBL-producing Enterobacteriaceae in wild birds. The distribution of CTX-M genes corresponds well with Swedish human isolates, indicating communication between the genetic pools of ESBLs in humans and wild birds. Urban ponds may serve as important natural reservoirs for antimicrobial resistance.
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38. |
- Hickman, Rachel A., et al.
(author)
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Dissemination of Resistant Escherichia coli Among Wild Birds, Rodents, Flies, and Calves on Dairy Farms
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- Antimicrobial resistance (AMR) in bacteria in the livestock is a growing problem, partly due to inappropriate use of antimicrobial drugs. Antimicrobial use (AMU) occurs in Swedish dairy farming but is restricted to the treatment of sick animals based on prescription by a veterinary practitioner. Despite these strict rules, calves shedding antimicrobial resistant Enterobacteriaceae have been recorded both in dairy farms and in slaughterhouses. Yet, not much is known how these bacteria disseminate into the local environment around dairy farms. In this study, we collected samples from four animal sources (fecal samples from calves, birds and rodents, and whole flies) and two environmental sources (cow manure drains and manure pits). From the samples, Escherichia coli was isolated and antimicrobial susceptibility testing performed. A subset of isolates was whole genome sequenced to evaluate relatedness between sources and genomic determinants such as antimicrobial resistance genes (ARGs) and the presence of plasmids were assessed. We detected both ARGs, mobile genetic elements and low rates of AMR. In particular, we observed four potential instances of bacterial clonal sharing in two different animal sources. This demonstrates resistant E. coli dissemination potential within the dairy farm, between calves and scavenger animals (rodents and flies). AMR dissemination and the zoonotic AMR risk is generally low in countries with low and restricted AMU. However, we show that interspecies dissemination does occur, and in countries that have little to no AMU restrictions this risk could be under-estimated.
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39. |
- Hickman, Rachel A., et al.
(author)
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Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts : A One Health Perspective
- 2021
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12
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Journal article (peer-reviewed)abstract
- Antibiotics are freqeuently used in the livestock sector in low- and middle-income countries for treatment, prophylaxis, and growth promotion. However, there is limited information into the zoonotic prevalence and dissemination patterns of antimicrobial resistance (AMR) within these environments. In this study we used pig farming in Thailand as a model to explore AMR; 156 pig farms were included, comprising of small-sized (<50 sows) and medium-sized (≥100 sows) farms, where bacterial isolates were selectively cultured from animal rectal and human fecal samples. Bacterial isolates were subjected to antimicrobial susceptibility testing (AST), and whole-genome sequencing. Our results indicate extensive zoonotic sharing of antibiotic resistance genes (ARGs) by horizontal gene transfer. Resistance to multiple antibiotics was observed with higher prevalence in medium-scale farms. Zoonotic transmission of colistin resistance in small-scale farms had a dissemination gradient from pigs to handlers to non-livestock contacts. We highly recommend reducing the antimicrobial use in animals’ feeds and medications, especially the last resort drug colistin.
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40. |
- Hoffman, Tove, et al.
(author)
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Reduced Binding between Omicron B.1.1.529 and the Human ACE2 Receptor in a Surrogate Virus Neutralization Test for SARS-CoV-2
- 2023
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In: Viruses. - : MDPI. - 1999-4915. ; 15:6
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Journal article (peer-reviewed)abstract
- The current gold standard assay for detecting neutralizing antibodies (NAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the conventional virus neutralization test (cVNT), which requires infectious virus and a biosafety level 3 laboratory. Here, we report the development of a SARS-CoV-2 surrogate virus neutralization test (sVNT) that, with Luminex technology, detects NAbs. The assay was designed to mimic the virus-host interaction and is based on antibody blockage between the human angiotensin-converting enzyme 2 (hACE2) receptor and the spike (S) protein of the Wuhan, Delta, and Omicron (B.1.1.529) variants of SARS-CoV-2. The sVNT proved to have a 100% correlation with a SARS-CoV-2 cVNT regarding qualitative results. Binding between the hACE2 receptor and the S1 domain of the B.1.1.529 lineage of the Omicron variant was not observed in the assay but between the receptor and an S1 + S2 trimer and the receptor binding domain (RBD) in a reduced manner, suggesting less efficient receptor binding for the B.1.1.529 Omicron variant. The results indicate that the SARS-CoV-2 sVNT is a suitable tool for both the research community and the public health service, as it may serve as an efficient diagnostic alternative to the cVNT.
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41. |
- Huber, Laura, et al.
(author)
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Geographic Drivers of Antimicrobial Use and Resistance in Pigs in Khon Kaen Province, Thailand
- 2021
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In: Frontiers in Veterinary Science. - : Frontiers Media S.A.. - 2297-1769. ; 8
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Journal article (peer-reviewed)abstract
- In Thailand, pig production has increased considerably in the last decades to meet a growing demand for pork. Antimicrobials are used routinely in intensive pig production to treat infections and increase productivity. However, the use of antimicrobials also contributes to the rise of antimicrobial resistance with potential consequences for animal and human health. Here, we quantify the association between antimicrobial use and resistance rates in extensive and intensive farms with a focus on geographic proximity between farm and drugstores. Of the 164 enrolled farms, 79% reported using antimicrobials for disease prevention, treatment, or as a feed additive. Antimicrobial-resistant E. coli were present in 63% of farms. These drugs included critically important antimicrobials, such as quinolones and penicillins. Medium-scale farms with intensive animal production practices showed higher resistance rates than small-scale farms with extensive practices. Farms with drug-resistant Escherichia coli were located closer to drugstores and a had a higher proportion of disease than farms without drug-resistant E. coli. We found no association between the presence of resistance in humans and antimicrobial use in pigs. Our findings call for actions to improve herd health to reduce the need for antimicrobials and systematic training of veterinarians and drugstore owners on judicious use of antimicrobials in animals to mitigate resistance.
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42. |
- Järhult, Josef D., 1975-
(author)
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Environmental resistance development to influenza antivirals : a case exemplifying the need for a multidisciplinary One Health approach including physicians
- 2018
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In: Acta Veterinaria Scandinavica. - : BioMed Central. - 0044-605X .- 1751-0147. ; 60
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Research review (peer-reviewed)abstract
- A multidisciplinary approach is a prerequisite for One Health. Physicians are important players in the One Health team, yet they are often hard to convince of the benefits of the One Health approach. Here, the case for multidisciplinarity including physicians is made using the example of environmental resistance development to influenza antivirals. Neuraminidase inhibitors are the major class of anti-influenza pharmaceuticals, and extensively stockpiled globally as a cornerstone of pandemic preparedness, especially important in the first phase before vaccines can be mass-produced. The active metabolite of oseltamivir that is excreted from treated patients degrades poorly in conventional sewage treatment processes and has been found in river waters. Dabbling ducks constitute the natural influenza A virus reservoir and often reside near sewage treatment plant outlets, where they may be exposed to neuraminidase inhibitor residues. In vivo experiments using influenza-infected Mallards exposed to neuraminidase inhibitors present in their water have shown resistance development and persistence, demonstrating that resistance may be induced and become established in the influenza strains circulating in natural hosts. Neuraminidase inhibitor resistance genes may become part of a human-adapted influenza virus with pandemic potential through reassortment or direct transmission. A pandemic caused by a neuraminidase inhibitor-resistant influenza virus is a serious threat as the first line defense in pandemic preparedness would be disarmed. To assess the risk for environmental influenza resistance development, a broad multidisciplinary team containing chemists, social scientists, veterinarians, biologists, ecologists, virologists, epidemiologists, and physicians is needed. Information about One Health early in high school and undergraduate training, an active participation of One Health-engaged physicians in the debate, and more One Health-adapted funding and publication possibilities are suggested to increase the possibility to engage physicians.
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43. |
- Järhult, Josef D., 1975-
(author)
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Tamiflu® - Use It and Lose It?
- 2011
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Doctoral thesis (other academic/artistic)abstract
- Influenza A viruses cause seasonal and pandemic outbreaks that range from mild infections to the disastrous Spanish Flu. Resistance to neuraminidase inhibitors (NAIs) is a growing problem as these drugs constitute a vital part of treatment strategies and pandemic preparedness plans worldwide. Oseltamivir (Tamiflu®) is the mostly used NAI. Its active metabolite, oseltamivir carboxylate (OC), is excreted from treated patients and degrades poorly in sewage treatment plants and surface water. Thus, OC can enter aquatic environments where the natural influenza reservoir, dabbling ducks, can be exposed to the substance and resistance could develop. If NAI resistance is established in influenza viruses circulating among wild birds, the resistance can form part of a virus re-entering the human population either by reassortment or by direct transmission. In this thesis, evidence is presented that OC is present in the waterways during a seasonal influenza outbreak in Japan, a country in which oseltamivir is liberally used. Furthermore, when mallards were infected with an influenza A/H1N1 virus and subjected to low, environmental-like concentrations of OC, resistance developed through acquisition of the well-known resistance mutation H274Y. The influenza infection in the mallards was mainly intestinal, had a rapid onset and was progressing in a longitudinal fashion in the intestine. Finally, influenza A viruses isolated from wild mallards in Sweden and containing resistance-related mutations were examined by a neuraminidase inhibition assay. The viruses did not have a decreased sensitivity to NAIs, but had mutations with a resistance-enhancing potential. Thus, OC is present in the environment and environmental-like concentrations of OC induce resistance in influenza viruses of dabbling ducks. The present resistance situation among wild birds is not well understood but the existence of H274Y among wild birds, though rare, and the spread of the former seasonal A/H1N1 virus containing H274Y among humans indicate that resistance mutations could establish themselves also among wild birds. An oseltamivir-resistant pandemic or a human-adapted highly-pathogenic avian influenza virus are frightening scenarios as oseltamivir is a cornerstone in the defense in those situations. There is a need for further studies, surveillance in wild birds and for a prudent use of antivirals.
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44. |
- Järhult, Josef D., 1975-, et al.
(author)
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The impact of viremia on organ failure, biomarkers and mortality in a Swedish cohort of critically ill COVID-19 patients
- 2021
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11
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Journal article (peer-reviewed)abstract
- The spread of virus via the blood stream has been suggested to contribute to extra-pulmonary organ failure in Coronavirus disease 2019 (COVID-19). We assessed SARS-CoV-2 RNAemia (RNAemia) and the association between RNAemia and inflammation, organ failure and mortality in critically ill COVID-19 patients. We included all patients with PCR verified COVID-19 and consent admitted to ICU. SARS-CoV-2 RNA copies above 1000/ml measured by PCR in plasma was defined as RNAemia and used as surrogate for viremia. In this cohort of 92 patients 59 (64%) were invasively ventilated. RNAemia was found in 31 patients (34%). Hypertension and corticosteroid treatment was more common in patients with RNAemia. Extra-pulmonary organ failure biomarkers and the extent of organ failure were similar in patients with and without RNAemia, but the former group had more renal replacement therapy and higher mortality (26 vs 16%; 35 vs 16%, respectively, p=0.04). RNAemia was not an independent predictor of death at 30 days after adjustment for age. SARS-CoV2 RNA copies in plasma is a common finding in ICU patients with COVID-19. Although viremia was not associated with extra pulmonary organ failure it was more common in patients who did not survive to 30 days after ICU admission.Trial registration: ClinicalTrials NCT04316884.
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45. |
- Karlsson, Philip A., et al.
(author)
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Antibiotic use during coronavirus disease 2019 intensive care unit shape multidrug resistance bacteriuria : A Swedish longitudinal prospective study
- 2023
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In: Frontiers in Medicine. - : Frontiers Media S.A.. - 2296-858X. ; 10
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Journal article (peer-reviewed)abstract
- Objectives: High frequency of antimicrobial prescription and the nature of prolonged illness in COVID-19 increases risk for complicated bacteriuria and antibiotic resistance. We investigated risk factors for bacteriuria in the ICU and the correlation between antibiotic treatment and persistent bacteria.Methods: We conducted a prospective longitudinal study with urine from indwelling catheters of 101 ICU patients from Uppsala University Hospital, Sweden. Samples were screened and isolates confirmed with MALDI-TOF and whole genome sequencing. Isolates were analyzed for AMR using broth microdilution. Clinical data were assessed for correlation with bacteriuria.Results: Length of stay linearly correlated with bacteriuria (R2 = 0.99, p ≤ 0.0001). 90% of patients received antibiotics, primarily the beta-lactams (76%) cefotaxime, piperacillin-tazobactam, and meropenem. We found high prevalence of Enterococcus (42%) being associated with increased cefotaxime prescription. Antibiotic-susceptible E. coli were found to cause bacteriuria despite concurrent antibiotic treatment when found in co-culture with Enterococcus.Conclusion: Longer stays in ICUs increase the risk for bacteriuria in a predictable manner. Likely, high use of cefotaxime drives Enterococcus prevalence, which in turn permit co-colonizing Gram-negative bacteria. Our results suggest biofilms in urinary catheters as a reservoir of pathogenic bacteria with the potential to develop and disseminate AMR.
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46. |
- Karlsson, Philip A., et al.
(author)
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Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden
- 2021
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 12
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Journal article (peer-reviewed)abstract
- The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.
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47. |
- Kontakis, M. G., et al.
(author)
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Antimicrobial and osteoconductive properties of two different types of titanium silver coating
- 2021
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In: European Cells & Materials. - : AO RESEARCH INSTITUTE DAVOS-ARI. - 1473-2262. ; 41, s. 694-706
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Journal article (peer-reviewed)abstract
- In prosthetic joint surgery, Ag coating of implant areas in direct contact with bone has been met with hesitation for fear of compromising osseointegration. The physicochemical, antibacterial and osteoconductive properties of three different Ti samples were studied: Ti6Al4V alloy that was grit-blasted (GB), Ti6Al4V alloy with an experimental Ti-Ag-nitride layer (SN) applied by physical vapour deposition (PVD) and commercially available PVD-coated Ti6Al4V alloy with a base Ag layer and a surface Ti-Ag-nitride layer (SSN, clinically known as PorAg (R)). Ag content on the surface of experimental SN and SSN discs was 27.7 %wt and 68.5 % wt, respectively. At 28 d, Ag release was 4 ppm from SN and 26.9 ppm from SSN substrates. Colonisation of discs by Staphylococcus aureus was the highest on GB [944 (+/- 91) x 10(4) CFU/mL], distinctly lower on experimental SN discs [414 (+/- 117) x 10(4) CFU/mL] and the lowest on SSN discs [307 (+/- 126) x 10(4) CFU/mL]. Primary human osteoblasts were abundant 28 d after seeding on GB discs but their adhesion and differentiation, measured by alkaline-phosphatase production, was suppressed by 73 % on SN and by 96 % on SSN discs, in comparison to GB discs. Thus, the PVD-applied Ag coatings differed considerably in their antibacterial effects and osteoconductivity. The experimental SN coating had similar antibacterial effects to the commercially available SSN coating while providing slightly improved osteoconductivity. Balancing the Ag content of Ti implants will be vital for future developments of implants designed for cementless fixation into bone.
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48. |
- Lazarinis, Stergios, 1971-, et al.
(author)
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Incidence of Rifampicin Resistance in Periprosthetic Joint Infection : A Single-Centre Cohort Study on 238 Patients
- 2023
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In: Antibiotics. - : MDPI. - 2079-6382. ; 12:10
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Journal article (peer-reviewed)abstract
- Background: Rifampicin is a pillar in the treatment of periprosthetic joint infection (PJI). However, rifampicin resistance is an increasing threat to PJI treatment. This study explores the incidence of rifampicin-resistant bacteria over time in a Swedish tertiary referral centre and the association of rifampicin resistance with infection-free survival after PJI.Methods: The study included 238 staphylococcal PJIs treated between 2001 and 2020 for which susceptibility data for rifampicin were available. Data on causative bacteria, rifampicin resistance, treatment, and outcome were obtained. Kaplan-Meier survival analysis and Cox regression modelling estimated the infection-free cumulative survival and adjusted hazard ratios (HRs) for the risk of treatment failure.Results: Rifampicin-resistant causative bacteria were identified in 40 cases (17%). The proportion of rifampicin-resistant agents decreased from 24% in 2010-2015 to 12% in 2016-2020. The 2-year infection-free survival rates were 78.6% (95% CI, 66.4-93.1%) for the rifampicin-resistant group and 90.0% (95% CI, 85.8-94.4%) for the rifampicin-sensitive group. Patients with PJI caused by rifampicin-resistant bacteria had an increased risk of treatment failure (adjusted HR, 4.2; 95% CI, 1.7-10.3).Conclusions: The incidence of PJI caused by rifampicin-resistant bacteria did not increase over the past 20 years. The risk of treatment failure in PJI caused by rifampicin-resistant bacteria is more than four times that caused by rifampicin-sensitive bacteria, highlighting the importance of limiting the development of rifampicin resistance.
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49. |
- Leangapichart, Thongpan, et al.
(author)
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Characterization of Klebsiella pneumoniae complex isolates from pigs and humans in farms in Thailand : population genomic structure, antibiotic resistance and virulence genes
- 2021
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In: Journal of Antimicrobial Chemotherapy. - : Oxford University Press. - 0305-7453 .- 1460-2091. ; 76:8, s. 2012-2016
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Journal article (peer-reviewed)abstract
- Objectives: To define characteristics of Klebsiella pneumoniae complex (hereafter KP) isolates from healthy pigs, farm workers and their householdmembers in Thailand. Methods: A total of 839 individual rectal swabs from pigs on 164 farms and 271 faecal samples of humans working on pig farms and persons living in the same household in Khon Kaen, Thailand were screened for gut colonization by KP. Genomic sequenceswere investigated for antibiotic resistance and virulence genes. Phylogenetic analyseswere performed in addition to comparison with isolates from previous studies from Thailand. Results: KP was detected in approximately 50% of pig and human samples. In total, 253 KP isolates were obtained: 39% from pigs, 34% from farmers and 26% from individuals living on the same farm but without animal contact. MLST revealed high genetic diversity with 196 different STs distributed over four phylogroups (Kp1 to Kp4). Low prevalence of ESBL-KP (7.5%) and colistin-resistant KP (3.2%) was observed among pigs and humans. Remarkably, four convergent MDR and hypervirulent strains were observed: one from pigs (ST290) and three from humans [ST35, ST3415 (strain 90CP1), ST17 (strain 90CM2)]. Sharing of KP clones among pigs and humans was identified for some STs including ST4788, ST661, ST3541 and ST29. Conclusions: The study indicated a low prevalence of ESBL and mcr genes among KP isolated from pigs and healthy humans in Thailand and suggested the possibility of zoonotic transmission for a subset of circulating KP clones.
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50. |
- Leangapichart, Thongpan, et al.
(author)
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Exploring the epidemiology of mcr genes, genetic context and plasmids in Enterobacteriaceae originating from pigs and humans on farms in Thailand
- 2023
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In: Journal of Antimicrobial Chemotherapy. - : Oxford University Press. - 0305-7453 .- 1460-2091. ; 78:6, s. 1395-1405
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Journal article (peer-reviewed)abstract
- Objectives In veterinary medicine, colistin has been widely used as therapeutic and prophylactic agent, and for growth promotion. However, colistin has been re-introduced into treatment of human MDR bacterial infections. We assessed the characteristics and spread of plasmid-borne colistin resistance among healthy pigs, workers with animal-contact and their household members in Thailand.Methods WGS and MIC data of 146 mcr-positive isolates from a cross-sectional One Health study were analysed. Long-read sequencing and conjugation were performed for selected isolates.Results mcr-carrying isolates were detected in 38% of pooled-pig samples and 16% of human faecal samples. Of 143 Escherichia coli and three Escherichia fergusonii, mcr-1, mcr-3, and mcr-9 variants were identified in 96 (65.8%), 61 (41.8%) and one (0.7%) isolate, respectively. Twelve E. coli co-harboured two mcr variants (mcr-1 and mcr-3). Clonal transmission was detected in five out of 164 farms. mcr-1 was mostly harboured by epidemic IncX4 and IncHI1 plasmids (89.9%). Conversely, mcr-3 was harboured by a range of different plasmids. Comparative plasmid studies suggested IncP and IncFII plasmids as possible endemic mcr-3 plasmids in Asian countries. Moreover, mcr-3 was associated with different mobile genetic elements including TnAs2, ISKpn40 and IS26/15DI. Detected genetic signatures (DRs) indicated recent mcr-3 transpositions, underlining the mobilizable nature of the mcr-3 cassette.Conclusions The epidemiology of mcr and the possible evolution of successful plasmids and transposition modules should be carefully monitored. Of special concern is the growing number of different horizontal gene transferring pathways encompassing various transposable modules the mcr genes can be shared between bacteria.
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