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Ahlstrom CA, Woksepp H, Sandegren L, Mohsin M, Hasan B, Muzyka D, Hernandez J, Aguirre F, Tok A, Söderman J, Olsen B, Ramey AM, Bonnedahl J. Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination. Sci Total Environ 2022; 824:153632. [PMID: 35124031 DOI: 10.1016/j.scitotenv.2022.153632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Carbapenem resistant Enterobacteriaceae (CRE) are a threat to public health globally, yet the role of the environment in the epidemiology of CRE remains elusive. Given that wild birds can acquire CRE, likely from foraging in anthropogenically impacted areas, and may aid in the maintenance and dissemination of CRE in the environment, a spatiotemporal comparison of isolates from different regions and timepoints may be useful for elucidating epidemiological information. Thus, we characterized the genomic diversity of CRE from fecal samples opportunistically collected from gulls (Larus spp.) inhabiting Alaska (USA), Chile, Spain, Turkey, and Ukraine and from black kites (Milvus migrans) sampled in Pakistan and assessed evidence for spatiotemporal patterns of dissemination. Within and among sampling locations, a high diversity of carbapenemases was found, including Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), oxacillinase (OXA), and Verona integron Metallo beta-lactamase (VIM). Although the majority of genomic comparisons among samples did not provide evidence for spatial dissemination, we did find strong evidence for dissemination among Alaska, Spain, and Turkey. We also found strong evidence for temporal dissemination among samples collected in Alaska and Pakistan, though the majority of CRE clones were transitory and were not repeatedly detected among locations where samples were collected longitudinally. Carbapenemase-producing hypervirulent K. pneumoniae was isolated from gulls in Spain and Ukraine and some isolates harbored antimicrobial resistance genes conferring resistance to up to 10 different antibiotic classes, including colistin. Our results are consistent with local acquisition of CRE by wild birds with spatial dissemination influenced by intermediary transmission routes, likely involving humans. Furthermore, our results support the premise that anthropogenically-associated wild birds may be good sentinels for understanding the burden of clinically-relevant antimicrobial resistance in the local human population.
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Affiliation(s)
- Christina A Ahlstrom
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA
| | - Hanna Woksepp
- Department of Development and Public Health, Kalmar County Hospital, Kalmar 391 85, Sweden; Department of Medicine and Optometry, Linnaeus University, Kalmar 391 85, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Infection biology, antimicrobial resistance and immunology, Uppsala University, Uppsala SE-75185, Sweden
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Badrul Hasan
- Department of Medical Biochemistry and Microbiology, Infection biology, antimicrobial resistance and immunology, Uppsala University, Uppsala SE-75185, Sweden; Animal Bacteriology Section, Microbial Sciences, Pests and Diseases, Agriculture Victoria Research, Bundoora, Victoria 3083, Australia
| | - Denys Muzyka
- National Scientific Center, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv 61023, Ukraine
| | - Jorge Hernandez
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar SE-39185, Sweden
| | - Filip Aguirre
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar SE-39185, Sweden
| | - Atalay Tok
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala SE-75185, Sweden
| | - Jan Söderman
- Laboratory Medicine, Jönköping, Region Jönköping County, Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Bjorn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala SE-75185, Sweden
| | - Andrew M Ramey
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 581 83, Sweden; Department of Infectious Diseases, Region Kalmar County, Kalmar 391 85, Sweden.
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Eminaga O, Semjonow A, Oezguer E, Herden J, Akbarov I, Tok A, Engelmann U, Wille S. An Electronic Specimen Collection Protocol Schema (eSCPS). Methods Inf Med 2018; 53:29-38. [PMID: 24317441 DOI: 10.3414/me13-01-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 11/04/2013] [Indexed: 11/09/2022]
Abstract
SummaryBackground: The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols.Materials and Methods: The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Fi -nally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS.Results: We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002).Conclusion: The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.
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Affiliation(s)
- O Eminaga
- Okyaz Eminaga, M.D., Department of Urology/Prostate Center, University Hospital Cologne, Kerpener Street 62, 50937 Cologne, Germany, E-mail:
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Hesson JC, Lundström JO, Tok A, Östman Ö, Lundkvist Å. Temporal Variation in Sindbis Virus Antibody Prevalence in Bird Hosts in an Endemic Area in Sweden. PLoS One 2016; 11:e0162005. [PMID: 27579607 PMCID: PMC5007008 DOI: 10.1371/journal.pone.0162005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/16/2016] [Indexed: 11/25/2022] Open
Abstract
Sindbis virus (SINV) is a mosquito-borne bird virus that occasionally causes human disease in Fennoscandia, suggested to have cyclic 7-year intervals between outbreaks. Reliable data on human infections in Sweden is however lacking. Here we investigated the SINV antibody prevalence among birds in a Swedish area endemic to SINV to scrutinize if a cyclic variation in antibody prevalence is present in the natural host of SINV. Serum from birds were sampled in the summers of 2002–2004 and 2009 in the floodplains of the River Dalälven in central Sweden, with 2002 and 2009 representing hypothesized years of SINV outbreaks. A total of 963 birds from 52 species (mainly passerines) were tested for the presence of SINV antibodies using a plaque reduction neutralization test. The highest SINV antibody prevalence was found in Turdidae species, specifically Fieldfare, Redwing and Song thrush in which more than 70% of sampled individuals had antibodies to SINV in 2009. The SINV antibody prevalence significantly varied between years with 2% in 2002, 8% in 2003, 14% in 2004 and 37% in 2009. Antibodies were found equally often in hatchlings and in adults and increased from early to late in the season. Clearly, the SINV antibody prevalence was not elevated in the bird hosts in the predicted outbreak year 2002, thus solid evidence of a cyclic occurrence of SINV in Sweden is still lacking.
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Affiliation(s)
- Jenny Christina Hesson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, Uppsala, Sweden.,Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Jan O Lundström
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, Uppsala, Sweden.,Swedish Biological Mosquito Control Project, Nedre Dalälvens Utvecklings AB, Gysinge, Sweden
| | - Atalay Tok
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, Uppsala, Sweden
| | - Örjan Östman
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, Uppsala, Sweden.,Laboratory of Clinical Microbiology, Uppsala University Hospital, Uppsala, Sweden
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Tok A, Eminaga O, Burghaus L, Herden J, Akbarov I, Engelmann U, Wille S. Age-stratified cut-off points for the nocturnal penile tumescence measurement using Nocturnal Electrobioimpedance Volumetric Assessment (NEVA(®) ) in sexually active healthy men. Andrologia 2015; 48:631-6. [PMID: 26498135 DOI: 10.1111/and.12492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2015] [Indexed: 11/29/2022] Open
Abstract
The current nocturnal penile tumescence (NPT) measurement is based on standard cut-off levels defined regardless of age. This study was conducted to provide age-stratified cut-off points for NPT measurement. Forty sexually active healthy men between 20 and 60 years old were enrolled and divided equally into four groups defined by age (20-29, 30-39, 40-49 and 50-60 years.). None of the candidates had sexual dysfunction or sleep disturbance or used supportive medication to enhance sexual function. Erectile function was evaluated by using the 5-item version of the international index of erectile function (IIEF-5). NPT was observed using the nocturnal electrobioimpedance volumetric assessment (NEVA(®) ). The NPT values of healthy men aged 20-60 years varied from 268.7% to 202.3%. The NPT differed significantly between age groups (P < 0.0009); however, no significant differences between men aged 30-39 and 40-49 (P = 0.593) were observed. Age was weakly associated with IIEF-5 scores (P = 0.004), whereas a strong and negative correlation between age and NPT (P < 0.0001) was found. IEF-5 scores were not significantly associated with NPT (P = 0.95). Therefore, the standard values for NPT testing should be considered in the evaluation of the nocturnal penile activity of men of all ages.
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Affiliation(s)
- A Tok
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - O Eminaga
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - L Burghaus
- Department of Neurology, University Hospital of Cologne, Cologne, Germany
| | - J Herden
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - I Akbarov
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - U Engelmann
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - S Wille
- Department of Urology, University Hospital of Cologne, Cologne, Germany
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Bhullar BAS, Morris ZS, Sefton EM, Tok A, Tokita M, Namkoong B, Camacho J, Burnham DA, Abzhanov A. A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution 2015; 69:1665-77. [PMID: 25964090 DOI: 10.1111/evo.12684] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/08/2015] [Indexed: 12/17/2022]
Abstract
The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches. We approached the problem of the mechanism behind this innovation using an approach bridging paleontology, comparative anatomy, and experimental developmental biology. First, we used fossil and extant data to show the beak is distinctive in consisting of fused premaxillae that are geometrically distinct from those of ancestral archosaurs. To elucidate underlying developmental mechanisms, we examined candidate gene expression domains in the embryonic face: the earlier frontonasal ectodermal zone (FEZ) and the later midfacial WNT-responsive region, in birds and several reptiles. This permitted the identification of an autapomorphic median gene expression region in Aves. To test the mechanism, we used inhibitors of both pathways to replicate in chicken the ancestral amniote expression. Altering the FEZ altered later WNT responsiveness to the ancestral pattern. Skeletal phenotypes from both types of experiments had premaxillae that clustered geometrically with ancestral fossil forms instead of beaked birds. The palatal region was also altered to a more ancestral phenotype. This is consistent with the fossil record and with the tight functional association of avian premaxillae and palate in forming a kinetic beak.
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Affiliation(s)
- Bhart-Anjan S Bhullar
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138. .,Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th St., Anatomy 306, Chicago, Illinois, 60637. .,Department of Geology and Geophysics, Yale University, P.O. Box 208109, New Haven, Connecticut, 06520. .,Peabody Museum of Natural History, Yale University, P.O. Box 208109, New Haven, Connecticut, 06520.
| | - Zachary S Morris
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Elizabeth M Sefton
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138.,Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts, 02138
| | - Atalay Tok
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Masayoshi Tokita
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Bumjin Namkoong
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Jasmin Camacho
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - David A Burnham
- Biodiversity Institute and Natural History Museum, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045
| | - Arhat Abzhanov
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138. .,Current address: Department of Life Sciences, Imperial College London, Silwood Park Campus Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom. .,Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
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Abstract
BACKGROUND Azoospermia is the absence of a measurable level of spermatozoa in the semen. It affects approximately 1% of all men, and the genetic basis of the majority of idiopathic cases is unknown. We investigated two unrelated consanguineous families with idiopathic azoospermia. In family 1, there were three azoospermic brothers and one oligozoospermic brother; and in family 2, there were three azoospermic brothers. Testis biopsy in the brothers in family 2 had led to the diagnosis of maturation arrest in the spermatid stage. METHODS Candidate disease loci were found via linkage mapping using data from single nucleotide polymorphism genome scans. Exome sequencing was applied to find the variants at the loci. RESULTS We identified two candidate loci in each family and homozygous truncating mutations p.R611X in TAF4B in family 1 and p.K507Sfs*3 in ZMYND15 in family 2. We did not detect any mutations in these genes in a cohort of 45 azoospermic and 15 oligozoospermic men. Expression studies for ZMYND15 showed that the highest expression was in the testis. CONCLUSIONS Both genes are known to have roles in spermatogenesis in mice but neither has been studied in humans. To our knowledge, they are the first genes identified for recessive idiopathic spermatogenic failure in men. Assuming that recessive genes for isolated azoospermia are as numerous in men as in mice, each gene is possibly responsible for only a small fraction of all cases.
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Affiliation(s)
- Özgecan Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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