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dc.contributor.authorSchneeberger, Pierre H.H.-
dc.contributor.authorBecker, Sören L.-
dc.contributor.authorPothier, Joël F.-
dc.contributor.authorDuffy, Brion-
dc.contributor.authorN'Goran, Eliézer K.-
dc.contributor.authorBeuret, Christian-
dc.contributor.authorFrey, Jürg E.-
dc.contributor.authorUtzinger, Jürg-
dc.date.accessioned2017-12-04T14:00:10Z-
dc.date.available2017-12-04T14:00:10Z-
dc.date.issued2016-06-
dc.identifier.issn1567-1348de_CH
dc.identifier.issn1567-7257de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/1666-
dc.description.abstractBackground: The intestinal microbiome is a complex community and its role in influencing human health is poorly understood. While conventional microbiology commonly attributes digestive disorders to a single microorganism, a metagenomics approach can detect multiple pathogens simultaneously and might elucidate the role of microbial communities in the pathogenesis of intestinal diseases. We present a proof-of-concept that a shotgun metagenomics approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples. Methods: In October 2012, we obtained stool specimens from patients with persistent diarrhea in south Côte d’Ivoire. Four stool samples were purposefully selected and subjected to microscopy, multiplex polymerase chain reaction (PCR), and a metagenomics approach. For the latter, we employed the National Center for Biotechnology Information nucleotide database and screened for 36 pathogenic organisms (bacteria, helminths, intestinal protozoa, and viruses) that may cause digestive disorders. We further characterized the bacterial population and the prevailing resistance patterns by comparing our metagenomics datasets with the genome-specific markers database and with the comprehensive antibiotic resistance database. Results: In the four patients, the metagenomics approach identified between eight and 11 pathogen classes that potentially cause digestive disorders. For bacterial pathogens, the diagnostic agreement between multiplex PCR and metagenomics was high; yet, metagenomics diagnosed several bacteria not detected by multiplex PCR. In contrast, some of the helminth and intestinal protozoa infections detected by microscopy were missed by metagenomics. The antimicrobial resistance analysis revealed the presence of genes conferring resistance to several commonly used antibiotics. Conclusions: A metagenomics approach provides detailed information on the presence and diversity of pathogenic organisms in human stool samples. Metagenomics studies allow for in-depth molecular characterization such as the antimicrobial resistance status, which may be useful to develop setting-specific treatment decisions. While metagenomics approaches remain challenging, the benefits of gaining new insights into intestinal microbial communities call for a broader application in epidemiologic studies.de_CH
dc.language.isoende_CH
dc.publisherElsevierde_CH
dc.relation.ispartofInfection, Genetics and Evolutionde_CH
dc.rightsLicence according to publishing contractde_CH
dc.subjectBacterial strain typingde_CH
dc.subjectCôte d'Ivoirede_CH
dc.subjectDiarrheade_CH
dc.subjectMetagenomicsde_CH
dc.subjectPathobiomede_CH
dc.subjectResistomede_CH
dc.subject.ddc570: Biologiede_CH
dc.titleMetagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept studyde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementLife Sciences und Facility Managementde_CH
zhaw.organisationalunitInstitut für Umwelt und Natürliche Ressourcen (IUNR)de_CH
zhaw.publisher.placeAmsterdamde_CH
dc.identifier.doi10.1016/j.meegid.2015.08.044de_CH
zhaw.funding.euNode_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.end397de_CH
zhaw.pages.start389de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume40de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.webfeedUmweltgenomikde_CH
zhaw.webfeedHealth Research Hub (LSFM)de_CH
zhaw.funding.zhawIn-depth molecular analysis of stool and water samples collected in Kampala, Ugandade_CH
Appears in collections:Publikationen Life Sciences und Facility Management

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Schneeberger, P. H. H., Becker, S. L., Pothier, J. F., Duffy, B., N’Goran, E. K., Beuret, C., Frey, J. E., & Utzinger, J. (2016). Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study. Infection, Genetics and Evolution, 40, 389–397. https://doi.org/10.1016/j.meegid.2015.08.044
Schneeberger, P.H.H. et al. (2016) ‘Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study’, Infection, Genetics and Evolution, 40, pp. 389–397. Available at: https://doi.org/10.1016/j.meegid.2015.08.044.
P. H. H. Schneeberger et al., “Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study,” Infection, Genetics and Evolution, vol. 40, pp. 389–397, Jun. 2016, doi: 10.1016/j.meegid.2015.08.044.
SCHNEEBERGER, Pierre H.H., Sören L. BECKER, Joël F. POTHIER, Brion DUFFY, Eliézer K. N’GORAN, Christian BEURET, Jürg E. FREY und Jürg UTZINGER, 2016. Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study. Infection, Genetics and Evolution. Juni 2016. Bd. 40, S. 389–397. DOI 10.1016/j.meegid.2015.08.044
Schneeberger, Pierre H.H., Sören L. Becker, Joël F. Pothier, Brion Duffy, Eliézer K. N’Goran, Christian Beuret, Jürg E. Frey, and Jürg Utzinger. 2016. “Metagenomic Diagnostics for the Simultaneous Detection of Multiple Pathogens in Human Stool Specimens from Côte d’Ivoire : A Proof-of-Concept Study.” Infection, Genetics and Evolution 40 (June): 389–97. https://doi.org/10.1016/j.meegid.2015.08.044.
Schneeberger, Pierre H. H., et al. “Metagenomic Diagnostics for the Simultaneous Detection of Multiple Pathogens in Human Stool Specimens from Côte d’Ivoire : A Proof-of-Concept Study.” Infection, Genetics and Evolution, vol. 40, June 2016, pp. 389–97, https://doi.org/10.1016/j.meegid.2015.08.044.


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