| Publikationstyp: | Beitrag in wissenschaftlicher Zeitschrift |
| Art der Begutachtung: | Peer review (Publikation) |
| Titel: | Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study |
| Autor/-in: | Schneeberger, Pierre H.H. Becker, Sören L. Pothier, Joël F. Duffy, Brion N'Goran, Eliézer K. Beuret, Christian Frey, Jürg E. Utzinger, Jürg |
| DOI: | 10.1016/j.meegid.2015.08.044 |
| Erschienen in: | Infection, Genetics and Evolution |
| Band(Heft): | 40 |
| Seite(n): | 389 |
| Seiten bis: | 397 |
| Erscheinungsdatum: | Jun-2016 |
| Verlag / Hrsg. Institution: | Elsevier |
| Verlag / Hrsg. Institution: | Amsterdam |
| ISSN: | 1567-1348 1567-7257 |
| Sprache: | Englisch |
| Schlagwörter: | Bacterial strain typing; Côte d'Ivoire; Diarrhea; Metagenomics; Pathobiome; Resistome |
| Fachgebiet (DDC): | 570: Biologie |
| Zusammenfassung: | Background: 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. |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/1666 |
| Volltext Version: | Publizierte Version |
| Lizenz (gemäss Verlagsvertrag): | Lizenz gemäss Verlagsvertrag |
| Departement: | Life Sciences und Facility Management |
| Organisationseinheit: | Institut für Umwelt und Natürliche Ressourcen (IUNR) |
| Publiziert im Rahmen des ZHAW-Projekts: | In-depth molecular analysis of stool and water samples collected in Kampala, Uganda |
| Enthalten in den Sammlungen: | Publikationen Life Sciences und Facility Management |
Dateien zu dieser Ressource:
Es gibt keine Dateien zu dieser Ressource.
Zur Langanzeige
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.
Alle Ressourcen in diesem Repository sind urheberrechtlich geschützt, soweit nicht anderweitig angezeigt.