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Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire : a proof-of-concept study

Schneeberger, Pierre H. H. and Becker, Sören L. and Pothier, Joël F. and Duffy, Brion and N'Goran, Eliézer K. and Beuret, Christian and Frey, Jürg E. and Utzinger, Jürg. (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.

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Official URL: http://edoc.unibas.ch/43732/

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Abstract

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 metagenomic 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 metagenomic approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples.; 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 metagenomic 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 metagenomic datasets with a genome-specific marker database and with a comprehensive antibiotic resistance database.; In the four patients, the metagenomic 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.; A metagenomic approach provides detailed information on the presence and diversity of pathogenic organisms in human stool samples. Metagenomic studies allow for in-depth molecular characterization such as the antimicrobial resistance status, which may be useful to develop setting-specific treatment algorithms. While metagenomic approaches remain challenging, the benefits of gaining new insights into intestinal microbial communities call for a broader application in epidemiologic studies.; ISRCTN86951400.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Eco System Health Sciences > Health Impact Assessment (Utzinger)
UniBasel Contributors:Schneeberger, Pierre and Becker, Sören Leif and Utzinger, Jürg
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Elsevier Science
ISSN:1567-1348
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:30 Aug 2016 09:22
Deposited On:30 Aug 2016 09:22

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