Title: Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d’Ivoire : a proof-of-concept study
Authors : Schneeberger, Pierre H.H.
Becker, Sören L.
Pothier, Joël F.
Duffy, Brion
N'Goran, Eliézer K.
Beuret, Christian
Frey, Jürg E.
Utzinger, Jürg
Published in : Infection, Genetics and Evolution
Volume(Issue) : 40
Pages : 389
Pages to: 397
Publisher / Ed. Institution : Elsevier
Publisher / Ed. Institution: Amsterdam
Issue Date: Jun-2016
License (according to publishing contract) : Licence according to publishing contract
Type of review: No review
Language : English
Subjects : Bacterial strain typing; Côte d'Ivoire; Diarrhea; Metagenomics; Pathobiome; Resistome
Subject (DDC) : 570: Biology
Abstract: 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.
Departement: Life Sciences and Facility Management
Organisational Unit: Institute of Natural Resource Sciences (IUNR)
Publication type: Article in scientific Journal
DOI : 10.1016/j.meegid.2015.08.044
ISSN: 1567-1348
URI: https://digitalcollection.zhaw.ch/handle/11475/1666
Published as part of the ZHAW project : In-depth molecular analysis of stool and water samples collected in Kampala, Uganda
Appears in Collections:Publikationen Life Sciences und Facility Management

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