title: Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study.
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.
authors.affiliation: Department of Diagnostics and Risk Assessment Plant Protection, Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland; Department of Virology, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland. Electronic address: pierre.schneeberger@unibas.ch.
authors.forename: Pierre H H
authors.initials: PHH
authors.lastname: Schneeberger
authors.affiliation: Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany. Electronic address: soeren.becker@becker-malente.de.
authors.forename: Sören L
authors.initials: SL
authors.lastname: Becker
authors.affiliation: Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland. Electronic address: joel.pothier@zhaw.ch.
authors.forename: Joël F
authors.initials: JF
authors.lastname: Pothier
authors.affiliation: Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland. Electronic address: brion.duffy@zhaw.ch.
authors.forename: Brion
authors.initials: B
authors.lastname: Duffy
authors.affiliation: Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire. Electronic address: eliezerngoran@yahoo.fr.
authors.forename: Eliézer K
authors.initials: EK
authors.lastname: N'Goran
authors.affiliation: Department of Virology, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland. Electronic address: christian.beuret@babs.admin.ch.
authors.forename: Christian
authors.initials: C
authors.lastname: Beuret
authors.affiliation: Department of Diagnostics and Risk Assessment Plant Protection, Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland. Electronic address: juerg.frey@agroscope.admin.ch.
authors.forename: Jürg E
authors.initials: JE
authors.lastname: Frey
authors.affiliation: Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland. Electronic address: juerg.utzinger@unibas.ch.
authors.forename: Jürg
authors.initials: J
authors.lastname: Utzinger
mesh_terms: D000293:Adolescent; D000328:Adult; D000890:Anti-Infective Agents / Q000494:pharmacology; D002648:Child; D002675:Child, Preschool; D015897:Comorbidity; D019295:Computational Biology / Q000379:methods; D007560:Cote d'Ivoire; D003967:Diarrhea / Q000175:diagnosis* / Q000453:epidemiology / Q000209:etiology*; D004352:Drug Resistance, Microbial; D005243:Feces / Q000382:microbiology* / Q000469:parasitology* / Q000821:virology; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D054892:Metagenome; D056186:Metagenomics / Q000379:methods / Q000592:standards; D015203:Reproducibility of Results; D055815:Young Adult
chemical_list: D000890:Anti-Infective Agents
keywords: Bacterial strain typing; Côte d'Ivoire; Diarrhea; Metagenomics; Pathobiome; Resistome