Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
EVALUATING THE POTENTIAL OF APPLYING A
METAGENOMICS ANALYSIS FOR INFECTIOUS
DISEASE CLINICAL DIAGNOSTICS AND HOTSPOT
SURVEILLANCE OF VULNERABLE POPULATIONS IN
CHALLENGING SETTINGS.
Wednesday, 1st June 12:20 La Fonda Ballroom Talk (OS‐2.05)
Oksana Lukjancenko 1 , Katrine Joensen 2 , Rene Hendriksen 1 , Patrick Munk 1 , Frank Aarestrup 1
1 Technical University of Denmark, National Food Institute, 2 Statens Serum Institute
World population faces the frequent appearance and rapid spread of infectious diseases. Diarrhea is a
major global disease burden estimated to encompass 1.7 billion cases each year. Diarrhea is typically
a symptom of a gastrointestinal infection, but may also be a symptom of several medical conditions
or a result of drug treatment, e.g. antibiotic‐associated diarrhea. Diarrhea of different infectious
origin (bacterial, viral or parasitic) cannot be distinguished based on history or clinical observations
and thus rapid analyses are important, since specific treatment as well as patient care depends
on the pathogen. In addition, rapid and accurate diagnostics, characterization and comparison of
pathogens are essential to identify both nosocomial and food borne outbreaks.
The current diagnostics involve numerous procedures and typically only result in identification of
a minority of diarrhea‐causing microbial agents, while often the pathogen is not identified in time
to guide clinical management, and in many clinical cases is never identified. With next‐generation
sequencing (NGS) becoming cheaper it has huge potential in routine diagnostics and infection surveillance.
NGS has already been used in clinical settings for elucidating bacterial outbreaks, and it has
been proposed for real‐time typing and surveillance of pathogens. NGS technology can be applied
directly to clinical or sewage samples, potentially advancing diagnostics and leading to even more
rapid diagnostic results.
Here, we evaluated the potential of NGS‐based diagnostics through 1) direct sequencing of fecal
samples from patients with diarrhea; and 2) sequencing of sewage samples, taken in the infor‐ mal
settlement, Kibera in Nairobi, Kenya. Species distribution was determined with MGmapper
(http://cge.cbs.dtu.dk/services/MGmapper/) and NGS‐based diagnostic prediction was performed
based on relative abundance of pathogenic bacteria, viruses, and parasites; and detection of bacterial
pathogen‐specific virulence genes. NGS‐based diagnostic results were compared to conventional
findings for clinical diarrheal samples; and epidemiological data for sewage samples.
The NGS‐based approach enabled pathogen detection comparable to the conventional diagnostics,
and the approach has potential to be extended for detection of all pathogens. Pathogen prediction
in sewage samples showed correspondence to the epidemiological data.
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