Messages from the first International Conference on Clinical Metagenomics (ICCMg).
Metagenomics is recently entering in the clinical microbiology and an increasing number of diagnostic laboratories are now proposing the sequencing & annotation of bacterial genomes and/or the analysis of clinical samples by direct or PCR-based metagenomics with short time to results. In this context, the first International Conference on Clinical Metagenomics (ICCMg) was held in Geneva in October 2016 and several key aspects have been discussed including: i) the need for improved resolution, ii) the importance of interpretation given the common occurrence of sequence contaminants, iii) the need for improved bioinformatic pipelines, iv) the bottleneck of DNA extraction, v) the importance of gold standards, vi) the need to further reduce time to results, vii) how to improve data sharing, viii) the applications of bacterial genomics and clinical metagenomics in better adapting therapeutics and ix) the impact of metagenomics and new sequencing technologies in discovering new microbes. Further efforts in term of reduced turnaround time, improved quality and lower costs are however warranted to fully translate metagenomics in clinical applications.
Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1205 Geneva, Switzerland. Electronic address: etienne.ruppe@hcuge.ch.
Etienne
E
Ruppé
Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland.
Gilbert
G
Greub
Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1205 Geneva, Switzerland; Bacteriology Laboratory, Service of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland.
Jacques
J
Schrenzel
D001424:Bacterial Infections / Q000175:diagnosis / Q000382:microbiology; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D016133:Polymerase Chain Reaction
Bio-informatics; Cancer; Intestinal microbiota; Metagenomics; Next-generation sequencing