Messages from the first International Conference on Clinical Metagenomics (ICCMg)

Etienne Ruppé,Gilbert Greub,Jacques Schrenzel

doi:10.1016/j.micinf.2017.01.005

Abstract

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.

Highlights

It has been suggested that prophages in the sequence type 398 (ST398) S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections
Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., Staphylococcal cassette chromosome mec (SCCmec) XI element, Tn916 transposon and non φ3-prophages) in a majority of bloodstream infection (BSI) isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections
Genome sequencing High-throughput sequencing technology was used to sequence the genomes of 22 ST398 isolates, including 16 BSI isolates randomly selected from our collection, and the six isolates representative of animal-associated isolates described in previous studies [6, 12]

Summary

Introduction

It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. Staphylococcus aureus sequence type 398 (ST398) is a lineage initially described in the early 2000s in colonized livestock pigs and in humans living in close contact with these animals [1, 2]. There has been a widening of the infection spectrum of these bacteria to include humans living in animal-free environments and companion and livestock animals other than pigs. ST398 has since become established as a major S. aureus clone responsible for BSIs in the analyzed area.

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