Comparison of two NGS platforms for metagenomic analysis of clinical samples

The advent of next generation sequencing platforms has greatly improved the direct assessment of human metagenomes permitting to obtain results in a time-frame compatible with diagnostic needs. The performances of two platforms, namely Roche 454 GS FLX+ and Illumina MiSeq, have been compared using a metagenomic approach aimed at the identification of the pathogenic agent, an RNA virus in this case, in a clinical sample. Both platforms resulted able to correctly identify the H1N1 virus in the sample, but also provided a similar overview of the microbial community. The detailed analysis of two very different but clinically relevant microorganisms that often co-infect patients, H1N1 and Streptococcus pneumoniae, showed differences in terms of depth of coverage and genome coverage, and showed that some genomic regions are more frequently represented in Illumina sequencing reads, while others in the 454 reads. These findings indicate that the platforms and the corresponding analysis procedures permit the high quality assembly of the H1N1 virus and the identification of the complex microbial community in the sample, supporting the usage of these approaches in a clincal setting.