Next-generation sequencing: what are the needs in routine clinical microbiology? A survey among clinicians involved in infectious diseases practice

BACKGROUND: The translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs. METHODS: To get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription. RESULTS: According to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics. CONCLUSION: A better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow.