Isolation of Harveyi clade Vibrio spp. collected in aquaculture farms: How can the identification issue be addressed?

International audienceAquaculture is a fast growing industry with its development hampered by bacterial diseases. Vibriosis caused byHarveyi clade strains is known for causing heavy loss especially in shrimp aquaculture farms. For farm treatmentand pathogen spread management, veterinarians and researchers need reliable bacterial identification tools. Arange of identification methods have been presented for Vibrio spp. in recent literature but little feedback on theirperformance have been made available to this day.This study aims at comparing Vibrio spp. identification methods and providing guidance on their use.Fifty farms were sampled and bacterial colonies were isolated using specific culture media before microscopicanalysis and genomic profiling using ERIC-PCR. A preliminary identification step was carried out using MALDIToFmass spectrometry. Four methods were compared for strain identification on 14 newly isolated Harveyiclade Vibrio spp. strains: whole genome sequencing (digital DNA DNA Hybridization (dDDH)), 5 MLSA schemes,ferric uptake regulation (fur) and lecithin-dependent haemolysin (ldh) single gene based identification methods.Apart from dDDH which is a reference method, no technique could identify all the isolates to the species level.The other tested techniques allowed a faster, cheaper but sub genus clade identification which can be interestingwhen absolute precision is not required. In this regard, MALDI-ToF and fur based identification seemed especiallypromising