Use of degenerate primers to detect and quantify torA gene harbored by specific spoilage organisms of fish

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Dehaut, Alexandre | Chollet, Marlène | Jacques, Philippe | Krzewinski, Frédéric | N'Guessan, Assi | Kol, Ossarath | Grard, Thierry | Brisabois, Anne | Duflos, Guillaume

Edité par CCSD -

International audience. Freshness is a key parameter of fish quality assessment. This matrix is highly perishable thus, objective tools for freshness estimation are required. Fish spoilage results from both autolytic activities and exogenous actions of specific spoilage organisms (SSO). The flesh of marine fish is characterized by the presence of Trimethylamine N-oxide (TMAO) involved in the osmoregulation process. TMAO can be used by bacteria from the genus Vibrio, Photobacterium, Shewanella as final electron acceptor and its reduction, thanks to TMAO reductase encoded by torA, leads to the production of TMA responsible of the specific fishy odor of spoiled fish.An in silico approach using biofinformatics tools combining R software, NRDB, NRPS primer (Laboratoire ProBioGEM) and AmplifX was set up to design and select primers. Forty torA sequences of Vibrio, nine of Shewanella and nine of Photobacterium were used to select a set of twelve primers. After a first in vitro screening of primers (absence of important primer dimers, ability to amplify a unique PCR product), a pair of primers amplifying a 400 bp fragment was selected to further analysis. The pair was tested on bacterial DNA of S.putrefaciens, P.phosphoreum, P.damselae, V.vulnificus, V.alginolyticus and two strains isolated from a spoiled whiting, identified as Burkholderia cepacia and member of S.putrefaciens group. Then, primer concentrations and annealing temperature were optimized for the selected pair with DNA from Photobacterium and Vibrio strains.Results on bacterial DNA are encouraging for Vibrio and Photobacterium species with a good efficiency (> 90%) and an acceptable range of quantification (µg.mL-1 to pg.mL-1). Selected primers showed a poor specificity on S.putrefaciens and whiting isolated strains but a 400 bp fragment is nevertheless observed. Secondly, total DNA extract from a few fresh and spoiled fish samples have been analyzed thanks to the selected pair of primers.

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