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Histamine intoxication is an important food safety and public health concern. Ripened cheeses are the most common dairy products in which histamine can accumulate. Histamine is formed by the microbiota present in cheese by decarboxylation of histidine, due to the action of the histidine decarboxylase. This study's objective was to identify the responsible for the formation of histamine accumulated in commercial cheeses. The content of histamine of 39 different types of cheeses marketed in Spain, of varying milk origin, was assessed. About one third of the cheeses analysed contained more than 200 mg/kg histamine; two cheeses exceeded 500 mg/kg histamine, the consumption of such cheeses can be harmful or even toxic for consumers. The five cheeses with the highest histamine concentrations were selected for in-depth molecular analysis. Firstly, bacterial and yeast isolates were obtained, and then the total genetic material from the cheeses was analysed, in order to verify the putative presence of the hdc histidine decarboxylase gene. In order to identify the histamine producing microorganisms, the nucleotide sequences of the histidine decarboxylase genes from the cheeses were amplified, and subjected them to Sanger sequencing. In four of the five selected cheeses, the main histamine producer was identified as Lentilactobacillus parabuchneri , whereas in the remaining cheese it was Tetragenococcus halophilus. The hdc gene was located in an unstable plasmid, only present in that cheese sample. Since all histamine producing microorganisms identified in this study are not part of the species used in cheese starter cultures, an improvement of hygienic manufacturing practices and/or thermal treatments for microbial inactivation in milk may be considered to prevent histamine accumulation in cheeses during ripening. [Display omitted] • Up to 51.2% of cheeses analysed contained detectable levels of histamine. • Cheeses containing histamine were made from raw milk (85%) and sheep milk (55%). • Total DNA from cheese is the best starting material to search for the hdc gene. • Lentilactobacillus parabuchneri is associated with commercial cheeses with ≥200 mg/kg histamine. • In one cheese, the hdc sequence corresponds to plasmid pHDC found in various species. [ABSTRACT FROM AUTHOR]