Resistome and virulome diversity of foodborne pathogens isolated from artisanal food production chain of animal origin in the Mediterranean region

Frédérique Pasquali; Lucia Gambi; Alessandra De Cesare; Cecilia Crippa; Vasco Cadavez; Ursula Gonzales-Barron; Antonio Valero; Fouad Achemchem; Alex Lucchi; Antonio Parisi; Gerardo Manfreda

doi:10.4081/ijfs.2022.10899

Resistome and virulome diversity of foodborne pathogens isolated from artisanal food production chain of animal origin in the Mediterranean region

Ital J Food Saf. 2022 Dec 5;11(4):10899. doi: 10.4081/ijfs.2022.10899.

Authors

Affiliations

¹ Department of Agricultural and Food Sciences, Alma Mater Studiorum Università di Bologna, Italy.
² Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Italy.
³ Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal.
⁴ Laboratório para a Sustentabilidade e Tecnologia em Regiões de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal.
⁵ Department of Food Science and Technology, UIC ENZOEM, Agrifood Campus of International Excellence (ceiA3), Universidad de Córdoba, Spain.
⁶ LASIME Laboratory, Agadir Superior School of Technology, Ibn Zohr University, Agadir, Morocco.
⁷ Experimental Zooprophylactic Institute of Puglia e della Basilicata, Bari, Italy.

Abstract

The aim of the present study was to investigate the resistome and virulome diversity of 43 isolates of Listeria monocytogenes, Salmonella enterica and S. aureus collected from artisanal fermented meat and dairy products and their production environments in Portugal, Spain, Italy and Morocco. After DNA extraction, genomes were sequenced, and de novo assembled. Genetic relationships among genomes were investigated by SNP calling and in silico 7- loci MLST. Genomes of the same species belonged to different ST-types demonstrating the circulation of different clones in in the same artisanal production plant. One specific clone included genomes of S. Paratyphi B belonging to ST43 and repeatedly isolated for more than a year in an artisanal sausage production plant. No genomes but three (belonging to Salmonella enterica), were predicted as multiresistant to different antimicrobials classes. Regarding virulence, genomes of L. monocytogenes belonging to ST1, ST3 and ST489, as well as genomes of S.enterica enterica (ST43, ST33, ST314, ST3667, ST1818, ST198) and ST121 S. aureus were predicted as virulent and hypervirulent. The occurrence of virulent and hypervirulent L. monocytogenes, Salmonella enterica and S. aureus strains in artisanal fermented meat and dairy productions as well as in their finished products suggests the need for a specific focus on prevention and control measures able to reduce the risk of these biological hazards in artisanal food productions.

Keywords: Artisanal food; antimicrobial resistance prediction; foodborne bacterial pathogens; virulence prediction.

Grants and funding

Funding: This work was funded within the EU H2020 PRIMA Project ArtiSaneFood “Innovative bio-interventions and risk modelling approaches for ensuring microbial safety and quality of Mediterranean artisanal fermented foods” (PRIMA/0001/2018). U. Gonzales-Barron and V. Cadavez are also grateful to the Portuguese Foundation for Science and Technology (FCT) for funding PRIMA/0001/2018; and for financial support through national funds FCT/MCTES (PIDDAC) to CIMO (UIDB/00690/2020 and UIDP/00690/2020) and SusTEC (LA/P/0007/2021).