Antibiotic susceptibility profiles of Pediococcus pentosaceus from various origins and their implications for the safety assessment of strains with food-technology applications

Abstract

In the fight against the spread of antibiotic resistance (ABR), authorities usually require that strains “intentionally added into the food chain” be tested for their antibiotic susceptibility. This applies to strains used in starter or adjunct cultures for the production of fermented foods, such as many strains of Pediococcus pentosaceus . The European Food Safety Authority (EFSA) recommends testing strains for their antibiotic susceptibility based on both genomic and phenotypic approaches. Furthermore, it proposes a set of antibiotics to assess, as well as a list of microbiological cutoffs (MCs) allowing classifying lactic acid bacteria as susceptible or resistant. Accurate MCs are essential, on the one hand, to avoid false negative strains, which may carry ABR genes and remain unnoticed, and on the other, to avoid false positive strains, which may be discarded while screening potential candidates for food-technology applications. Due to relatively scarce data, MCs have been defined for the whole Pediococcus genus, although differences between different species should be expected. In this study, we investigated the antibiotic susceptibility of thirty-five strains of P. pentosaceus isolated from various matrices in the last seventy years. Minimal inhibitory concentrations (MICs) were determined using a standard protocol, and MIC distributions were established. Phenotypic analyses were complemented with genome sequencing and by seeking known antibiotic resistance genes. The genomes of all the strains were free of known antibiotic resistance genes, but most displayed MICs above the currently defined MCs for chloramphenicol, and all showed excessive MICs for tetracycline. Based on the distributions, we calculated and proposed new MCs for chloramphenicol (16 instead of 4 mg/L) and tetracycline (256 instead of 8 mg/L).