The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.

Food safety can be compromised by some bioactive compounds such as biogenic amines that can be specially found in fermented foods due to the bacterial decarboxylation of some amino acids by fermentative or spoilage bacteria. Cava lees are a winery by-product rich in fiber and phenolic compounds and previous works have raised their revalorization from a food safety point of view. The aim of the current work was to investigate whether the use of cava lees can help to control biogenic amine formation in bread and fermented sausages. In bread, only very low levels of biogenic amines (putrescine, cadaverine, and/or spermidine) were found, whose content did not vary with the addition of different amounts of lees. However, the addition of lees in fermented sausages significantly reduced the formation of tyramine and cadaverine. In sausages spontaneously fermented and inoculated with Salmonella spp., the presence of cadaverine and putrescine diminished by 62 and 78%, respectively, due to the addition of cava lees. The addition of cava lees phenolic extract also showed an anti-aminogenic effect (21% for cadaverine and 40% for putrescine), although in a lesser extent than cava lees. Cava lees and their phenolic extract were shown to be an effective strategy to control the undesirable accumulation of high levels of biogenic amines during the production of fermented products.

The revalorization of food processing by-products not only reduces the environmental impact of their disposal, but also generates added economic value. Cava lees consist of inactive cells of Saccharomyces cerevisiae, and though regarded as a valueless winery by-product, they are rich in fiber and phenolic compounds. In this study, a challenge test was performed to assess the effect of cava lees and a phenolic extract (LPE) derived therefrom on the behaviour of technological microbiota (lactic acid bacteria used as a starter culture) and the foodborne pathogens Salmonella spp. and Listeria monocytogenes during the fermentation and ripening of pork sausages. Ten batches of fermented sausages were prepared with and without cava lees or the LPE, and with or without different strains of Latilactobacillus sakei (CTC494 or BAP110). The addition of cava lees reduced the pH values of the meat batter throughout the fermentation and ripening process. No growth-promoting effect on spontaneous lactic acid bacteria (LAB) or the starter culture was observed. In contrast, the presence of cava lees prevented the growth of the tested pathogens (Salmonella and L. monocytogenes), as did the starter culture, resulting in significantly lower counts compared to the control batch. In addition, the combination of cava lees with L. sakei CTC494 had a bactericidal effect on Salmonella. LPE supplementation did not affect the pH values or LAB counts but reduced the mean counts of Salmonella, which were 0.71 log₁₀ lower than the control values at the end of the ripening. The LPE did not exert any additional effect to that of the starters applied alone. The revalorization of cava lees as a natural ingredient to improve the microbiological safety of fermented sausages is a feasible strategy that would promote a circular economy and benefit the environment.

Listeria monocytogenes, the causative agent of listeriosis, is a relevant pathogen in dry fermented sausages (DFSs), and the application of antilisterial starter cultures is an effective intervention strategy to control the pathogen during DFS production. The effect of factors in relation to DFS formulation and production, NaCl (0–40 g/L), Mn (0.08–0.32 g/L), glucose (0–40 g/L) and temperature (3–37 °C), on the behaviour of L. monocytogenes when cocultured with Latilactobacillus sakei 23K (non-bacteriocinogenic) and CTC494 (bacteriocinogenic) strains was studied through a central composite design in meat simulation media. L. sakei and L. monocytogenes counts, pH, lactic acid production and bacteriocin activity were determined in mono and coculture. The pH decrease and lactic acid production were highly influenced by glucose, while production of sakacin K by L. sakei CTC494 was observed at moderate (10 and 20 °C), but not at the lowest (3 °C) and highest (37 °C), temperatures. Coculture growth had no effect on the acidification and bacteriocin production but inhibited and inactivated L. monocytogenes when L. sakei 23K entered the early stationary phase and when L. sakei CTC494 produced sakacin K. Optimal conditions for achieving a 5-log units reduction of L. monocytogenes were at 20 °C, 20 g/L of NaCl, 0.20 g/L of Mn and 40 g/L of glucose, those highlighting the importance of considering product formulation and fermentation conditions for bioprotective starter cultures application.

Dry fermented sausage innovation trends are linked to consumer preferences for clean label and sodium-reduced foods. This study aims to evaluate the effect of the formulation and production process temperature on the dynamics of bacterial communities in fuet-type dry fermented sausages using metataxonomics. Six fuet batches were manufactured, including formulations without and with the addition of nitrifying salts (replaced or not by pork liver auto-hydrolysate as a colouring agent), processed at 3 to 12 °C, and a partial replacement of NaCl by KCl, processed at 12 °C. Fermentation was performed spontaneously or by a starter culture. Physicochemical characterisation and culture-dependent and independent bacterial analyses were performed at day 0, 4 and 12, at the end of ripening (a_w < 0.90) and after storage. Temperature was the most important factor determining the change in pH, a_w and lactic acid bacteria levels while the presence of a starter culture promoted a pH decrease. Metataxonomic analysis showed that low temperature processes and the absence of nitrifying salts allowed the growth of spoilage-related species, while sausages submitted to a mild temperature containing a starter culture and nitrifying salts showed less bacterial diversity. Liver auto-hydrolysate added putative probiotic species to the product. This study provides valuable information to manufacturers who want to innovate safely.

Salmonella enterica serovar Agona is a globally distributed pathogen associated with several hosts, environments and foodborne outbreaks. In this study, we conducted a comprehensive analysis of 4,202 genomes, including an in-depth investigation of 233 French isolates, to elucidate population structure, global dissemination patterns and the genetic determinants underlying ecological adaptation and epidemiological success. Our analyses confirmed the polyphyletic nature of this serotype and identified at least two major genomic lineages differing notably in the presence of fimbrial genes (faeCDE), type VI secretion system (T6SS) gene cluster located in Salmonella pathogenicity island 6 (SPI-6), and SPI-17. The dominant lineage, primarily associated with MLST profile ST13, accounts for approximately 99% of publicly available genomes and exhibits a worldwide distribution across continents, hosts, and ecological niches.The core genome MLST (cgMLST) analysis revealed a major global cluster encompassing 84% of the analyzed genomes, suggesting a common ancestral origin followed by extensive international dissemination. Despite the overall stability of the core genome, Hierarchical Clustering (HC) HC5 analysis uncovered substantial microdiversity within the population, identifying 1,771 distinct clusters. Of these, 1,294 were singletons, while 477 grouped multiple genomes, including several globally distributed clones. Phylogenetic analysis of the 233 French isolates identified 21 well-supported groups linking human infections to poultry, dairy products, environmental sources and imported foods, thereby highlighting complex transmission routes and that a single clone was responsible of the outbreaks occurred in France in 2005 and 2017.Analysis of the accessory genome revealed a broad repertoire of genes associated with tolerance to metals, biocides and antimicrobial compounds, along with the ubiquitous presence of major efflux pump systems, underscoring the strong adaptive capacity of S. Agona to anthropogenic environments. Two Salmonella Genomic Island (SGI)-4-like integrative elements were independently acquired within the French collection and a total of 133 plasmids were predicted, twenty-six of which carried antimicrobial resistance genes. Although our findings suggest that combinations of conserved and accessory determinants (virulence and resistence genes, SGI, plasmids, etc…) contribute to the emergence of clones with epidemic and spread potential. Overall, this study provides new insights into the evolutionary dynamics, ecological versatility and public health relevance of this serotype.