Assessment of antibiotic resistance in staphylococci involved in fermented meat product processing

Metagenomic profiles of the antimicrobial resistance in traditional Chinese fermented meat products: Core resistome and co-occurrence patterns

Antimicrobial resistance (AMR) poses a significant challenge to global health, and the presence of antibiotic resistance genes (ARGs) in food poses a potential threat to public health. Traditional Chinese fermented meat products (FMPs) are highly favored because of their unique flavors and cultural value. However, microbial safety and the potential distribution and composition of AMR in these products remain unclear. In this study, a comprehensive analysis of bacterial composition and antibiotic-resistant populations in 216 samples of traditional fermented meat products from different regions of China was conducted using a metagenomic approach. Staphylococcus was the most abundant genus in the samples, accounting for an average abundance of 29.9 %, followed by Tetragenococcus (17.1 %), and Latilactobacillus (3.6 %). A core resistome of FMP samples was constructed for the first time using co-occurrence network analysis, which revealed the distribution and interrelationships of ARGs and bio/metal-resistant genes (BMRGs). Random forest analysis identified the lincosamide nucleotidyltransferase lnuA and the multidrug and toxic compound extrusion (MATE) transporter abeM as potential indicators for assessing the overall abundance of the core resistome. Additionally, Staphylococcus, Acinetobacter, and Pseudomonas were identified as hosts constituting the core resistome. Despite their low abundance, the latter two still serve as major reservoirs of antibiotic resistance genes. Notably, Lactococcus cremoris was identified as the key host for tetracycline resistance genes in the samples, highlighting the need for enhanced resistance monitoring in lactic acid bacteria. Based on our findings, in the microbial safety assessment of fermented meat products, beyond common foodborne pathogens, attention should be focused on detecting and controlling coagulase-negative Staphylococcus, Acinetobacter, and Pseudomonas, and addressing bacterial resistance. The quantitative detection of lnuA and abeM could provide a convenient and rapid method for assessing the overall abundance of the core resistome. Our findings have important implications for the control of bacterial resistance and prevention of pathogenic bacteria in fermented meat products.

Technological and Safety Characterization of Coagulase-Negative Staphylococci Isolated from Sardinian Fermented Sausage Made by Ovine Meat

Ripened sheep sausages are widely consumed in Italy, particularly in Sardinia. Despite their driving role in flavor and color development, coagulase-negative staphylococci in these products have been rarely investigated. A total of 70 CoNS cultures isolated from Sardinian sheep sausages were characterized by rep-PCR and M13-RAPD typing and identified by 16S rDNA sequencing. S. xylosus and S. equorum accounted for more than 70% of the total isolates, whilst S. pasteuri (8.5%), S. succinus (2.8%), and S. haemolyticus (2.8%) were less represented. The genes encoding the synthesis of putrescine, tyramine, cadaverine, and histamine were evaluated by PCR. None of the strains hosted genes for decarboxylases, except one S. pasteuri strain that was potentially a tyramine-producer. Antibiotic resistance was evaluated, along with nitrate reductase, lipolytic, and proteolytic activity, in a pool of selected cultures. Resistance to the primary antibiotics was rather widespread. S. xylosus, S. equorum, and S. pasteuri strains were all resistant to amoxicillin and kanamycin. S. equorum strains were sensitive to all tested antibiotics. S. xylosus strains were all resistant to penicillin B. Conversely, all S. pasteuri strains were resistant to both ampicillin and penicillin B, and four out of five strains exhibited tetracycline resistance. The high variability in the production of sheep sausages makes the search for adjunct cultures of crucial relevance. According to this perspective, the characterization of the autochthonous CSN population represents the first step to approach a starter selection.

The regulation of key flavor of traditional fermented food by microbial metabolism: A review

The beneficial microorganisms in food are diverse and complex in structure. These beneficial microorganisms can produce different and unique flavors in the process of food fermentation. The unique flavor of these fermented foods is mainly produced by different raw and auxiliary materials, fermentation technology, and the accumulation of flavor substances by dominant microorganisms during fermentation. The succession and metabolic accumulation of microbial flora significantly impacts the distinctive flavor of fermented foods. The investigation of the role of microbial flora changes in the production of flavor substances during fermentation can reveal the potential connection between microbial flora succession and the formation of key flavor compounds. This paper reviewed the evolution of microbial flora structure as food fermented and the key volatile compounds that contribute to flavor in the food system and their potential relationship. Further, it was a certain guiding significance for food industrial production.

High-pressure processing effect on conjugal antibiotic resistance genes transfer in vitro and in the food matrix among strains from starter cultures

This study analyzed the effect of high-pressure processing (HPP) on the frequency of conjugal gene transfer of antibiotic resistance genes among strains obtained from starter cultures. Gene transfer ability was analyzed in vitro and in situ in the food matrix. It was found that the transfer of aminoglycoside resistance genes did not occur after high-pressure treatment, either in vitro or in situ. After exposure to HPP, the transfer frequencies of tetracycline, ampicillin and chloramphenicol resistance genes increased significantly compared to the control sample, both in vitro and in situ. The frequency of resistance genes transfer in the food matrix in the pressurized samples did not differ significantly from the in vitro transfer rate. Minimum Inhibitory Concentrations (MICs) for these antibiotics determined for transconjugants were lower or equal to MICs determined for the donors. No significant differences were observed between the MIC values determined for the transconjugants obtained in vitro and in situ. The results suggest that HPP may contribute to the spread of antibiotic resistance. This points to the need to verify starter cultures strains for their antibiotic resistance and pressurization parameters to avoid spreading antibiotic resistance genes.

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.