A note on challenge trials to determine the growth of Listeria monocytogenes on mushrooms (Agaricus bisporus)

peer-reviewedIn the EU, food is considered safe with regard to Listeria monocytogenes if the number of micro-organisms does not exceed 100 colony forming units (cfu)/g throughout its shelf-life. Therefore, it is important to determine if a food supports growth of L. monocytogenes. Guidelines for conducting challenge tests for growth assessment of L. monocytogenes on foods were published by the European Union Reference Laboratory (EURL) in 2014. The aim of this study was to use these guidelines to determine if refrigerated, fresh, whole, closed-cap, prepackaged mushrooms (Agaricus bisporus) support the growth of L. monocytogenes. Three batches of mushrooms were artificially inoculated at approximately 100 cfu/g with a three-strain mix of L. monocytogenes and incubated for 2 days at 8°C followed by 4 days at 12°C. L. monocytogenes numbers were determined (in triplicate for each batch) on days 0, 2 and 6. Water activity, pH and total bacterial counts were also determined. There was no increase in the number of L. monocytogenes above the threshold of 0.5 log cfu/g in any of the replicates. In 8 of 9 replicates, the numbers decreased indicating that A. bisporus do not support the growth of L. monocytogenes. As the EU regulations allow < 100 cfu/g if the food cannot support growth of L. monocytogenes, the significance of this study is that mushrooms with < 100 cfu/g may be within the regulations and therefore, quantitative rather than qualitative determination may be required.Safefoo

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries

peer-reviewedMicroorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.Science Foundation Ireland(SFI)Grant Number 13/SIRG/215

Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

peer-reviewedPhenotypic, chemotaxonomic and genotypic data from 12 strains of Escherichia coli were collected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems for E. coli and to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157 E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing of E. coli to species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification of E. coli. The results showed that identification of E. coli strains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.The authors acknowledge the financial contribution of the Spanish INIA, the Research Council of Norway (project 178230/I10), Foundation for Levy on Foods, the Norwegian Research Fees Fund for Agricultural Goods, the Norwegian Independent Meat and Poultry Association, Nortura SA and NHO Matog Landbruk

New Weapons to Fight Old Enemies: Novel Strategies for the (Bio)control of Bacterial Biofilms in the Food Industry

peer-reviewedBiofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, DNA and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. Biofilm formation enhances the ability of the producer/s to persist in a given environment. Pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem for the healthcare and food industries, as their biofilm-forming ability protects them from common cleaning processes and allows them to remain in the environment post-sanitation. In the food industry, persistent bacteria colonize the inside of mixing tanks, vats and tubing, compromising food safety and quality. Strategies to overcome bacterial persistence through inhibition of biofilm formation or removal of mature biofilms are therefore necessary. Current biofilm control strategies employed in the food industry (cleaning and disinfection, material selection and surface preconditioning, plasma treatment, ultrasonication, etc.), although effective to a certain point, fall short of biofilm control. Efforts have been explored, mainly with a view to their application in pharmaceutical and healthcare settings, which focus on targeting molecular determinants regulating biofilm formation. Their application to the food industry would greatly aid efforts to eradicate undesirable bacteria from food processing environments and, ultimately, from food products. These approaches, in contrast to bactericidal approaches, exert less selective pressure which in turn would reduce the likelihood of resistance development. A particularly interesting strategy targets quorum sensing systems, which regulate gene expression in response to fluctuations in cell-population density governing essential cellular processes including biofilm formation. This review article discusses the problems associated with bacterial biofilms in the food industry and summarizes the recent strategies explored to inhibit biofilm formation, with special focus on those targeting quorum sensing.Science Foundation Irelan

Inactivation of indicator microorganisms and biological hazards by standard and/or alternative processing methods in Category 2 and 3 animal by-products and derived products to be used as organic fertilisers and/or soil improvers

The European Commission requested EFSA to assess if different thermal processes achieve a 5 log10 reduction in Enterococcus faecalis or Salmonella Senftenberg (775W) and (if relevant) a 3 log10 reduction in thermoresistant viruses (e.g. Parvovirus) as well as if different chemical processes achieve a 3 log10 reduction of eggs of Ascaris sp., in eight groups of Category 2 and 3 derived products and animal by-products (ABP). These included (1) ash derived from incineration, co-incineration and combustion; (2) glycerine derived from the production of biodiesel and renewable fuels; (3) other materials derived from the production of biodiesel and renewable fuels; (4) hides and skins; (5) wool and hair; (6) feathers and down; (7) pig bristles; and (8) horns, horn products, hooves and hoof products. Data on the presence of viral hazards and on thermal and chemical inactivation of the targeted indicator microorganisms and biological hazards under relevant processing conditions were extracted via extensive literature searches. The evidence was assessed via expert knowledge elicitation. The certainty that the required log10 reductions in the most resistant indicator microorganisms or biological hazards will be achieved for each of the eight groups of materials mentioned above by the thermal and/or chemical processes was (1) 99–100% for the two processes assessed; (2) 98–100% in Category 2 ABP, at least 90–99% in Category 3 ABP; (3) 90–99% in Category 2 ABP; at least 66–90% in Category 3 ABP; (4) 10–66% and 33–66%; (5) 1–33% and 10–50%; (6) 66–90%; (7) 33–66% and 50–95%; (8) 66–95%, respectively. Data generation on the occurrence and reduction of biological hazards by thermal and/or chemical methods in these materials and on the characterisation of the usage pathways of ABP as organic fertilisers/soil improvers is recommended

Update of the list of QPS-recommended microbiological agents intentionally added to food or feed as notified to EFSA 16: suitability of taxonomic units notified to EFSA until March 2022

The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Of the 50 microorganisms notified to EFSA in October 2021 to March 2022 (inclusive), 41 were not evaluated: 10 filamentous fungi, 1 Enterococcus faecium, 1 Clostridium butyricum, 3 Escherichia coli and 1 Streptomyces spp. because are excluded from QPS evaluation, and 25 TUs that have already a QPS status. Nine notifications, corresponding to seven TUs were evaluated: four of these, Streptococcus salivarius, Companilactobacillus formosensis, Pseudonocardia autotrophica and Papiliotrema terrestris, being evaluated for the first time. The other three, Microbacterium foliorum, Pseudomonas fluorescens and Ensifer adhaerens were re-assessed. None of these TUs were recommended for QPS status: Ensifer adhaerens, Microbacterium foliorum, Companilactobacillus formosensis and Papiliotrema terrestris due to a limited body of knowledge, Streptococcus salivarius due to its ability to cause bacteraemia and systemic infection that results in a variety of morbidities, Pseudonocardia autotrophica due to lack of body of knowledge and uncertainty on the safety of biologically active compounds which can be produced, and Pseudomonas fluorescens due to possible safety concerns

Biofilms from a Food Microbiology Perspective: Structures, Functions and Control Strategies

Materials and equipment in food processing industries are colonized by surface-associated microbial communities called biofilms. In these biostructures microorganisms are embedded in a complex organic matrix composed essentially of polysaccharides, nucleic acids and proteins. This organic shield contributes to the mechanical biofilm cohesion and triggers tolerance to environmental stresses such as dehydratation or nutrient deprivation. Notably, cells within a biofilm are more tolerant to sanitation processes and the action of antimicrobial agents than their free living (or planktonic) counterparts. Such properties make conventional cleaning and disinfection protocols normally not effective in eradicating these biocontaminants. Biofilms are thus a continuous source of persistent microorganisms, including spoilage and pathogenic microorganisms, leading to repeated contamination of processed food with important economic and safety impact. Alternatively, in some particular settings, biofilm formation by resident or technological microorganisms can be desirable, due to possible enhancement of food fermentations or as a means of bioprotection against the settlement of pathogenic microorganisms. In the last decades substantial research efforts have been devoted to unravelling mechanisms of biofilm formation, deciphering biofilm architecture and understanding microbial interactions within those ecosystems. However, biofilms present a high level of complexity and many aspects remain yet to be fully understood. A lot of attention has been also paid to the development of novel strategies for preventing or controlling biofilm formation in industrial settings. Further research needs to be focused on the identification of new biocides effective against biofilm-associated microorganisms, the development of control strategies based on the inhibition of cell-to-cell communication, and the potential use of bacteriocins, bacteriocin-producing bacteria, phage, and natural antimicrobials as anti-biofilm agents, among others. This Research Topic aims to provide an avenue for dissemination of recent advances within the “biofilms” field, from novel knowledge on mechanisms of biofilm formation and biofilm architecture to novel strategies for biofilm control in food industrial settings

Industrial and Host Associated Stress Responses in Food Microbes. Implications for Food Technology and Food Safety

Throughout the food processing chain and after ingestion by the host, food associated bacteria have to cope with a range of stress factors such as thermal and/or non-thermal inactivation treatments, refrigeration temperatures, freeze-drying, high osmolarity, acid pH in the stomach or presence of bile salts in the intestine, that threaten bacterial survival. The accompanying plethora of microbial response and adaptation phenomena elicited by these stresses has important implications for food technology and safety. Indeed, while resistance development of pathogenic and spoilage microorganisms may impose health risks for the consumer and impart great economic losses to food industries, reduced survival of probiotic bacteria may strongly compromise their claimed health benefit attributes. As a result, substantial research efforts have been devoted in the last decades to unravel the mechanisms underlying stress response and resistance development in food associated microorganisms in order to better predict and improve (i) the inactivation of foodborne pathogens and spoilage microorganisms on the one hand and (ii) the robustness and performance of beneficial microorganisms on the other. Moreover, the recent implementation of system-wide omics and (single-)cell biology approaches is greatly boosting our insights into the modes of action underlying microbial inactivation and survival. This Research Topic aims to provide an avenue for dissemination of recent advances within the field of microbial stress response and adaptation, with a particular focus not only on food spoilage and pathogenic microorganisms but also on beneficial microbes in foods

A Systematic Review of Bacterial Foodborne Outbreaks Related to Red Meat and Meat Products

Our investigation focused on foodborne outbreaks related to meat and meat products, published in peer reviewed journals in the period 1980–2015. Most of the outbreaks, investigated in this study, were caused by Escherichia coli and Salmonella, causing 33 and 21 outbreaks, respectively, mostly in Europe and the United States. In the E. coli outbreaks, the total number of reported cases was 1966, of which 1543 were laboratory confirmed. The number of cases requiring hospitalization was 476, of whom 233 cases had a hemolytic-uremic syndrome (HUS), and the reported deaths were 32. All of the E. coli outbreaks, except four, were caused by serovar O157:H7. The other four outbreaks were caused by the following serovars: O111:H8, O26:H11, O111, and O103:H25. Fresh processed meat products were the category most frequently implicated. In the Salmonella outbreaks, the total number of all reported cases was 2279, of whom 1891 were laboratory confirmed. The number of reported cases requiring hospitalization was 94, and seven were reported dead. Regarding Salmonella, eight serovars caused those outbreaks. The most common serovar causing Salmonella-related outbreaks was Salmonella Typhimurium. The food category most frequently implicated in those outbreaks was raw-cured fermented sausages. Other organisms linked to meat-associated outbreaks, but less frequently reported, were Staphylococcus aureus, Bacillus cereus, Clostridium perfringens, Clostridium botulinum, and Listeria monocytogenes. Issues of the burden of outbreaks, the challenges of comparing global outbreaks, food attribution, and how the meat industry works to meet consumer demands while maintaining food safety are discussed