Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation

Ozone-based treatments for inactivation of Salmonella enterica in tree nuts: Inoculation protocol and surrogate suitability considerations

The feasibility of using gaseous ozone, alone or in combination with other treatments, to decontaminate in-shell almonds and pistachios, prepared under different pathogen-inoculation conditions, was explored. Nuts were inoculated with either Salmonella enterica serovar Enteritidis or a potential Salmonella surrogate, Enterococcus faecium OSY 31284. The effect of inoculation method (with or without vacuum application), and of drying inoculated nuts (up to three days) on treatment efficacy was investigated. Inoculated nuts were subjected to gaseous ozone alone (almonds, pistachios) or ozone in combination with heating in brine solution (pistachios). Ozone treatment included application of vacuum (10 in Hg), followed by vessel pressurization to 12.5 psig with ozone‑oxygen mixture (160 g ozone/m³ gas mixture) and holding for 30 min. Heating was conducted in a brine solution (5% NaCl) at 70 °C, for 10 min. Ozone-based treatments were significantly more effective (P < 0.05) on almonds than pistachios, with maximum S. Enteritidis reduction of 2.9 vs. 0.8 log CFU/g, regardless of inoculation method or the drying time. Treatment of inoculated pistachios with heated brine and gaseous ozone reduced S. Enteritidis population by 5.0 to 7.0 log CFU/g and was not significantly more effective than treatment with heated brine alone (reduction of 4.8 to 7.1 log CFU/g). Application of vacuum during inoculation increased bacterial population on nut kernels by approximately 1.2 log CFU/g, but the increase in inoculum population had no effect on inactivation of either species of inoculated bacteria. Decontamination treatments were less effective against both bacteria by up to 2 log CFU/g when drying time of inoculated nuts increased. E. faecium was significantly more resistant to heat and ozone treatment (P < 0.05) than was S. Enteritidis on pistachios, but not on almonds. Results of this study show that laboratory methodology affects observed treatment effectiveness. Considering its high resistance to the heat-ozone combination, E. faecium may not be a suitable surrogate for S. Enteritidis during processing of pistachios by this treatment. Efficacy of ozone gas to decontaminate S. Enteritidis-inoculated nuts depends heavily on the type of nut. Although reductions of S. Enteritidis populations on in-shell pistachios are low, treatment of in-shell almonds resulted in greater reductions, indicating the promise of this technology to enhance the safety of specific nut products.

Decontamination of Chia and Flax Seed Inoculated with Salmonella and Surrogate, Enterococcus faecium NRRL B-2354, Using a Peracetic Acid Sanitizing Solution: Antimicrobial Efficacy and Impact on Seed Functionality

Raw chia and flax seeds are increasingly associated with Salmonella contamination. However, intervention technologies for these seeds that maintain them in a raw state, without causing clumping because of mucilage production upon moisture exposure, are limited. In this study, a commercial ethanol and paracetic acid sanitizing solution meeting these criteria was evaluated for efficacy against Salmonella and Enterococcus faecium NRRL B-2354, a known Salmonella surrogate for thermal intervention technologies. Samples (100 g each) of chia and flax seeds ( n = 5) were inoculated with either a cocktail of Salmonella Newport, Senftenberg, Oranienburg, Saintpaul, Typhimurium DT104, and Cubana or E. faecium NRRL B-2354. After overnight acclimatization, samples were treated with 4 mL of sanitizing solution per sample and then held at ambient temperature (20 to 25°C) for 1 h before bacterial enumeration. Separate 1-kg-treated batches were evaluated for germination ability (4 replicates of 100-g samples), as well as nutrient content and rancidity ( n = 3), compared with untreated control. Following the posttreatment holding time, these batches were dried back to original moisture content at 70°C to evaporate residual sanitizing solution, thereby stopping treatment. The sanitizing solution was found to be an effective intervention method for chia and flax seeds, reducing Salmonella to below the level of detection by more than 4 and more than 5 average log CFU/g, respectively. Germination was not significantly affected ( P ≥ 0.05) for chia seed. For both seeds, nutrition and rancidity were not significantly affected ( P ≥ 0.05). Furthermore, E. faecium NRRL B-2354 was found to be an appropriate Salmonella surrogate for treatment of chia and flax seeds with this sanitizing solution, showing comparable but higher resistance to treatment with the sanitizing solution than the Salmonella cocktail.

Validation of Enterococcus faecium as a surrogate for Salmonella under different processing conditions for peanuts and pecans

Food Safety and Modernization Act (FSMA) Preventive Control rules require nut processors validate thermal processes to ensure a desirable log reduction of Salmonella is achieved. Due to the complex nature of nut and nut products, processes and equipment, it is difficult to use one validation study for all and may requires individual equipment be validated at the plant level. In plant validation studies, pathogens such as Salmonella cannot be used due to the risk of contamination, thus the suitability of a non-pathogenic organism, Enterococcus faecium as a surrogate for Salmonella was evaluated for peanut and pecan thermal processing. Stagnant and forced dry air heating conditions, (120 °C (20, 30, 40 min), 130 °C (10, 20, 30 min), 140 °C (10, 20, 30 min)) were evaluated for unblanched peanut kernels. Oil heating conditions (116 °C, 121 °C, and 127 °C for 0.5, 1.0, 1.5, 2.0, 2.5 min) were evaluated for pecan kernels. Inshell pecans are conditioned in hot or cold water to facilitate the shelling process. Water heating conditions (75 °C (20, 40, 80, 120 s), 80 °C (20, 40, 80, 120 s), 85 °C (20, 40, 80, 120 s), 90 °C (20, 40, 60, 80 s), and 95 °C (20, 40, 60, 80 s)) were evaluated for inshell pecans. Under conditions, except forced air treatment, E. faecium reductions (Log N/N₀) were either not significantly different (P > 0.05) or significantly lower than Salmonella (P < 0.05), making it a suitable surrogate for the processes evaluated.

Radio-Frequency Processing for Inactivation of Salmonella enterica and Enterococcus faecium NRRL B-2354 in Black Peppercorn

Several Salmonella outbreaks linked to black pepper call for effective inactivation processes, because current decontamination methods result in quality deterioration. Radio-frequency (RF) heating provides a rapid heating rate and volumetric heating, resulting in a shorter come-up time. This allows for choosing a high-temperature and short-time combination to achieve the desired inactivation with minimal quality deterioration. The objectives of this study were to evaluate RF heating for inactivation of Salmonella enterica and Enterococcus faecium in black peppercorn and evaluate quality changes of RF-treated black peppercorn. Black peppercorns were inoculated with a five-strain cocktail of Salmonella or E. faecium to attain initial population levels of 6.8 and 7.3 log CFU/g, respectively, and were then adjusted to a moisture content of 12.7% (wet basis) and a water activity of 0.60 at room temperature. A stability test was performed to quantify the microbial reduction during inoculation and equilibration before RF heating inactivation. During RF heating, the cold spot was determined to be at the center on the top surface of the treated sample. In addition to inoculating the entire sample, an inoculated packed sample was placed at the cold spot of the tray. An RF heating time of 2.5 min provided a 5.31- and 5.26-log CFU/g reduction in the entire sample contained in the tray for Salmonella and E. faecium, respectively. Color parameters (L*, a*, b*), piperine content, total phenolics, scavenging activity, and most of the volatile compounds of 2.5-min RF-treated samples were not significantly different from those of the control samples. These data suggest that RF heating is a promising thermal inactivation treatment for Salmonella without significant quality deterioration, and E. faecium seems to be a suitable surrogate for Salmonella to validate the efficacy of RF heating of black peppercorn.

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

BACKGROUND

Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.

RESULTS

E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.

CONCLUSIONS

Beyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.

Testing a Nonpathogenic Surrogate Microorganism for Validating Desiccation-Adapted Salmonella Inactivation in Physically Heat-Treated Broiler Litter

Thermal resistance of desiccation-adapted Salmonella Senftenberg 775W was compared with that of Enterococcus faecium NRRL B-2354 in aged broiler litter. Aged broiler litter with 20, 30, and 40% moisture contents was inoculated separately with desiccation-adapted Salmonella Senftenberg 775W and E. faecium NRRL B-2354 at ca. 5 to 6 log CFU/g and then heat treated at 75, 85, and 150°C. At all tested temperatures, desiccation-adapted E. faecium NRRL B-2354 was more heat resistant than desiccation-adapted Salmonella Senftenberg 775W ( P < 0.05). During the treatments at 75 and 85°C, E. faecium NRRL B-2354 in aged broiler litter with all moisture contents was reduced by 2.89 to 4.12 log and was above the detection limit of direct plating (1.30 log CFU/g), whereas Salmonella Senftenberg 775W could not be detected by enrichment (>5-log reduction) during holding time at these temperatures. At 150°C, E. faecium NRRL B-2354 in aged broiler litter with 20 and 30% moisture contents was still detectable by enrichment after heat exposure for up to 15 min, whereas Salmonella Senftenberg 775W in aged broiler litter with all moisture contents could not be detected throughout the entire treatment. Our results revealed that E. faecium NRRL B-2354 can be used as a surrogate for Salmonella to validate the thermal processing of poultry litter by providing a sufficient safety margin. This study provides a practical tool for poultry litter processors to evaluate the effectiveness of their thermal processing.

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

Enterococcus durans KLDS6.0930 has previously been shown to have probiotic potential. However, being a potential clinical pathogen, it becomes necessary to evaluate its safety status for novel potential probiotic use. The purpose of this study is to systematically evaluate the safety of E. durans KLDS6.0930 based on its genomics, phenotypic characteristics and oral toxicity. The complete genome of E. durans KLDS6.0930 was sequenced and analyzed for safety-related genes. Antibiotic susceptibility and the production of harmful metabolites were tested. A 28-day repeated oral dose toxicity test was implemented in rats. In vitro, E. durans KLDS6.0930 was resistant to five antibiotics, with intrinsic resistances to four antibiotics and no identified genes for the last. E. durans KLDS6.0930 was not hemolytic and virulence factors were non-functional in its genome. E. durans KLDS6.0930 produced a small amount of tyramine and phenethylamine; genes encoding tyramine decarboxylase were identified. In addition, genotype and phenotype analyses showed that the strain did not have the ability to generate D-lactic acid, indole, or nitroreductase. In vivo, E. durans KLDS6.0930 did not induce adverse effects on the organs, hematological and serum biochemical parameters, or cecal bacterial populations in the oral toxicity test. These results indicate that E. durans KLDS6.0930 can be safely used as a potential probiotic for human consumption and animal feed.

Safety assessment and functional properties of four enterococci strains isolated from regional Argentinean cheese

The members of the Enterococcus genus are widely distributed in nature. Its strains have been extensively reported to be present in plant surfaces, soil, water and food. In an attempt to assess their potential application in food industry, four Enterococcus faecium group-strains recently isolated from Argentinean regional cheese products were evaluated using a combination of whole genome analyses and in vivo assays. In order to identify these microorganisms at species level, in silico analyses using their newly reported sequences were conducted. The average nucleotide identity (ANI), in silico DNA-DNA hybridization, and phylogenomic trees constructed using core genome data allowed IQ110, GM70 and GM75 strains to be classified as E. faecium while IQ23 strain was identified as E. durans. Besides their common origin, the strains showed differences in their genetic structure and mobile genetic element content. Furthermore, it was possible to determine the absence or presence of specific features related to growth in milk, cheese ripening, probiotic capability and gut adaptation including sugar, amino acid, and peptides utilization, flavor compound production, bile salt tolerance as well as biogenic amine production. Remarkably, all strains encoded for peptide permeases, maltose utilization, bile salt tolerance, diacetyl and tyramine production genes. On the other hand, some variability was observed regarding citrate and lactose utilization, esterase, and cell wall-associated proteinase. In addition, while strains were predicted to be non-human pathogens by the in silico inspection of pathogenicity and virulence factors, only the GM70 strain proved to be non-virulent in Galleria mellonella model. In conclusion, we propose that, in order to improve the rational selection of strains for industrial applications, a holistic approach involving a comparative genomic analysis of positive and negative features as well as in vivo evaluation of virulence behavior should be performed.

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening

Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce

Despite continuing efforts to reduce foodborne pathogen contamination of fresh produce, significant outbreaks continue to occur. Identification of appropriate surrogates for foodborne pathogens facilitates relevant research to identify reservoirs and amplifiers of these contaminants in production and processing environments. Therefore, the objective of this study was to identify environmental Escherichia coli isolates from manures (poultry, swine and dairy) and surface water sources with properties similar to those of the produce associated foodborne pathogens E. coli O157:H7 and Salmonella enterica serotype Typhimurium. The most similar environmental E. coli isolates were from poultry (n=3) and surface water (n=1) sources. The best environmental E. coli surrogates had cell surface characteristics (zeta potential, hydrophobicity and exopolysaccharide composition) that were similar (i.e., within 15%) to those of S. Typhimurium and/or formed biofilms more often when grown in low nutrient media prepared from lettuce lysates (24%) than when grown on high nutrient broth (7%). The rate of attachment of environmental isolates to lettuce leaves was also similar to that of S. Typhimurium. In contrast, E. coli O157:H7, a commonly used E. coli quality control strain and swine isolates behaved similarly; all were in the lowest 10% of isolates for biofilm formation and leaf attachment. These data suggest that the environment may provide a valuable resource for selection of surrogates for foodborne pathogens.

Approaches toward Identification of Surrogates To Validate Antimicrobial Washes as Preventive Controls for Fresh-Cut Leafy Greens

In fresh-cut produce production, antimicrobials may be used during washing to control the risk of cross-contamination by microbial hazards. Surrogate microorganisms have long been used to validate processes, but none have been identified for validating the efficacy of antimicrobial washing of fresh-cut produce. The objective of this study was to develop procedures by which surrogates may be identified for use in validating the control of cross-contamination for fresh-cut lettuce operations. Four microbial characteristics, which may be important factors in cross-contamination events, were quantitatively evaluated in potential surrogate microorganisms for comparison to a reasonably foreseeable hazard, Escherichia coli O157:H7: sensitivity to chlorine in solution, sensitivity to chlorine on lettuce leaf surfaces, shedding from contaminated lettuce leaves into the water during washing, and cross-contamination from inoculated to uninoculated lettuce leaves during chorine washing. A procedure of practical quantitative experiments for comparing the characteristics reduced the original pool of 80 potential strains, which consisted of lactic acid bacteria, probiotics, and isolates obtained from lettuce enrichment cultures, to five strains: Lactobacillus plantarum, Pediococcus pentosaceus, probiotic 22C, and two lettuce enrichment isolates. These strains may be evaluated in additional studies involving comparisons to other reasonably foreseeable hazards and including other potential process variables that should be understood and controlled to prevent cross-contamination in fresh-cut lettuce operations.

Selection of Surrogate Bacteria for Use in Food Safety Challenge Studies: A Review

Nonpathogenic surrogate bacteria are prevalently used in a variety of food challenge studies in place of foodborne pathogens such as Listeria monocytogenes, Salmonella, Escherichia coli O157:H7, and Clostridium botulinum because of safety and sanitary concerns. Surrogate bacteria should have growth characteristics and/or inactivation kinetics similar to those of target pathogens under given conditions in challenge studies. It is of great importance to carefully select and validate potential surrogate bacteria when verifying microbial inactivation processes. A validated surrogate responds similar to the targeted pathogen when tested for inactivation kinetics, growth parameters, or survivability under given conditions in agreement with appropriate statistical analyses. However, a considerable number of food studies involving putative surrogate bacteria lack convincing validation sources or adequate validation processes. Most of the validation information for surrogates in these studies is anecdotal and has been collected from previous publications but may not be sufficient for given conditions in the study at hand. This review is limited to an overview of select studies and discussion of the general criteria and approaches for selecting potential surrogate bacteria under given conditions. The review also includes a list of documented bacterial pathogen surrogates and their corresponding food products and treatments to provide guidance for future studies.

Ultraviolet (UV-C) inactivation of Enterococcus faecium, Salmonella choleraesuis and Salmonella typhimurium in porcine plasma

The objective of this study was to assess the effectiveness of an ultraviolet (UV-C, 254 nm) irradiation system on reducing the load of Salmonella typhimurium (S. typhimurium), Salmonella choleraesuis (S. choleraesuis) resistant to streptomycin and Enterococcus faecium (E. faecium) inoculated in sterile porcine plasma and then subjected to different UV-C irradiation doses (750, 1500, 3000, 6000 and 9000 J/L) using a pilot plant UV-C device working under turbulent flow. Results indicated that UV-C treatment induced a viability reduction of 0.38, 1.18, 3.59, 4.72 and 5.06 log10 S. typhimurium when irradiated at 750, 1500, 3000, 6000 and 9000 J/L, respectively. The observed log10 reduction of S. choleraesuis was 1.44, 2.68, 5.55, 7.07 and 7.97 at 750, 1500, 3000, 6000 and 9000 J/L, respectively. The best-fit inactivation for S. choleraesuis was the Weibull distribution curve, while the best-fit curve for S. typhimurium was the Weibull plus tail model, indicating that around 10² cfu/mL resistant S. typhimurium was detected when the liquid plasma was UV-C irradiated at doses up to 9000 J/L. Viability reduction for E. faecium was 0.44, 1.01, 3.70, 5.61 and 6.22 log10 when irradiated at 750, 1500, 3000, 6000 and 9000 J/L, respectively, with no bacterial resistance observed with UV-C doses of 6000 J/L or higher. The biphasic model was the best fit model for the inactivation curve for E. faecium. For the three microorganisms tested, about a 4 log-unit reduction was achieved when the liquid plasma was irradiated at 3000J/L. Overall results demonstrate the usefulness of the UV-C system to inactivate bacteria in liquid plasma before spray-drying. We conclude that the UV-C system can provide an additional biosafety feature that can be incorporated into the manufacturing process for spray-dried animal plasma.

Amylolytic Enzymes Acquired from L-Lactic Acid Producing Enterococcus faecium K-1 and Improvement of Direct Lactic Acid Production from Cassava Starch

An amylolytic lactic acid bacterium isolate K-1 was isolated from the wastewater of a cassava starch manufacturing factory and identified as Entercoccus faecium based on 16S rRNA gene sequence analysis. An extracellular α-amylase was purified to homogeneity and the molecular weight of the purified enzyme was approximately 112 kDa with optimal pH value and temperature measured of 7.0 and 40 °C, respectively. It was stable at a pH range of 6.0-7.0, but was markedly sensitive to high temperatures and low pH conditions, even at a pH value of 5. Ba²⁺, Al³⁺, and Co²⁺ activated enzyme activity. This bacterium was capable of producing 99.2% high optically pure L-lactic acid of 4.3 and 8.2 g/L under uncontrolled and controlled pH at 6.5 conditions, respectively, in the MRS broth containing 10 g/L cassava starch as the sole carbon source when cultivated at 37 °C for 48 h. A control pH condition of 6.5 improved and stabilized the yield of L-lactic acid production directly from starch even at a high concentration of starch at up to 150 g/L. This paper is the first report describing the properties of purified α-amylase from E. faecium. Additionally, pullulanase and cyclodextrinase activities were also firstly recorded from E. faecium K-1.

Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods

Certain strains of Enterococcus faecium contribute beneficially to human health and food fermentation. However, other E. faecium strains are opportunistic pathogens due to the acquisition of virulence factors and antibiotic resistance determinants. To characterize E. faecium from soybean fermentation, we sequenced the genomes of 10 E. faecium strains from Korean soybean-fermented foods and analyzed their genomes by comparing them with 51 clinical and 52 non-clinical strains of different origins. Hierarchical clustering based on 13,820 orthologous genes from all E. faecium genomes showed that the 10 strains are distinguished from most of the clinical strains. Like non-clinical strains, their genomes are significantly smaller than clinical strains due to fewer accessory genes associated with antibiotic resistance, virulence, and mobile genetic elements. Moreover, we identified niche-associated gene gain and loss from the soybean strains. Thus, we conclude that soybean E. faecium strains might have evolved to have distinctive genomic features that may contribute to its ability to thrive during soybean fermentation.

Validation of Baking To Control Salmonella Serovars in Hamburger Bun Manufacturing, and Evaluation of Enterococcus faecium ATCC 8459 and Saccharomyces cerevisiae as Nonpathogenic Surrogate Indicators

This study was conducted to validate a simulated commercial baking process for hamburger buns to destroy Salmonella serovars and to determine the appropriateness of using nonpathogenic surrogates (Enterococcus faecium ATCC 8459 or Saccharomyces cerevisiae) for in-plant process validation studies. Wheat flour was inoculated (∼6 log CFU/g) with three Salmonella serovars (Typhimurium, Newport, or Senftenberg 775W) or with E. faecium. Dough was formed, proofed, and baked to mimic commercial manufacturing conditions. Buns were baked for up to 13 min in a conventional oven (218.3°C), with internal crumb temperature increasing to ∼100°C during the first 8 min of baking and remaining at this temperature until removal from the oven. Salmonella and E. faecium populations were undetectable by enrichment (>6-log CFU/g reductions) after 9.0 and 11.5 min of baking, respectively, and ≥5-log-cycle reductions were achieved by 6.0 and 7.75 min, respectively. D-values of Salmonella (three-serovar cocktail) and E. faecium 8459 in dough were 28.64 and 133.33, 7.61 and 55.67, and 3.14 and 14.72 min at 55, 58, and 61°C, respectively, whereas D-values of S. cerevisiae were 18.73, 5.67, and 1.03 min at 52, 55, and 58°C, respectivly. The z-values of Salmonella, E. faecium, and S. cerevisiae were 6.58, 6.25, and 4.74°C, respectively. A high level of thermal lethality was observed for baking of typical hamburger bun dough, resulting in rapid elimination of high levels of the three-strain Salmonella cocktail; however, the lethality and microbial destruction kinetics should not be extrapolated to other bakery products without further research. E. faecium demonstrated greater thermal resistance compared with Salmonella during bun baking and could serve as a conservative surrogate to validate thermal process lethality in commercial bun baking operations. Low thermal tolerance of S. cerevisiae relative to Salmonella serovars limits its usefulness as a surrogate for process validations.

Screening probiotic strains for safety: Evaluation of virulence and antimicrobial susceptibility of enterococci from healthy Chinese infants

The aim of this study was to evaluate the safety of enterococci isolated from Chinese infants and screen out potential probiotic candidates. One hundred eight strains were isolated from feces of 34 healthy infants, and 38 strains of Enterococcus spp. were categorized as follows: E. faecalis (22), E. faecium (10), E. hirae (3), E. durans (2), and E. casseliflavus (1). Of these, 72.7% of E. faecalis came from infants delivered by cesarean and 62.5% of E. faecium from infants delivered vaginally. For safety evaluation of strains, we determined presence of virulence genes; production of hemolysin, gelatinase, and biofilm; and antimicrobial susceptibility of enterococci. Six out of 14 virulence genes were detected with a distribution of gelE (26.3%), cylA (39.4%), esp (15.8%), efaA (63.2%), asa1 (50.0%), and ace (50.0%). In phenotype analysis, 36.8% of the strains exhibited positive hemolytic activity and 17.5% were positive for production of gelatinase. Results of antimicrobial susceptibility showed that different percentages of the strains were resistant to ciprofloxacin (5.2%), vancomycin (7.8%), rifampicin (10.5%), erythromycin (52.6%), and gentamycin (52.6%); remarkably, none of the strains were resistant to ampicillin or chloramphenicol. In total, 10 strains, including 6 E. faecium, which are free of virulence determinants and sensitive to common antimicrobial agents (e.g., ampicillin and vancomycin), were further assessed for their probiotic properties. All strains survived well in simulated gastric fluid and intestinal tract, with maximum reductions of 0.600 and 0.887 log cfu/mL, respectively. Six strains of E. faecium could resist 0.3 to 1.0% bile salt, of which E. faecium WEFA23 presented the highest growth (75.06%) at 1.0% bile salt. All strains showed bile salt hydrolase activity on glycodeoxycholic acid, but only 3 of E. faecium showed activity on taurodeoxycholic acid. These results deliver useful information on the safety of enterococci in infants in China, and provide a protocol to screen probiotics for absence of virulence and antimicrobial susceptibility of enterococci.

Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study

Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information.

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

Enterococcus faecium , a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium . However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium . cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

Development of a Dry Inoculation Method for Thermal Challenge Studies in Low-Moisture Foods by Using Talc as a Carrier for Salmonella and a Surrogate (Enterococcus faecium)

The objective of this study was to obtain dry inocula of Salmonella Tennessee and Enterococcus faecium, a surrogate for thermal inactivation of Salmonella in low-moisture foods, and to compare their thermal resistance and stability over time in terms of survival. Two methods of cell growth were compared: cells harvested from a lawn on tryptic soy agar (TSA-cells) and from tryptic soy broth (TSB-cells). Concentrated cultures of each organism were inoculated onto talc powder, incubated at 35 °C for 24 h, and dried for additional 24 h at room temperature (23 ± 2 °C) to achieve a final water activity of ≤ 0.55 before sieving. Cell reductions of Salmonella and E. faecium during the drying process were between 0.14 and 0.96 log CFU/g, depending on growth method used. There was no difference between microbial counts at days 1 and 30. Heat resistance of the dry inoculum on talc inoculated into a model peanut paste (50 % fat and 0.6 water activity) was determined after 1 and 30 days of preparation, using thermal death time tests conducted at 85 °C. For Salmonella, there was no significant difference between the thermal resistance (D(85 °C)) for the TSB-cells and TSA-cells (e.g. day 1 cells D(85 °C) = 1.05 and 1.07 min, respectively), and there was no significant difference in D(85 °C) between dry inocula on talc used either 1 or 30 days after preparation (P > 0.05). However, the use the dry inocula of E. faecium yielded different results: the TSB-grown cells had a significantly (P < 0.05) greater heat resistance than TSA-grown cells (e.g. D(85 °C) for TSB-cells = 3.42 min versus 2.60 min for TSA-cells). E. faecium had significantly (P < 0.05) greater heat resistance than Salmonella Tennessee regardless what cell type was used for dry inoculum preparation; therefore, it proved to be a conservative but appropriate surrogate for thermal inactivation of Salmonella in low-moisture food matrices under the tested conditions.

Evaluating Pediococcus acidilactici and Enterococcus faecium NRRL B-2354 as Thermal Surrogate Microorganisms for Salmonella for In-Plant Validation Studies of Low-Moisture Pet Food Products

Pediococcus acidilactici ATCC 8042 and Enterococcus faecium NRRL B-2354 were investigated as potential surrogates for Salmonella serovars using thermal death time kinetics in products such as dry pet foods. The D-values of P. acidilactici ATCC 8042, E. faecium NRRL B-2354, and a cocktail of seven Salmonella serovars associated with low-moisture products were determined in a preservative-free dry pet food product at moisture levels of 9.1, 17.9, and 27.0% and heated between 76.7 and 87.8°C. The D-values were calculated by least squares linear regression. The D-values of P. acidilactici ATCC 8042 were higher than those for the Salmonella serovar cocktail but lower than those for E. faecium NRRL 2354. At 9.1% moisture, D-values of 6.54, 11.51, and 11.66 min at 76.7°C, 2.66, 3.22, and 4.08 min at 82.2°C, and 1.07, 1.29, and 1.69 min at 87.8°C were calculated for Salmonella serovars, P. acidilactici ATCC 8042, and E. faecium NRRL B-2354, respectively. The data suggest that the thermal inactivation characteristics of P. acidilactici ATCC 8042 can be utilized as a surrogate to predict the response of Salmonella in dry pet food products that are thermally processed at <90°C.

Identification of Multiple Bacteriocins in Enterococcus spp. Using an Enterococcus-Specific Bacteriocin PCR Array

Twenty-two bacteriocin-producing Enterococcus isolates obtained from food and animal sources, and demonstrating activity against Listeria monocytogenes, were screened for bacteriocin-related genes using a bacteriocin PCR array based on known enterococcal bacteriocin gene sequences in the NCBI GenBank database. The 22 bacteriocin-positive (Bac+) enterococci included En. durans (1), En. faecalis (4), En. faecium (12), En. hirae (3), and En. thailandicus (2). Enterocin A (entA), enterocins mr10A and mr10B (mr10AB), and bacteriocin T8 (bacA) were the most commonly found structural genes in order of decreasing prevalence. Forty-five bacteriocin genes were identified within the 22 Bac+ isolates, each containing at least one of the screened structural genes. Of the 22 Bac+ isolates, 15 possessed two bacteriocin genes, seven isolates contained three different bacteriocins, and three isolates contained as many as four different bacteriocin genes. These results may explain the high degree of bactericidal activity observed with various Bac+ Enterococcus spp. Antimicrobial activity against wild-type L. monocytogenes and a bacteriocin-resistant variant demonstrated bacteriocins having different modes-of-action. Mixtures of bacteriocins, especially those with different modes-of-action and having activity against foodborne pathogens, such as L. monocytogenes, may play a promising role in the preservation of food.

Behavior of Shiga toxigenic Escherichia coli relevant to lettuce washing processes and consideration of factors for evaluating washing process surrogates

Postharvest processes for fresh produce commonly include washing in water containing antimicrobial chemicals, such as chlorine; however, if the antimicrobials are not present in sufficient levels, washing can promote the spread of contamination that might be present. To understand cross-contamination risk during washing, we tested a collection of Shiga toxigenic Escherichia coli (STEC), including O157:H7 and other non-O157 strains, for certain traits during washing of fresh-cut lettuce, i.e., sensitivity to sublethal chlorine levels and ability to cross-contaminate (detach from and attach to) lettuce in the presence of sublethal chlorine levels. Nonpathogenic E. coli Nissle 1917 (EcN) and Pediococcus pentosaceus lactic acid bacterial species (LAB) were included as potential washing process validation surrogates. As measured by extension of the lag phase of growth in media containing 0.15 ppm of chlorine, chlorine sensitivity varied among the STECs. Cross-contamination was assessed by evaluating transfer of bacteria from inoculated to uninoculated leaves during washing. Without chlorine, similar transfer to wash water and uninoculated leaves was shown. In 1 ppm of chlorine, cross-contamination was not detected with most strains, except for the substantial transfer by a STEC O111 strain and EcN in some replicates. Strain O111 and EcN showed less inactivation in 0.25 ppm of chlorine water compared with O157 (P < 0.05). LAB showed similar transfer and similar chlorine inactivation to O157. Considering together the sublethal chlorine sensitivity and detachment/attachment traits, neither EcN nor LAB displayed optimal characteristics as washing process surrogates for the STEC strains, although further evaluation is needed. This work demonstrated a range of behaviors of STEC strains during lettuce washing and may be helpful in hazard characterization, identifying factors to consider for evaluating washing process efficacy, and identifying phenotypic traits to select surrogates to validate washing processes.