Lag time variability in individual spores of Clostridium botulinum

Germination and outgrowth of Bacillus mycoides KBAB4 spores are impacted by environmental pH, quantitatively analyzed at single cell level with sporetracker

Quantifying spore germination and outgrowth heterogeneity is challenging. Single cell level analysis should provide supplementary knowledge regarding the impact of unfavorable conditions on germination and outgrowth dynamics. This work aimed to quantify the impact of pH on spore germination and outgrowth, investigating the behavior of individual spore crops, produced under optimal and suboptimal conditions. Bacillus mycoides (formerly B. weihenstephanensis) KBAB4 spores, produced at pH 7.4 and at pH 5.5 were incubated at different pH values, from pH 5.2 to 7.4. The spores were monitored by microscopy live imaging, in controlled conditions, at 30 °C. The images were analyzed using SporeTracker, to determine the state of single cells. The impact of pH on germination and outgrowth times and rates was estimated and the correlation between these parameters was quantified. The correlation between germination and outgrowth times was significantly higher at low pH. These results suggest that an environmental pressure highlights the heterogeneity of spore germination and outgrowth within a spore population. Results were consistent with previous observations at population level, now confirmed and extended to single cell level. Therefore, single cell level analyses can be used to quantify the heterogeneity of spore populations, which is of interest in order to control the development of spore-forming bacteria, responsible for food safety issues.

Uptake of UVc induced photoproducts of dipicolinic acid by Bacillus subtilis spores - Effects on the germination and UVc resistance of the spores

Dipicolinic acid (DPA) is a specific molecule of bacterial spores which is essential to their resistance to various stresses such as ultraviolet (UV) exposure and to their germination. DPA has a particular photochemistry that remains imperfectly understood. In particular, due to its ability to absorb UVc radiation, it is likely to form in vitro a wide variety of photoproducts (DPAp) of which only about ten have been recently identified. The photochemical reactions resulting in DPAp, especially those inside the spores, are still poorly understood. Only one of these DPAp, which probably acts as a photosensitizer of DNA upon exposure to UVc, has been identified as having an impact on spores. However, as UVc is required to form DPAp, it is difficult to decouple the overall effect of UVc exposure from the possible effects of DPAp alone. In this study, DPAp were artificially introduced into the spores of the FB122 mutant strain of Bacillus subtilis, one that does not produce DPA. These experiments revealed that some DPAp may play a positive role for the spore. These benefits are visible in an improvement in spore germination rate and kinetics, as well as in an increase in their resistance to UVc exposure.

Moderate high-pressure superdormancy in Bacillus spores: properties of superdormant spores and proteins potentially influencing moderate high-pressure germination

Resistant bacterial spores are a major concern in industrial decontamination processes. An approach known as pressure-mediated germination-inactivation strategy aims to artificially germinate spores by isostatic pressure to mitigate their resistance to inactivation processes. The successful implementation of such a germination-inactivation strategy relies on the germination of all spores. However, germination is heterogeneous, with some “superdormant” spores germinating extremely slowly or not at all. The present study investigated potential underlying reasons for moderate high-pressure (150 MPa; 37°C) superdormancy of Bacillus subtilis spores. The water and dipicolinic acid content of superdormant spores was compared with that of the initial dormant spore population. The results suggest that water and dipicolinic acid content are not major drivers of moderate high-pressure superdormancy. A proteomic analysis was used to identify proteins that were quantified at significantly different levels in superdormant spores. Subsequent validation of the germination capacity of deletion mutants revealed that the presence of protein YhcN is required for efficient moderate high-pressure germination and that proteins MinC, cse60, and SspK may also play a role, albeit a minor one.

IMPORTANCE Spore-forming bacteria are ubiquitous in nature and, as a consequence, inevitably enter the food chain or other processing environments. Their presence can lead to significant spoilage or safety-related issues. Intensive treatment is usually required to inactivate them; however, this treatment harms important product quality attributes. A pressure-mediated germination-inactivation approach can balance the need for effective spore inactivation and retention of sensitive ingredients. However, superdormant spores are the bottleneck preventing the successful and safe implementation of such a strategy. An in-depth understanding of moderate high-pressure germination and the underlying causes of superdormancy is necessary to advance the development of mild high pressure-based spore control technologies. The approach used in this work allowed the identification of proteins that have not yet been associated with reduced germination at moderate high pressure. This research paves the way for further studies on the germination and superdormancy mechanisms in spores, assisting the development of mild spore inactivation strategies.

An Accurate Method for Studying Individual Microbial Lag: Experiments and Computations

Variability in the behavior of microbial foodborne pathogens and spoilers causes difficulties in predicting the safety and quality of food products during their shelf life. Therefore, the quantification of the individual microbial lag phase distribution is of high relevance to the field of quantitative microbial risk assessment. To construct models that predict the effect of changes in environmental conditions on the individual lag, an accurate determination of these distributions is required. Therefore, the current research focuses on the development of an experimental and computational method for accurate determination of individual lag phase distribution. The experimental method is unique in the sense that full liquid volumes are sampled without using dilutions to detect the final population, thereby minimizing experimental errors. Moreover, the method does not aim at the isolation of single cells but at a low number of cells. The fact that several cells can be present in the initial samples instead of having a single cell is considered by the computational method. This method relies on Monte Carlo simulation to predict the individual lag phase distribution for a given set of distribution parameters and maximum likelihood estimation to find the parameters that describe the experimental data best. The method was validated both through simulation and experiments and was found to deliver a desired accuracy.

Bacillus spore germination at moderate high pressure: A review on underlying mechanisms, influencing factors, and its comparison with nutrient germination

Spore-forming bacteria are resistant to stress conditions owing to their ability to form highly resistant dormant spores. These spores can survive adverse environmental conditions in nature, as well as decontamination processes in the food and related industries. Bacterial spores may return to their vegetative state through a process called germination. As spore germination is critical for the loss of resistance, outgrowth, and development of pathogenicity and spoilage potential, the germination pathway has piqued the interest of the scientific community. The inhibition and induction of germination have critical applications in the food industry. Targeted germination can aid in decreasing the resistance of spores and allow the application of milder inactivation procedures. This germination-inactivation strategy allows better maintenance of important food quality attributes. Different stimuli are reported to trigger germination. Among those, isostatic high pressure (HP) has gained increasing attention due to its potential applications in industrial processes. However, pressure-mediated spore germination is extremely heterogeneous as some spores germinate rapidly, while others exhibit slow germination or do not undergo germination at all. The successful and safe implementation of the germination-inactivation strategy, however, depends on the germination of all spores. Therefore, there is a need to elucidate the mechanisms of HP-mediated germination. This work aimed to critically review the current state of knowledge on Bacillus spore germination at a moderate HP of 50-300 MPa. In this review, the germination mechanism, heterogeneity, and influencing factors have been outlined along with knowledge gaps.

Strain-Dependent Cheese Spoilage Potential of Clostridium tyrobutyricum

Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid concentration, moisture and fat content, and the presence of other microorganisms. Previous studies revealed high intraspecies diversity of C. tyrobutyricum strains and variable tolerance toward pH, temperatures, and salt concentrations. These findings indicate that strain-dependent characteristics may be relevant to assess the risk for cheese spoilage if clostridial contamination occurs. In this study, we aimed to compare the phenotypes of 12 C. tyrobutyricum strains which were selected from 157 strains on the basis of genotypic and proteotypic variability. The phenotypic analysis comprised the assessment of gas production and organic acid concentrations in an experimental cheese broth incubated at different temperatures (37, 20, and 14 °C). For all tested strains, delayed gas production at lower incubation temperatures and a strong correlation between gas production and the change in organic acid concentrations were observed. However, considering the time until gas production was visible at different incubation temperatures, a high degree of heterogeneity was found among the tested strains. In addition, variation among replicates of the same strain and differences due to different inoculum levels became evident. This study shows, that, among other factors, strain-specific germination and growth characteristics should be considered to evaluate the risk of cheese spoilage by C. tyrobutyricum.

Suboptimal Bacillus licheniformis and Bacillus weihenstephanensis Spore Incubation Conditions Increase Heterogeneity of Spore Outgrowth Time

Changes with time of a population of Bacillus weihenstephanensis KBAB4 and Bacillus licheniformis AD978 dormant spores into germinated spores and vegetative cells were followed by flow cytometry, at pH ranges of 4.7 to 7.4 and temperatures of 10°C to 37°C for B. weihenstephanensis and 18°C to 59°C for B. licheniformis Incubation conditions lower than optimal temperatures or pH led to lower proportions of dormant spores able to germinate and extended time of germination, a lower proportion of germinated spores able to outgrow, an extension of their times of outgrowth, and an increase of the heterogeneity of spore outgrowth time. A model based on the strain growth limits was proposed to quantify the impact of incubation temperature and pH on the passage through each physiological stage. The heat treatment temperature or time acted independently on spore recovery. Indeed, a treatment at 85°C for 12 min or at 95°C for 2 min did not have the same impact on spore germination and outgrowth kinetics of B. weihenstephanensis despite the fact that they both led to a 10-fold reduction of the population. Moreover, acidic sporulation pH increased the time of outgrowth 1.2-fold and lowered the proportion of spores able to germinate and outgrow 1.4-fold. Interestingly, we showed by proteomic analysis that some proteins involved in germination and outgrowth were detected at a lower abundance in spores produced at pH 5.5 than in those produced at pH 7.0, maybe at the origin of germination and outgrowth behavior of spores produced at suboptimal pH.IMPORTANCE Sporulation and incubation conditions have an impact on the numbers of spores able to recover after exposure to sublethal heat treatment. Using flow cytometry, we were able to follow at a single-cell level the changes in the physiological states of heat-stressed spores of Bacillus spp. and to discriminate between dormant spores, germinated spores, and outgrowing vegetative cells. We developed original mathematical models that describe (i) the changes with time of the proportion of cells in their different states during germination and outgrowth and (ii) the influence of temperature and pH on the kinetics of spore recovery using the growth limits of the tested strains as model parameters. We think that these models better predict spore recovery after a sublethal heat treatment, a common situation in food processing and a concern for food preservation and safety.

Superdormant Spores as a Hurdle for Gentle Germination-Inactivation Based Spore Control Strategies

Bacterial spore control strategies based on the germination-inactivation principle can lower the thermal load needed to inactivate bacterial spores and thus preserve food quality better. However, the success of this strategy highly depends on the germination of spores, and a subpopulation of spores that fail to germinate or germinate extremely slowly hinders the application of this strategy. This subpopulation of spores is termed 'superdormant (SD) spores.' Depending on the source of the germination stimulus, SD spores are categorized as nutrient-SD spores, Ca2+-dipicolinic acid SD spores, dodecylamine-SD spores, and high pressure SD spores. In recent decades, research has been done to isolate these different groups of SD spores and unravel the cause of their germination deficiency as well as their germination capacities. This review summarizes the challenges caused by SD spores, their isolation and characterization, the underlying mechanisms of their germination deficiency, and the future research directions needed to tackle this topic in further depth.

Electrical discharges in water induce spores' DNA damage

Bacterial spores are one of the most resilient life forms on earth and are involved in many human diseases, such as infectious diarrhea, fatal paralytic illnesses and respiratory infections. Here, we investigated the mechanisms involved in the death of Bacillus pumilus spores after exposure to electric arcs in water. Cutting-edge microscopies at the nanoscale did not reveal any structural disorganization of spores exposed to electric arcs. This result suggested the absence of physical destruction by a propagating shock wave or an exposure to an electric field. However, Pulsed-Field Gel Electrophoresis (PFGE) revealed genomic DNA damage induced by UV radiation and Reactive Oxygen Species (ROS). UV induced single-strand DNA breaks and thymine dimers while ROS were mainly involved in base excision. Our findings revealed a correlation between DNA damage and the treatment of spores with electrical discharges.

Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores

Bacterial spores are ubiquitous in nature and can withstand both chemical and physical stresses. Spores can survive food preservation processes and upon outgrowth cause food spoilage as well as safety risks. The heterogeneous germination and outgrowth behavior of isogenic spore populations exacerbates this risk. A major unknown factor of spores is likely to be the inherently heterogeneous spore protein composition. The proteomics methods discussed here help in broadening the knowledge about spore structure and identification of putative target proteins from spores of different spore formers. Approaches to synchronize Bacillus subtilis spore formation, and to analyze spore proteins as well as the physiology of spore germination and outgrowth are also discussed. Live-imaging and fluorescence microscopy techniques discussed here allow analysis, at single cell level, of the 'germinosome', the process of spore germination itself, spore outgrowth and the spore intracellular pH dynamics. For the latter, a recently published improved pHluorin (IpHluorin) under control of the ptsG promoter is applicable. While the data obtained from such tools offers novel insight in the mechanisms of bacterial spore awakening, it may also be used to probe candidate antimicrobial compounds for inhibitory effects on spore germination and strengthen microbial risk assessment.

Development and validation of predictive models for the effect of storage temperature and pH on the growth boundaries and kinetics of Alicyclobacillus acidoterrestris ATCC 49025 in fruit drinks

This study was undertaken to provide quantitative tools for predicting the behavior of the spoilage bacterium Alicyclobacillus acidoterrestris ATCC 49025 in fruit drinks. In the first part of the study, a growth/no growth interface model was developed, predicting the probability of growth as a function of temperature and pH. For this purpose, the growth ability of A. acidoterrestris was studied at different combinations of temperature (15-45 °C) and pH (2.02-5.05). The minimum pH and temperature where growth was observed was 2.52 (at 35 and 45 °C) and 25 °C (at pH ≥ 3.32), respectively. Then a logistic polynomial regression model was fitted to the binary data (0: no growth, 1: growth) and, based on the concordance index (98.8%) and the Hosmer-Lemeshow statistic (6.226, P = 0.622), a satisfactory goodness of fit was demonstrated. In the second part of the study, the effects of temperature (25-55 °C) and pH (3.03-5.53) on A. acidoterrestris growth rate were investigated and quantitatively described using the cardinal temperature model with inflection and the cardinal pH model, respectively. The estimated values for the cardinal parameters T_min, T_max, T_opt and pH_min, pH_max, pH_opt were 18.11, 55.68, 48.60 °C and 2.93, 5.90, 4.22, respectively. The developed models were validated against growth data of A. acidoterrestris obtained in eight commercial pasteurized fruit drinks. The validation results showed a good performance of both models. In all cases where the growth/no growth interface model predicted a probability lower than 0.5, A. acidoterrestris was, indeed, not able to grow in the tested fruit drinks; similarly, when the model predicted a probability above 0.9, growth was observed in all cases. A good agreement was also observed between growth predicted by the kinetic model and the observed kinetics of A. acidoterrestris in fruit drinks at both static and dynamic temperature conditions.

Spore Germination

Despite being resistant to a variety of environmental insults, the bacterial endospore can sense the presence of small molecules and respond by germinating, losing the specialized structures of the dormant spore, and resuming active metabolism, before outgrowing into vegetative cells. Our current level of understanding of the spore germination process in bacilli and clostridia is reviewed, with particular emphasis on the germinant receptors characterized in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. The recent evidence for a local clustering of receptors in a "germinosome" would begin to explain how signals from different receptors could be integrated. The SpoVA proteins, involved in the uptake of Ca2+-dipicolinic acid into the forespore during sporulation, are also responsible for its release during germination. Lytic enzymes SleB and CwlJ, found in bacilli and some clostridia, hydrolyze the spore cortex: other clostridia use SleC for this purpose. With genome sequencing has come the appreciation that there is considerable diversity in the setting for the germination machinery between bacilli and clostridia.

Effect of storage temperature on the lag time of Geobacillus stearothermophilus individual spores

The lag times (λ) of Geobacillus stearothermophilus single spores were studied at different storage temperatures ranging from 45 to 59 °C using the Bioscreen C method. A significant variability of λ was observed among individual spores at all temperatures tested. The storage temperature affected both the position and the spread of the λ distributions. The minimum mean value of λ (i.e. 10.87 h) was observed at 55 °C, while moving away from this temperature resulted in an increase for both the mean and standard deviation of λ. A Cardinal Model with Inflection (CMI) was fitted to the reverse mean λ, and the estimated values for the cardinal parameters T_min, T_max, T_opt and the optimum mean λ of G. stearothermophilus were found to be 38.1, 64.2, 53.6 °C and 10.3 h, respectively. To interpret the observations, a probabilistic growth model for G. stearothermophilus individual spores, taking into account λ variability, was developed. The model describes the growth of a population, initially consisting of N₀ spores, over time as the sum of cells in each of the N₀ imminent subpopulations originating from a single spore. Growth simulations for different initial contamination levels showed that for low N₀ the number of cells in the population at any time is highly variable. An increase in N₀ to levels exceeding 100 spores results in a significant decrease of the above variability and a shorter λ of the population. Considering that the number of G. stearothermophilus surviving spores in the final product is usually very low, the data provided in this work can be used to evaluate the probability distribution of the time-to-spoilage and enable decision-making based on the "acceptable level of risk".

Intracellular survival of Clostridium chauvoei in bovine macrophages

Clostridium chauvoei is the etiological agent of blackleg, a severe disease of domestic ruminants, causing myonecrosis and serious toxemia with high mortality. Despite the known importance of this agent, studies evaluating its pathogenesis of blackleg are scarce, and many are based on an unproven hypothesis that states that macrophages are responsible for carrying C. chauvoei spores from the intestines to muscles in the early stages of blackleg. Therefore, the present study aimed to investigate the survival of C. chauvoei vegetative cells or spores after phagocytosis by a murine macrophage cell line (RAW 264.7) and bovine monocyte-derived macrophages and to profile inflammatory and anti-inflammatory cytokine transcripts of bovine macrophages infected with C. chauvoei vegetative cells or spores. Both vegetative cells and spores of C. chauvoei remain viable after internalization by murine and bovine macrophages. Bovine macrophages infected with vegetative cells showed a pro-inflammatory profile, while those infected with spores displayed an anti-inflammatory profile. Together, these results corroborate the classical hypothesis that macrophages may play a role in the early pathogenesis of blackleg. Moreover, this is the first study to evaluate the infection kinetics and cytokine profile of bovine monocyte-derived macrophages infected with a Clostridium species.

Systematic Assessment of Nonproteolytic Clostridium botulinum Spores for Heat Resistance

Heat treatment is an important controlling factor that, in combination with other hurdles (e.g., pH, aw), is used to reduce numbers and prevent the growth of and associated neurotoxin formation by nonproteolytic C. botulinum in chilled foods. It is generally agreed that a heating process that reduces the spore concentration by a factor of 10(6) is an acceptable barrier in relation to this hazard. The purposes of the present study were to review the available data relating to heat resistance properties of nonproteolytic C. botulinum spores and to obtain an appropriate representation of parameter values suitable for use in quantitative microbial risk assessment. In total, 753 D values and 436 z values were extracted from the literature and reveal significant differences in spore heat resistance properties, particularly those corresponding to recovery in the presence or absence of lysozyme. A total of 503 D and 338 z values collected for heating temperatures at or below 83°C were used to obtain a probability distribution representing variability in spore heat resistance for strains recovered in media that did not contain lysozyme.

IMPORTANCE

In total, 753 D values and 436 z values extracted from literature sources reveal significant differences in spore heat resistance properties. On the basis of collected data, two z values have been identified, z = 7°C and z = 9°C, for spores recovered without and with lysozyme, respectively. The findings support the use of heat treatment at 90°C for 10 min to reduce the spore concentration by a factor of 10(6), providing that lysozyme is not present during recovery. This study indicates that greater heat treatment is required for food products containing lysozyme, and this might require consideration of alternative recommendation/guidance. In addition, the data set has been used to test hypotheses regarding the dependence of spore heat resistance on the toxin type and strain, on the heating technique used, and on the method of D value determination used.

Recovery of Heat Treated Bacillus cereus Spores Is Affected by Matrix Composition and Factors with Putative Functions in Damage Repair

The ability of spores to recover and grow out after food processing is affected by cellular factors and by the outgrowth conditions. In the current communication we studied the recovery and outgrowth of individually sorted spores in BHI and rice broth media and on agar plates using flow cytometry. We show that recovery of wet heat treated Bacillus cereus ATCC 14579 spores is affected by matrix composition with highest recovery in BHI broth or on rice agar plates, compared to BHI agar plates and rice broth. Data show that not only media composition but also its liquid or solid state affect the recovery of heat treated spores. To determine the impact of factors with putative roles in recovery of heat treated spores, specific genes previously shown to be highly expressed in outgrowing heat-treated spores were selected for mutant construction. Spores of nine B. cereus ATCC 14579 deletion mutants were obtained and their recovery from wet heat treatment was evaluated using BHI and rice broth and agar plates. Deletion mutant spores showed different capacity to recover from heat treatment compared to wild type with the most pronounced effect for a mutant lacking BC5242, a gene encoding a membrane protein with C2C2 zinc finger which resulted in over 95% reduction in recovery compared to the wild type in BHI broth. Notably, similar relative performance of wild type and mutants was observed using the other recovery conditions. We obtained insights on the impact of matrix composition and state on recovery of individually sorted heat treated spores and identified cellular factors with putative roles in this process. These results may provide leads for future developments in design of more efficient combined preservation treatments.

Quantifying the effect of water activity and storage temperature on single spore lag times of three moulds isolated from spoiled bakery products

The inhibitory effect of water activity (a_w) and storage temperature on single spore lag times of Aspergillus niger, Eurotium repens (Aspergillus pseudoglaucus) and Penicillium corylophilum strains isolated from spoiled bakery products, was quantified. A full factorial design was set up for each strain. Data were collected at levels of a_w varying from 0.80 to 0.98 and temperature from 15 to 35°C. Experiments were performed on malt agar, at pH5.5. When growth was observed, ca 20 individual growth kinetics per condition were recorded up to 35days. Radius of the colony vs time was then fitted with the Buchanan primary model. For each experimental condition, a lag time variability was observed, it was characterized by its mean, standard deviation (sd) and 5^th percentile, after a Normal distribution fit. As the environmental conditions became stressful (e.g. storage temperature and a_w lower), mean and sd of single spore lag time distribution increased, indicating longer lag times and higher variability. The relationship between mean and sd followed a monotonous but not linear pattern, identical whatever the species. Next, secondary models were deployed to estimate the cardinal values (minimal, optimal and maximal temperatures, minimal water activity where no growth is observed anymore) for the three species. That enabled to confirm the observation made based on raw data analysis: concerning the temperature effect, A. niger behaviour was significantly different from E. repens and P. corylophilum: T_opt of 37.4°C (standard deviation 1.4°C) instead of 27.1°C (1.4°C) and 25.2°C (1.2°C), respectively. Concerning the a_w effect, from the three mould species, E. repens was the species able to grow at the lowest a_w (aw_min estimated to 0.74 (0.02)). Finally, results obtained with single spores were compared to findings from a previous study carried out at the population level (Dagnas et al., 2014). For short lag times (≤5days), there was no difference between lag time of the population (ca 2000 spores inoculated in one spot) and mean (nor 5^th percentile) of single spore lag time distribution. In contrast, when lag time was longer, i.e. under more stressful conditions, there was a discrepancy between individual and population lag times (population lag times shorter than 5^th percentiles of single spore lag time distribution), confirming a stochastic process. Finally, the temperature cardinal values estimated with single spores were found to be similar to those obtained at the population level, whatever the species. All these findings will be used to describe better mould spore lag time variability and then to predict more accurately bakery product shelf-life.

Identification of CdnL, a Putative Transcriptional Regulator Involved in Repair and Outgrowth of Heat-Damaged Bacillus cereus Spores

Spores are widely present in the environment and are common contaminants in the food chain, creating a challenge for food industry. Nowadays, heat treatments conventionally applied in food processing may become milder to comply with consumer desire for products with higher sensory and nutritional values. Consequently subpopulations of spores may emerge that are sublethally damaged rather than inactivated. Such spores may germinate, repair damage, and eventually grow out leading to uncontrolled spoilage and safety issues. To gain insight into both the behaviour of damaged Bacillus cereus spores, and the process of damage repair, we assessed the germination and outgrowth performance using OD595 measurements and microscopy combined with genome-wide transcription analysis of untreated and heat-treated spores. The first two methods showed delayed germination and outgrowth of heat-damaged B. cereus ATCC14579 spores. A subset of genes uniquely expressed in heat-treated spores was identified with putative roles in the outgrowth of damaged spores, including cdnL (BC4714) encoding the putative transcriptional regulator CdnL. Next, a B. cereus ATCC14579 cdnL (BC4714) deletion mutant was constructed and assessment of outgrowth from heat-treated spores under food relevant conditions showed increased damage compared to wild type spores. The approach used in this study allows for identification of candidate genes involved in spore damage repair. Further identification of cellular parameters and characterisation of the molecular processes contributing to spore damage repair may provide leads for better control of spore outgrowth in foods.

Quantification of Nonproteolytic Clostridium botulinum Spore Loads in Food Materials

We have produced data and developed analysis to build representations for the concentration of spores of nonproteolytic Clostridium botulinum in materials that are used during the manufacture of minimally processed chilled foods in the United Kingdom. Food materials are categorized into homogenous groups which include meat, fish, shellfish, cereals, fresh plant material, dairy liquid, dairy nonliquid, mushroom and fungi, and dried herbs and spices. Models are constructed in a Bayesian framework and represent a combination of information from a literature survey of spore loads from positive-control experiments that establish a detection limit and from dedicated microbiological tests for real food materials. The detection of nonproteolytic C. botulinum employed an optimized protocol that combines selective enrichment culture with multiplex PCR, and the majority of tests on food materials were negative. Posterior beliefs about spore loads center on a concentration range of 1 to 10 spores kg(-1). Posterior beliefs for larger spore loads were most significant for dried herbs and spices and were most sensitive to the detailed results from control experiments. Probability distributions for spore loads are represented in a convenient form that can be used for numerical analysis and risk assessments.

Implant Placement in Failed Endodontic Sites: A Review

Dental implants may fail to osseointegrate in sites of endodontic failure. This may occur as a result colonization by various anaerobic and facultative bacterial species. If an implant is placed in a site where vegetative bacteria are residing, the implant may fail to integrate if a bacterial colonization proceeds coronally. If the implant apical cortical bone is thin or if there is an apical fenestration, the colonization may proceed through the thin or nonexistent bone through the covering mucosa, relieving inflammatory pressure to create an apical (retrograde) peri-implantitis. Enterococcus faecalis may be the prime culprit in these types of implant failures. After thorough debridement, the implant may be immediately placed after extraction of an endodontically failed tooth, and the patient treated with an appropriate antibiotic. Alternatively waiting for postextraction healing and subsequent implant placement can be done. Nevertheless, either way may allow for the formation of bacterial vegetative forms or biofilms. The implant surface may be colonized when the surface is exposed to the bacteria. Thorough debridement is crucial. Nonetheless, organisms may persist. Randomized controlled trials are needed to elucidate this issue.

Colonial vs. planktonic type of growth: mathematical modeling of microbial dynamics on surfaces and in liquid, semi-liquid and solid foods

Predictive models are mathematical expressions that describe the growth, survival, inactivation, or biochemical processes of foodborne bacteria. During processing of contaminated raw materials and food preparation, bacteria are entrapped into the food residues, potentially transferred to the equipment surfaces (abiotic or inert surfaces) or cross-contaminate other foods (biotic surfaces). Growth of bacterial cells can either occur planktonically in liquid or immobilized as colonies. Colonies are on the surface or confined in the interior (submerged colonies) of structured foods. For low initial levels of bacterial population leading to large colonies, the immobilized growth differs from planktonic growth due to physical constrains and to diffusion limitations within the structured foods. Indeed, cells in colonies experience substrate starvation and/or stresses from the accumulation of toxic metabolites such as lactic acid. Furthermore, the micro-architecture of foods also influences the rate and extent of growth. The micro-architecture is determined by (i) the non-aqueous phase with the distribution and size of oil particles and the pore size of the network when proteins or gelling agent are solidified, and by (ii) the available aqueous phase within which bacteria may swarm or swim. As a consequence, the micro-environment of bacterial cells when they grow in colonies might greatly differs from that when they grow planktonically. The broth-based data used for modeling (lag time and generation time, the growth rate, and population level) are poorly transferable to solid foods. It may lead to an over-estimation or under-estimation of the predicted population compared to the observed population in food. If the growth prediction concerns pathogen bacteria, it is a major importance for the safety of foods to improve the knowledge on immobilized growth. In this review, the different types of models are presented taking into account the stochastic behavior of single cells in the growth of a bacterial population. Finally, the recent advances in the rules controlling different modes of growth, as well as the methodological approaches for monitoring and modeling such growth are detailed.

Apertures in the Clostridium sporogenes spore coat and exosporium align to facilitate emergence of the vegetative cell

Clostridium sporogenes forms highly heat resistant endospores, enabling this bacterium to survive adverse conditions. Subsequently, spores may germinate, giving rise to vegetative cells that multiply and lead to food spoilage. Electron microscopy was used to visualise changes in spore structures during germination, emergence and outgrowth. C. sporogenes spores were surrounded by an exosporium that was oval in shape and typically 3 μm in length. An aperture of 0.3–0.4 μm was observed at one end of the exosporium. The rupture of the spore coats occurs adjacent to the opening in the exosporium. The germinated cell emerges through this hole in the spore coat and then through the pre-existing aperture in the exosporium, before eventually being released, leaving behind a largely intact exosporium with an enlarged aperture (0.7–1.0 μm) and coat shell. The formation of this aperture, its function and its alignment with the spore coat is discussed.

•

Electron microscopy was used to study structures of Clostridium sporogenes spores.

•

Spore exosporia possessed either a terminal aperture or a lipped protrusion.

•

Cells emerged through the preformed aperture or sporiduct of the spore.

•

Apertures in the spore coat and exosporium were aligned, and may be predetermined.

Influence of food matrix on outgrowth heterogeneity of heat damaged Bacillus cereus spores

Spoilage of heat treated foods can be caused by the presence of surviving spore-formers. It is virtually impossible to prevent contamination at the primary production level as spores are ubiquitous present in the environment and can contaminate raw products. As a result spore inactivation treatments are widely used by food producing industries to reduce the microbial spore loads. However consumers prefer mildly processed products that have less impact on its quality and this trend steers industry towards milder preservation treatments. Such treatments may result in damaged instead of inactivated spores, and these spores may germinate, repair, and grow out, possibly leading to quality and safety issues. The ability to repair and grow out is influenced by the properties of the food matrix. In the current communication we studied the outgrowth from heat damaged Bacillus cereus ATCC 14579 spores on Anopore membrane, which allowed following outgrowth heterogeneity of individual spores on broccoli and rice-based media as well as standard and mildly acidified (pH 5.5) meat-based BHI. Rice, broccoli and BHI pH 5.5 media resulted in delayed outgrowth from untreated spores, and increased heterogeneity compared to BHI pH 7.4, with the most pronounced effect in rice media. Exposure to wet heat for 1 min at 95 °C caused 2 log inactivation and approximately 95% of the spores in the surviving fraction were damaged resulting in substantial delay in outgrowth based on the time required to reach a maximum microcolony size of 256 cells. The delay was most pronounced for heat-treated spores on broccoli medium followed by spores on rice media (both untreated and treated). Interestingly, the increase in outgrowth heterogeneity of heat treated spores on BHI pH 7.4 was more pronounced than on rice, broccoli and BHI pH 5.5 conceivably reflecting that conditions in BHI pH 7.4 better support spore damage repair. This study compares the effects of three main factors, namely heat treatment, pH of BHI and the effect of food matrix highlighting the impact of different (model) food recovery media on outgrowth efficiency and heterogeneity of non-heat-treated and heat-damaged B. cereus spores.

Pressure-Based Strategy for the Inactivation of Spores

Since the first application of high hydrostatic pressure (HHP) for food preservation more than 100 years ago, a wealth of knowledge has been gained on molecular mechanisms underlying the HHP-mediated destruction of microorganisms. However, one observation made back then is still valid, i.e. that HHP alone is not sufficient for the complete inactivation of bacterial endospores. To achieve "commercial sterility" of low-acid foods, i.e. inactivation of spores capable of growing in a specific product under typical storage conditions, a combination of HHP with other hurdles is required (most effectively with heat (HPT)). Although HPT processes are not yet industrially applied, continuous technical progress and increasing consumer demand for minimally processed, additive-free food with long shelf life, makes HPT sterilization a promising alternative to thermal processing.In recent years, considerable progress has been made in understanding the response of spores of the model organism B. subtilis to HPT treatments and detailed insights into some basic mechanisms in Clostridium species shed new light on differences in the HPT-mediated inactivation of Bacillus and Clostridium spores. In this chapter, current knowledge on sporulation and germination processes, which presents the basis for understanding development and loss of the extreme resistance properties of spores, is summarized highlighting commonalities and differences between Bacillus and Clostridium species. In this context, the effect of HPT treatments on spores, inactivation mechanism and kinetics, the role of population heterogeneity, and influence factors on the results of inactivation studies are discussed.

The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types

Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.

We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.

Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10⁹ CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10⁶ and 1.4 × 10⁶ CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked.

Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota.

Genomes, neurotoxins and biology of Clostridium botulinum Group I and Group II

Recent developments in whole genome sequencing have made a substantial contribution to understanding the genomes, neurotoxins and biology of Clostridium botulinum Group I (proteolytic C. botulinum) and C. botulinum Group II (non-proteolytic C. botulinum). Two different approaches are used to study genomics in these bacteria; comparative whole genome microarrays and direct comparison of complete genome DNA sequences. The properties of the different types of neurotoxin formed, and different neurotoxin gene clusters found in C. botulinum Groups I and II are explored. Specific examples of botulinum neurotoxin genes are chosen for an in-depth discussion of neurotoxin gene evolution. The most recent cases of foodborne botulism are summarised.

Functional characterisation of germinant receptors in Clostridium botulinum and Clostridium sporogenes presents novel insights into spore germination systems

Clostridium botulinum is a dangerous pathogen that forms the highly potent botulinum toxin, which when ingested causes a deadly neuroparalytic disease. The closely related Clostridium sporogenes is occasionally pathogenic, frequently associated with food spoilage and regarded as the non-toxigenic equivalent of Group I C. botulinum. Both species form highly resistant spores that are ubiquitous in the environment and which, under favourable growth conditions germinate to produce vegetative cells. To improve the control of botulinum neurotoxin-forming clostridia, it is imperative to comprehend the mechanisms by which spores germinate. Germination is initiated following the recognition of small molecules (germinants) by a specific germinant receptor (GR) located in the spore inner membrane. The present study precisely defines clostridial GRs, germinants and co-germinants. Group I C. botulinum ATCC3502 contains two tricistronic and one pentacistronic GR operons, while C. sporogenes ATCC15579 has three tricistronic and one tetracistronic GR operons. Insertional knockout mutants, allied with characterisation of recombinant GRs shows for the first time that amino acid stimulated germination in C. botulinum requires two tri-cistronic encoded GRs which act in synergy and cannot function individually. Spore germination in C. sporogenes requires one tri-cistronic GR. Two other GRs form part of a complex involved in controlling the rate of amino-acid stimulated germination. The suitability of using C. sporogenes as a substitute for C. botulinum in germination studies and food challenge tests is discussed.

Clostridium botulinum is a dangerous pathogen that forms the deadly botulinum neurotoxin. Strains of C. botulinum are present in the environment as spores. Under suitable conditions, the dormancy of the bacterial spore is broken, and germination occurs. Germination is initiated following the recognition of small molecules by a specific germinant receptor (GR) located within spores. Currently, the identification and characterisation of these GRs remains unknown, but is critical if strategies are to be developed to either prevent spore germination altogether, or to germinate all the spores and then inactivate the emergent sensitive vegetative cells. The present study has characterised two functionally active GRs in C. botulinum which act in synergy and cannot function individually, and a related functionally active GR in C. sporogenes. These GRs respond to amino acids. Other GRs appear to form part of a complex involved in controlling the speed of germination, or are not functionally active. This study provides new insights into the mechanisms involved in germination and will allow us to develop new strategies to control this deadly pathogen.

New targets in the search for preventive and therapeutic agents for botulism

Botulism is a severe neuroparalytic disease resulting from exposure to one of the most poisonous toxins to humans. Because of this high potency and the use of toxins as biological weapons, botulism is a public health concern and each case represents an emergency. Current therapy involves respiratory supportive care and anti-toxins administration. As a preventive measure, vaccination against toxins represents an effective strategy but is undesirable due the rarity of botulism and the effectiveness of toxins in treating several neuromuscular disorders. This paper summarizes the current issues in botulism treatment and prevention, highlighting the challenge for future researches.

Botulism outbreaks in natural environments - an update

Clostridium botulinum comprises a diverse group of botulinum toxin-producing anaerobic rod-shaped spore-forming bacteria that are ubiquitously distributed in soils and aquatic sediments. Decomposition of plants, algae, and animals creates anaerobic environments that facilitate growth of C. botulinum, which may then enter into food webs leading to intoxication of animals. Via saprophytic utilization of nutrients, the bacteria rapidly sporulate, creating a reservoir of highly robust spores. In the present review, we focus on the occurrence of C. botulinum in non-clinical environments, and examine factors influencing growth and environmental factors associated with botulism outbreaks. We also outline cases involving specific environments and their biota. In wetlands, it has been found that some C. botulinum strains can associate with toxin-unaffected organisms–-including algae, plants, and invertebrates–-in which the bacteria appear to germinate and stay in the vegetative form for longer periods of time. We suggest the need for future investigations to resolve issues related to the environments in which C. botulinum spores may accumulate and germinate, and where the vegetative forms may multiply.

Monitoring of commitment, blocking, and continuation of nutrient germination of individual Bacillus subtilis spores

Short exposures of Bacillus spores to nutrient germinants can commit spores to germinate when germinants are removed or their binding to the spores' nutrient germinant receptors (GRs) is inhibited. Bacillus subtilis spores were exposed to germinants for various periods, followed by germinant removal to prevent further commitment. Release of spore dipicolinic acid (DPA) was then measured by differential interference contrast microscopy to monitor germination of multiple individual spores, and spores did not release DPA after 1 to 2 min of germinant exposure until ~7 min after germinant removal. With longer germinant exposures, percentages of committed spores with times for completion of DPA release (Trelease) greater than the time of germinant removal (Tb) increased, while the time Tlag - Tb, where Tlag represents the time when rapid DPA release began, was decreased but rapid DPA release times (ΔTrelease = Trelease - Tlag) were increased; Factors affecting average Trelease values and the percentages of committed spores were germinant exposure time, germinant concentration, sporulation conditions, and spore heat activation, as previously shown for commitment of spore populations. Surprisingly, germination of spores given a 2nd short germinant exposure 30 to 45 min after a 1st exposure of the same duration was significantly higher than after the 1st exposure, but the number of spores that germinated in the 2nd germinant exposure decreased as the interval between germinant exposures increased up to 12 h. The latter results indicate that spores have some memory, albeit transient, of their previous exposure to nutrient germinants.

Quantification of the impact of single and multiple mild stresses on outgrowth heterogeneity of Bacillus cereus spores

Outgrowth heterogeneity of bacterial spore populations complicates both prediction and efficient control of spore outgrowth. In this study, the impact of mild preservation stresses on outgrowth of Bacillus cereus ATCC 14579 spores was quantified during the first stages of outgrowth. Heterogeneity in outgrowth of heat-treated (90°C for 10 min) and non-heat-treated germinated single spores to the maximum micro-colony stage of 256 cells was assessed by direct imaging on Anopore strips, placed on BHI plates at pH7 and pH5.5, without and with added NaCl or sorbic acid (HSA). At pH7 non-heated and heat-treated germinated spores required 6h to reach the maximum microcolony stage with limited heterogeneity, and these parameters were only slightly affected with both types of spores when incubated at pH7 with added NaCl. Notably, the most pronounced effects were observed during outgrowth of spores at pH5.5 without and with added NaCl or HSA. Non-heat-treated germinated spores showed again efficient outgrowth with limited heterogeneity reaching the maximum microcolony stage after 6h at pH5.5, which increased to 12h and 16 h with added NaCl and HSA, respectively. In contrast, heat-treated spores displayed a strong delay between initial germination and swelling and further outgrowth at pH5.5, resulting in large heterogeneity and low numbers of fastest growers reaching the maximum microcolony stage after 10, 12 and 24h, without and with added NaCl or HSA, respectively. This work shows that Anopore technology provides quantitative information on the impact of combined preservation stresses on outgrowth of single spores, showing that outgrowth of germinated heat-treated spores is significantly affected at pH5.5 with a large fraction of spores arrested in the early outgrowth stage, and with outgrowing cells showing large heterogeneity with only a small fraction committed to relatively fast outgrowth.

Monitoring rates and heterogeneity of high-pressure germination of bacillus spores by phase-contrast microscopy of individual spores

Germination of Bacillus spores with a high pressure (HP) of ∼150 MPa is via activation of spores' germinant receptors (GRs). The HP germination of multiple individual Bacillus subtilis spores in a diamond anvil cell (DAC) was monitored with phase-contrast microscopy. Major conclusions were that (i) >95% of wild-type spores germinated in 40 min in a DAC at ∼150 MPa and 37°C but individual spores' germination kinetics were heterogeneous; (ii) individual spores' HP germination kinetic parameters were similar to those of nutrient-triggered germination with a variable lag time (Tlag) prior to a period of the rapid release (ΔTrelease) of the spores' dipicolinic acid in a 1:1 chelate with Ca(2+) (CaDPA); (iii) spore germination at 50 MPa had longer average Tlag values than that at ∼150 MPa, but the ΔTrelease values at the two pressures were identical and HPs of <10 MPa did not induce germination; (iv) B. subtilis spores that lacked the cortex-lytic enzyme CwlJ and that were germinated with an HP of 150 MPa exhibited average ΔTrelease values ∼15-fold longer than those for wild-type spores, but the two types of spores exhibited similar average Tlag values; and (v) the germination of wild-type spores given a ≥30-s 140-MPa HP pulse followed by a constant pressure of 1 MPa was the same as that of spores exposed to a constant pressure of 140 MPa that was continued for ≥35 min; (vi) however, after short 150-MPa HP pulses and incubation at 0.1 MPa (ambient pressure), spore germination stopped 5 to 10 min after the HP was released. These results suggest that an HP of ∼150 MPa for ≤30 s is sufficient to fully activate spores' GRs, which remain activated at 1 MPa but can deactivate at ambient pressure.

Development of a time-to-detect growth model for heat-treated Bacillus cereus spores

The microbiological safety and quality of Refrigerated Processed Foods of Extended Durability (REPFEDs) relies on a combination of mild heat treatment and refrigeration, sometimes in combination with other inhibitory agents that are ineffective when used alone. In this context, a predictive model describing the time-to-detect growth (measured by turbidimetry) of psychrotrophic Bacillus cereus spores submitted to various combinations of pH, water activity (aw), heat treatment and storage temperature was developed. As the inoculum was high, the time-to-detect growth was the sum of two times: for a large part of the spore lag time (time before germination and outgrowth) and to a lesser extent of the time to have subsequent vegetative cells growing up to a detectable level. A dataset of 434 combinations (of pH, aw, heat treatment, storage temperature and B. cereus strain), originally collected at Ghent University to build a growth/no-growth model for two Bacillus cereus strains, was re-interpreted as time-to-detect growth values. In the growth area (223 combinations) the time-to-detect growth was set as the longest time where none, or only one, of the 8 replicated wells showed growth. In the no-growth area (211 combinations) the time-to-detect growth was set as longer than the time where the experiment was stopped (60days or more) and analysed as a censored response. The factors of variation were heat-treatment intensity (85°C, 87°C and 90°C in a time range of 1 to 38min), storage temperature (8-30°C), pH (5.2-6.4) and aw (0.973-0.995). Two different strains were analysed. The model had a Gamma multiplicative structure; it was solved by Bayesian inference with informative prior distributions. To be implemented in a decision tool, for instance to calculate the process and formulation conditions required to achieve a given detection time, each Gamma term had some constraints: they had to be monotonous, continuous and algebraically simple mathematical functions (i.e. having analytical solution). Overall, the cumulative effect of various stressful conditions (pasteurisation process, low temperature, and low pH) enables to extend the time-to-detect growth up to 60days or more, whereas the heat-treatment on its own did not have a similar effect. For example, with the most heat resistant strain (strain 1, FF140), for a product at aw0.99, stored at 10°C, heat-treated at 90°C for 10min, a time-to-detect growth of 2days was expected when the pH equalled 6.5. Under the same conditions, if the pH was reduced to 5.8, the time-to-detect growth was predicted to be 11days (and 33days at pH5.5). After a pasteurisation at 90°C for 10min, for a product kept at 10°C, combinations of pH and aw such as pH6.0-aw0.97, pH5.7-aw0.98 or pH5.5-aw0.99 were predicted to extend the time-to-detect growth up to 30days. The developed model is a useful tool for REPFED producers to guarantee the safety of their products towards psychrotrophic B. cereus.

Live cell imaging of germination and outgrowth of individual bacillus subtilis spores; the effect of heat stress quantitatively analyzed with SporeTracker

Spore-forming bacteria are a special problem for the food industry as some of them are able to survive preservation processes. Bacillus spp. spores can remain in a dormant, stress resistant state for a long period of time. Vegetative cells are formed by germination of spores followed by a more extended outgrowth phase. Spore germination and outgrowth progression are often very heterogeneous and therefore, predictions of microbial stability of food products are exceedingly difficult. Mechanistic details of the cause of this heterogeneity are necessary. In order to examine spore heterogeneity we made a novel closed air-containing chamber for live imaging. This chamber was used to analyze Bacillus subtilis spore germination, outgrowth, as well as subsequent vegetative growth. Typically, we examined around 90 starting spores/cells for ≥4 hours per experiment. Image analysis with the purposely built program “SporeTracker” allows for automated data processing from germination to outgrowth and vegetative doubling. In order to check the efficiency of the chamber, growth and division of B. subtilis vegetative cells were monitored. The observed generation times of vegetative cells were comparable to those obtained in well-aerated shake flask cultures. The influence of a heat stress of 85°C for 10 min on germination, outgrowth, and subsequent vegetative growth was investigated in detail. Compared to control samples fewer spores germinated (41.1% less) and fewer grew out (48.4% less) after the treatment. The heat treatment had a significant influence on the average time to the start of germination (increased) and the distribution and average of the duration of germination itself (increased). However, the distribution and the mean outgrowth time and the generation time of vegetative cells, emerging from untreated and thermally injured spores, were similar.