Generation Times and Modeling of Enterotoxin-Positive and Enterotoxin-Negative Strains of Clostridium perfringens in Laboratory Media and Ground Beef

Probe-based bacterial single-cell RNA sequencing predicts toxin regulation

Clonal bacterial populations rely on transcriptional variation across individual cells to produce specialized states that increase fitness. Understanding all cell states requires studying isogenic bacterial populations at the single-cell level. Here we developed probe-based bacterial sequencing (ProBac-seq), a method that uses libraries of DNA probes and an existing commercial microfluidic platform to conduct bacterial single-cell RNA sequencing. We sequenced the transcriptome of thousands of individual bacterial cells per experiment, detecting several hundred transcripts per cell on average. Applied to Bacillus subtilis and Escherichia coli, ProBac-seq correctly identifies known cell states and uncovers previously unreported transcriptional heterogeneity. In the context of bacterial pathogenesis, application of the approach to Clostridium perfringens reveals heterogeneous expression of toxin by a subpopulation that can be controlled by acetate, a short-chain fatty acid highly prevalent in the gut. Overall, ProBac-seq can be used to uncover heterogeneity in isogenic microbial populations and identify perturbations that affect pathogenicity.

Time-dependent microbial shifts during crayfish decomposition in freshwater and sediment under different environmental conditions

Fossilization processes and especially the role of bacterial activity during the preservation of organic material has not yet been well understood. Here, we report the results of controlled taphonomic experiments with crayfish in freshwater and sediment. 16S rRNA amplicon analyzes showed that the development of the bacterial community composition over time was correlated with different stages of decay and preservation. Three dominating genera, Aeromonas, Clostridium and Acetobacteroides were identified as the main drivers in the decomposition of crayfish in freshwater. Using micro-computed tomography (µ-CT), scanning electron microscopy (SEM) and confocal Raman spectroscopy (CRS), calcite clusters were detected after 3-4 days inside crayfish carcasses during their decomposition in freshwater at 24 °C. The precipitation of calcite clusters during the decomposition process was increased in the presence of the bacterial genus Proteocatella. Consequently, Proteocatella might be one of the bacterial genera responsible for fossilization.

The complex role of microbial metabolic activity in fossilization

Bacteria play an important role in the fossilization of soft tissues; their metabolic activities drive the destruction of the tissues and also strongly influence mineralization. Some environmental conditions, such as anoxia, cold temperatures, and high salinity, are considered widely to promote fossilization by modulating bacterial activity. However, bacteria are extremely diverse, and have developed metabolic adaptations to a wide range of stressful conditions. Therefore, the influence of the environment on bacterial activity, and of their metabolic activity on fossilization, is complex. A number of examples illustrate that simple, general assumptions about the role of bacteria in soft tissue fossilization cannot explain all preservational pathways: (i) experimental results show that soft tissues of cnidaria decay less in oxic than anoxic conditions, and in the fossil record are found more commonly in fossil sites deposited under oxic conditions rather than anoxic environments; (ii) siderite concretions, which often entomb soft tissue fossils, precipitate due to a complex mixture of sulfate- and iron reduction by some bacterial species, running counter to original theories that iron reduction is the primary driver of siderite concretion growth; (iii) arthropod brains, now widely accepted to be preserved in many Cambrian fossil sites, are one of the first structures to decay in taphonomic experiments, indicating that their fossilization processes are complex and influenced by bacterial activity. In order to expand our understanding of the complex process of bacterially driven soft tissue fossilization, more research needs to be done, on fossils themselves and in taphonomic experiments, to determine how the complex variation in microbial metabolic activity influences decay and mineralization.

Clinical relevance of Clostridium bacteremia: An 8-year retrospective study

Clostridium spp. are recovered from 25% of the blood culture positive with anaerobes. However, the clinical relevance of Clostridium bacteremia has been controverted in the literature, particularly for C. perfringens. We aimed to evaluate the clinical relevance of Clostridium bacteremia, either due to C. perfringens or other Clostridium species, and to identify the risk factors of mortality in these patients. A retrospective cohort study was conducted from January 2010 to April 2018. All the patients with at least one blood culture positive with any Clostridium species were included. Eighty-one patients with a least one blood culture positive with any Clostridium species were included. Seventy patients (86.4%) fulfilled the criteria for clinically relevant bacteremia. Bacteremia due to C. perfringens tended to be less clinically relevant than other Clostridium species but this was not statistically significant (76% vs 91.2%, P = 0.09). In case of clinically relevant bacteremia, the 30-day mortality rate was 31.4%. In multivariate analysis, adequate empiric antimicrobial therapy was significantly associated with survival (P = 0.03). In conclusion, bacteremia due to C. perfringens or other Clostridium species is usually clinically relevant. This finding was also supported by an improved survival at 30 days when adequate empiric antimicrobial therapy was administered.

Effect of combination of Oxyrase and sodium thioglycolate on growth of Clostridium perfringens from spores under aerobic incubation

Clostridium perfringens is a strictly anaerobic pathogen that requires absence of oxygen for its growth in laboratory experiments, which is usually attained by using an anaerobic chamber or anaerobic jars. However, it has been demonstrated that C. perfringens may survive for short periods of times due to its adaptive response to O₂. Therefore, the objective of this study was to explore the application of Oxyrase (OX) and sodium thioglycolate (ST) as oxygen scavengers, used alone or in combination, for observation of the growth of C. perfringens under aerobic incubation. The growth of C. perfringens from spores in Schaedler Anaerobe Agar containing different levels and combinations of OX and ST was observed at temperatures between 20 and 50 °C. The kinetic parameters, including lag time, specific growth rate, and maximum cell concentrations in the stationary phase, were determined. The results indicated that ST at concentrations of 0.025 and 0.05% (w/w), although allowing eventual growth of C. perfringens, prolonged its lag times, while OX at 1.5% only allowed growth at a lower growth rate in comparison to anaerobic incubation. OX at 3% enhanced the growth of C. perfringens at temperatures between 30 and 50 °C, while higher levels of OX were needed in the medium to support the growth of C. perfringens during storage at 25 °C (>6% OX) and 20 °C (>9% OX), due to the effect of temperature on enzyme activity. No significant difference was found in the kinetic parameters of C. perfringens incubated aerobically with OX and the control (without OX or ST) in an anaerobic chamber. Therefore, OX at appropriate concentrations may allow the observation of the growth of C. perfringens under aerobic incubation conditions without the need of an anaerobic device.

A Systematic Review of Beef Meat Quantitative Microbial Risk Assessment Models

Each year in Europe, meat is associated with 2.3 million foodborne illnesses, with a high contribution from beef meat. Many of these illnesses are attributed to pathogenic bacterial contamination and inadequate operations leading to growth and/or insufficient inactivation occurring along the whole farm-to-fork chain. To ensure consumer health, decision-making processes in food safety rely on Quantitative Microbiological Risk Assessment (QMRA) with many applications in recent decades. The present study aims to conduct a critical analysis of beef QMRAs and to identify future challenges. A systematic approach, the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, was used to collate beef QMRA models, identify steps of the farm-to-fork chain considered, and analyze inputs and outputs included as well as modelling methods. A total of 2343 articles were collected and 67 were selected. These studies focused mainly on western countries and considered Escherichia coli (EHEC) and Salmonella spp. pathogens. Future challenges were identified and included the need of whole-chain assessments, centralization of data collection processes, and improvement of model interoperability through harmonization. The present analysis can serve as a source of data and information to inform QMRA framework for beef meat and will help the scientific community and food safety authorities to identify specific monitoring and research needs.

The Biokinetic Spectrum for Temperature and optimal Darwinian fitness

Darwinian fitness is maximised at a temperature below T_opt, but what this temperature is remains unclear. By linking our previous work on the Biokinetic Spectrum for Temperature with a model for temperature-dependent biological growth rate we obtain a plausible value for such a temperature. We find this approach reveals considerable commonalities in how life responds to temperature with implications that follow in evolution, physiology and ecology. We described a data set consisting of 17,021 observations of temperature-dependent population growth rates from 2411 bacterial, archaeal and eukaryal strains. We fitted a thermodynamic model to describe the strains' temperature-dependent growth rate curves that assumed growth was limited by a single rate-limiting enzyme. We defined U_mes as an empirical measure of the temperature at which strains grew as fast and also as efficiently as possible. We propose that Darwinian fitness is optimised at U_mes by trading-off growth rate and physiological efficiency. Using the full data set we calculated the Biokinetic Spectrum for Temperature (BKST): the distribution of temperature-dependent growth rates for each temperature. We used quantile regression to fit alternative models to the BKST to obtain quantile curves. A quantile is a value that contains a particular proportion of the data. The quantile curves suggested commonalities in temperature-dependencies spanning taxa and ecotype, consistent with the single rate-limiting enzyme concept. We showed that on the log scale, the slopes of the quantile curves were the same as the slopes of the thermodynamic model growth curves at U_mes. This was true for Bacteria, Archaea, and Eukarya, and across other conditions (pH, water activity, metabolic type and trophic type). We showed that the quantile curves were the loci of the temperatures and growth rates that optimised Darwinian fitness for each strain at a given temperature-dependence and independently of other conditions. The quantile curves for Archaea and Bacteria shared a number of similarities attributable to the influence of the properties of water on protein folding. Other implications have impact on evolutionary biology, ecology, and physiology. The model predicts the existence of eurythermic strains that grow with about equal efficiency over a broad temperature range. These strains will have higher evolutionary rates with lower mutational costs that are independent of environmental conditions, a factor likely to have been significant during the Precambrian if the early Earth was warmer than today. The model predicts that random mutations are likely to result in shifts along the quantile curves and not across them. It predicts that some psychrophiles will be capable of performing well under climate change, and that selection will favour faster growth rates as the temperature increases. Last, it predicts trade-offs between growth rate and soma production, so that temperature-dependence, and possibly Darwinian fitness, remain constant over a broad temperature range and growth rates.

Evaluation of the Epithelial Barrier Function and Ileal Microbiome in an Established Necrotic Enteritis Challenge Model in Broiler Chickens

Necrotic enteritis (NE) is a recognized multifactorial disease that cost annually to the poultry industry around $2 billion. However, diverse aspects related to its presentation are not completely understood, requiring further studies using known induction experimental models. Therefore, the purpose of this study was to measure the changes occurring in performance, intestinal integrity and ileal microbiome using a previously established NE-challenge model. Chickens were assigned to a negative control group (NC) or a positive control group (PC). In the PC, broilers were orally gavaged with Salmonella Typhimurium (ST) (1 × 107 cfu/chick) at day 1, Eimeria maxima (EM) (2.5 × 104 oocyst/chick) at day 18 and Clostridium perfringens (CP) (1 × 108 cfu/chick/day) at 23-24 days of age. Weekly, body weight (BW), body weight gain (BWG), feed intake (FI) and feed conversion ratio (FCR) were evaluated. Morbidity and mortality were determined throughout the study, and NE lesion scores were recorded at day 25. Additionally, blood and liver samples were collected to measure gut permeability as determined by levels of serum fluorescein isothiocyanate-dextran (FITC-d) and bacterial translocation (BT). Ileal contents were processed for 16S rRNA gene-based microbiome analysis. Performance parameters and intestinal permeability measurements were negatively impacted in the PC resulting in elevated serum FITC-d and BT with a -6.4% difference in BWG. The NE lesion score in PC (1.97 vs. 0.00) was significantly higher in comparison to NC, although there was no difference in mortality. The microbiome analysis showed a dramatic shift of ileal microbiomes in PC groups as compared to NC (ANOSIM: R = 0.76, P = 0.001). The shift was characterized by reduced abundance of the phylum Actinobacteria (P < 0.01), and increased abundance of the genera Butyrivibrio, Lactobacillus, Prevotella and Ruminococcus in PC compared to NC (P < 0.05). Expectedly, Clostridium was found higher in PC (2.98 ± 0.71%) as compared to NC (1.84 ± 0.36%), yet the difference was not significant. In conclusion, results of the present study showed the different intestinal epithelial and microbiological alterations occurring in an established NE-challenge model that considers paratyphoid Salmonella infections in young chicks as an important predisposing factor for presentation of NE.

Distribution of Enterotoxin- and Epsilon-Positive Clostridium perfringens Spores in U.S. Retail Spices

The role of spices as vehicles of foodborne illness prompted an examination of bacterial spores in these products. Here, we report on the levels and characteristics of spores of Clostridium perfringens associated with 247 U.S. retail spices. Forty-three confirmed isolates from 17% of samples were obtained, present at levels ranging from 3.6 to 2,400/g. Twenty-seven (63%) of C. perfringens isolates were positive for the enterotoxin gene ( cpe). Seven random spice isolates produced enterotoxin at levels of between 4 and 16 ng/mL, compared with three outbreak (control) strains that each produced enterotoxin levels of >1,024 ng/mL. D_95°C levels (1.0 to 3.3 min) of spores of four randomly selected spice isolates suggests a plasmid-localized cpe, while one had D_95°C (>45 min) consistent with chromosomally located cpe. Five of the 43 isolates possessed the epsilon toxin gene ( etx, as well as cpe). Foods could easily become contaminated with spores of cpe-positive C. perfringens by the addition of spices. Because of its spore-forming ability, its rapid generation times at elevated temperatures, improper heating, cooling, and holding conditions could lead to elevated levels of C. perfringens in foods, a requirement for its implication in foodborne outbreaks.

Homeostatic Cell Growth Is Accomplished Mechanically through Membrane Tension Inhibition of Cell-Wall Synthesis

Feedback mechanisms are required to coordinate balanced synthesis of subcellular components during cell growth. However, these coordination mechanisms are not apparent at steady state. Here, we elucidate the interdependence of cell growth, membrane tension, and cell-wall synthesis by observing their rapid re-coordination after osmotic shocks in Gram-positive bacteria. Single-cell experiments and mathematical modeling demonstrate that mechanical forces dually regulate cell growth: while turgor pressure produces mechanical stress within the cell wall that promotes its expansion through wall synthesis, membrane tension induces growth arrest by inhibiting wall synthesis. Tension inhibition occurs concurrently with membrane depolarization, and depolarization arrested growth independently of shock, indicating that electrical signals implement the negative feedback characteristic of homeostasis. Thus, competing influences of membrane tension and cell-wall mechanical stress on growth allow cells to rapidly correct for mismatches between membrane and wall synthesis rates, ensuring balanced growth.

The Divided Bacterial Genome: Structure, Function, and Evolution

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.

Identity, Abundance, and Reactivation Kinetics of Thermophilic Fermentative Endospores in Cold Marine Sediment and Seawater

Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50°C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H2 began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained ∼105-106 inducible TFEs cm-3. TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 × 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment.

Assessing the usefulness of clostridia spores for evaluating sewage sludge hygienization

The capability of clostridia spores to act as pathogen indicators in sewage sludge treatment was investigated. Sulfite-reducing clostridia and E. coli levels were monitored during waste activated sludge pre-treatments (alkali and ultrasound) and its subsequent mesophilic anaerobic digestion. E. coli was maintained or reduced depending on treatment type and intensity. However, alkali pre-treatment (35.3gNaOH/kgTS) by itself and alkali (157gNaOH/kgTS) and ultrasound (27,000kJ/kgTS) pre-treatments followed by anaerobic digestion provoked reproducible clostridia increases. Specifically, up to 2.7log₁₀ after 35.3gNaOH/kgTS pre-treatment and up to 1.9 and 1.1log₁₀ after digesting the 157gNaOH/kg TS and 27,000kJ/kgTS pre-treated sludge, respectively. Having rejected the hypotheses of sporulation and floc dissipation, the most plausible explanation for these clostridia increases is re-growth. These results question the suitability of clostridia spores as indicators of sludge treatment and other biological treatments where clostridia may have a role.

Evaluating the Performance of a New Model for Predicting the Growth of Clostridium perfringens in Cooked, Uncured Meat and Poultry Products under Isothermal, Heating, and Dynamically Cooling Conditions

Clostridium perfringens type A is a significant public health threat and its spores may germinate, outgrow, and multiply during cooling of cooked meats. This study applies a new C. perfringens growth model in the USDA Integrated Pathogen Modeling Program-Dynamic Prediction (IPMP Dynamic Prediction) Dynamic Prediction to predict the growth from spores of C. perfringens in cooked uncured meat and poultry products using isothermal, dynamic heating, and cooling data reported in the literature. The residual errors of predictions (observation-prediction) are analyzed, and the root-mean-square error (RMSE) calculated. For isothermal and heating profiles, each data point in growth curves is compared. The mean residual errors (MRE) of predictions range from -0.40 to 0.02 Log colony forming units (CFU)/g, with a RMSE of approximately 0.6 Log CFU/g. For cooling, the end point predictions are conservative in nature, with an MRE of -1.16 Log CFU/g for single-rate cooling and -0.66 Log CFU/g for dual-rate cooling. The RMSE is between 0.6 and 0.7 Log CFU/g. Compared with other models reported in the literature, this model makes more accurate and fail-safe predictions. For cooling, the percentage for accurate and fail-safe predictions is between 97.6% and 100%. Under criterion 1, the percentage of accurate predictions is 47.5% for single-rate cooling and 66.7% for dual-rate cooling, while the fail-dangerous predictions are between 0% and 2.4%. This study demonstrates that IPMP Dynamic Prediction can be used by food processors and regulatory agencies as a tool to predict the growth of C. perfringens in uncured cooked meats and evaluate the safety of cooked or heat-treated uncured meat and poultry products exposed to cooling deviations or to develop customized cooling schedules. This study also demonstrates the need for more accurate data collection during cooling.

Behavior and Inactivation of Enterotoxin-Positive Clostridium perfringens in Pork Picadillo and Tamales Filled with Pork Picadillo under Different Cooking, Storage, and Reheating Conditions

This study analyzed the behavior of Clostridium perfringens in individual ingredients and tamales containing different pathogen concentrations upon exposure to different temperatures and methods of cooking, storage, and reheating. In ground pork, C. perfringens cells were inactivated when exposed to 95°C for 30 min. Three lots of picadillo inoculated with 0, 3, and 5 log CFU/g C. perfringens cells, respectively, were exposed to different storage temperatures. At 20°C, cell counts increased 1 log in all lots, whereas at 8°C, counts decreased by 2 log. Four lots of tamales prepared with picadillo inoculated with 0, 2, 3, and 7 log CFU/g prior to the final cooking step exhibited no surviving cells (91°C for 90, 45, or 35 min). Four lots of tamales were inoculated after cooking with concentrations of 0, 0.6, 4, and 6 log CFU/g of the pathogen and then stored at different temperatures. In these preparations, after 24 h at 20°C, the count increased by 1.4, 1.7, and 1.8 log in the tamales inoculated with 0.6, 4, and 6 log inoculum, respectively. When they were stored at 8°C for 24 h, enumerations decreased to <1, 2.5, and 1.9 log in the tamales inoculated with 0.6, 4, and 6 log of C. perfringens cells, respectively. However, when the lots were exposed to 20°C and then 8°C, 0.8, 1.8, and 2.4 log changes were observed for the tamales inoculated with 0.6, 4, and 6 log, respectively. Microwaving, steaming, and frying to reheat tamales inoculated with 6 log CFU/g C. perfringens cells showed that the pathogen was inactivated after 2 min of exposure in the microwave and after 5 min of exposure to steam. In contrast, no inactivation was observed after 5 min of frying. The tamales inoculated with spores (7 log most probable number [MPN]/g) showed a decrease of 2 log after steaming or frying, and no survival was observed after microwaving. Tamales inoculated with spores (7 log MPN/g) after cooking were susceptible to microwaves, but 2.4 and 255 MPN/g remained after frying and steaming, respectively.

Metabolism at evolutionary optimal States

Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization.

Differential outgrowth potential of Clostridium perfringens food-borne isolates with various cpe-genotypes in vacuum-packed ground beef during storage at 12°C

In the current study, the outgrowth of spores of 15 different food isolates of Clostridium perfringens was evaluated in vacuum-packed ground beef during storage at 12°C and 25°C. This included enterotoxic strains carrying the gene encoding the CPE enterotoxin on the chromosome (C-cpe), on a plasmid (P-cpe) and cpe-negative strains. The 15 strains were selected from a larger group of strains that were first evaluated for their ability to sporulate in modified Duncan-Strong sporulating medium. Sporulation ability varied greatly between strains but was not associated with a particular cpe genotype. In line with previous studies, the tested C-cpe strains produced spores with significantly higher heat resistance than the cpe-negative and P-cpe strains (both IS1151 and IS1470-like) with the exception of strain VWA009. Following inoculation of vacuum-packed cooked ground beef with spores, the heat-resistant C-cpe strains showed lower outgrowth potential in this model food stored at 12°C than the P-cpe and cpe-negative strains, while no significant differences were observed at 25°C. These results suggest that the latter strains may have a competitive advantage over C-cpe strains at reduced temperatures during storage of foods that support the growth of C. perfringens. While spores of P-cpe strains are readily inactivated by heat processing, post-processing contamination by food handlers who may carry P-cpe strains that have a better growth potential at lower temperatures must be avoided. The varying responses of C. perfringens spores to heat and the differences in outgrowth capacity at different temperatures are factors to be considered in strain selection for challenge tests, and for predictive modelling of C. perfringens.

Systems and photosystems: cellular limits of autotrophic productivity in cyanobacteria

Recent advances in the modeling of microbial growth and metabolism have shown that growth rate critically depends upon the optimal allocation of finite proteomic resources among different cellular functions and that modeling growth rates becomes more realistic with the explicit accounting for the costs of macromolecular synthesis, most importantly, protein expression. The "proteomic constraint" is considered together with its application to understanding photosynthetic microbial growth. The central hypothesis is that physical limits of cellular space (and corresponding solvation capacity) in conjunction with cell surface-to-volume ratios represent the underlying constraints on the maximal rate of autotrophic microbial growth. The limitation of cellular space thus constrains the size the total complement of macromolecules, dissolved ions, and metabolites. To a first approximation, the upper limit in the cellular amount of the total proteome is bounded this space limit. This predicts that adaptation to osmotic stress will result in lower maximal growth rates due to decreased cellular concentrations of core metabolic proteins necessary for cell growth owing the accumulation of compatible osmolytes, as surmised previously. The finite capacity of membrane and cytoplasmic space also leads to the hypothesis that the species-specific differences in maximal growth rates likely reflect differences in the allocation of space to niche-specific proteins with the corresponding diminution of space devoted to other functions including proteins of core autotrophic metabolism, which drive cell reproduction. An optimization model for autotrophic microbial growth, the autotrophic replicator model, was developed based upon previous work investigating heterotrophic growth. The present model describes autotrophic growth in terms of the allocation protein resources among core functional groups including the photosynthetic electron transport chain, light-harvesting antennae, and the ribosome groups.

Growth potential of Clostridium perfringens from spores in acidified beef, pork, and poultry products during chilling

The ability of Clostridium perfringens to germinate and grow in acidified ground beef as well as in 10 commercially prepared acidified beef, pork, and poultry products was assessed. The pH of ground beef was adjusted with organic vinegar to achieve various pH values between 5.0 and 5.6; the pH of the commercial products ranged from 4.74 to 6.35. Products were inoculated with a three-strain cocktail of C. perfringens spores to achieve ca. 2-log (low) or 4-log (high) inoculum levels, vacuum packaged, and cooled exponentially from 54.4 to 7.2°C for 6, 9, 12, 15, 18, or 21 h to simulate abusive cooling; the U.S. Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) recommends a cooling time of 6.5 h. Total germinated C. perfringens populations were determined after plating on tryptose-sulfite-cycloserine agar and incubating the plates anaerobically at 37°C for 48 h. In addition, C. perfringens growth from spores was assessed at an isothermal temperature of 44°C. Growth from spores was inhibited in ground beef with a pH of 5.5 or below, even during extended cooling from 54.4 to 7.2°C in 21 h. In ground beef with a pH of 5.6, the growth was >1 log after 18 h of cooling from 54.4 to 7.2°C. However, 15 h of cooling controlled the growth to <1 log, regardless of the inoculum level. In addition, no growth was observed in any product with a pH ranging from 4.74 to 5.17, both during exponential abusive cooling periods of up to 21 h and during storage for 21 h at 44°C. While <1-log growth of C. perfringens from spores was observed in the pH 5.63 product cooled exponentially from 54.4 to 7.2°C in 15 h or less, the pH 6.35 product supported growth, even after 6 h of cooling from 54.4 to 7.2°C. These challenge tests demonstrate that adjustment of ground beef to pH of 5.5 or less and of barbeque products to pH of 5.63 or less inhibits C. perfringens spore germination and outgrowth during extended cooling periods from 54.4 to 7.2°C up to 15 h. Therefore, safe cooling periods for products with homogeneous, lower pHs can be substantially longer.

Forces that influence the evolution of codon bias

The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the variation among species appears to be due to biased patterns of mutation. The strength of selection on codon usage can be estimated by two different approaches. First, the extent of bias in favour of translationally optimal codons in highly expressed genes, compared to that in genes where selection is weak, reveals the long-term effectiveness of selection. Here we show that the strength of selected codon usage bias is highly correlated with bacterial growth rate, suggesting that selection has favoured translational efficiency. Second, the pattern of bias towards optimal codons at polymorphic sites reveals the ongoing action of selection. Using this approach we obtained results that were completely consistent with the first method; importantly, the frequency spectra of optimal codons at polymorphic sites were similar to those predicted under an equilibrium model. Highly expressed genes in Escherichia coli appear to be under continuing strong selection, whereas selection is very weak in genes expressed at low levels.

Potential for growth of Clostridium perfringens from spores in pork scrapple during cooling

We conducted stabilization studies to determine the ability of Clostridium perfringens spores to germinate and grow during exponential cooling of a commercial formulation of pork scrapple. Scrapple was inoculated with a mixture of three strains of C. perfringens spores (NTCC 8238, NCTC 8239, and ATCC 10288), vacuum packaged, and reheated (20 min/93.3 degrees C) in a circulating water bath. The cooked samples were cooled (30 s) in an ice bath before being transferred to a programmable water bath to cool through the temperature range of 54.4 degrees C to 7.2 degrees C in 12, 14, or 21 h to simulate deviations from the required cooling time of 6.5 h. After cooling, the samples, in duplicate, were analyzed to determine if growth from spores had occurred. The samples were plated onto tryptose-sulfite-cycloserine agar and incubated anaerobically at 37 degrees C for 48 h before counting the colonies. Minimal growth (less than 1.0 log) was observed during a 12- or 14 h cooling period. However, when the time to achieve 7.2 degrees C was extended to 21 h, C. perfringens spores germinated and grew from an inoculum of approximately 3.0 log(10) to approximately 7.8 log(10) CFU/g. Thus, scrapple must be cooled after cooking to 7.2 degrees C within 6.5 h, but for no more than 14 h, to prevent a food safety hazard from outgrowth of C. perfringens spores during cooling.

Development of an integrated model for heat transfer and dynamic growth of Clostridium perfringens during the cooling of cooked boneless ham

Numerous small meat processors in the United States have difficulties complying with the stabilization performance standards for preventing growth of Clostridium perfringens by 1 log10 cycle during cooling of ready-to-eat (RTE) products. These standards were established by the Food Safety and Inspection Service (FSIS) of the US Department of Agriculture in 1999. In recent years, several attempts have been made to develop predictive models for growth of C. perfringens within the range of cooling temperatures included in the FSIS standards. Those studies mainly focused on microbiological aspects, using hypothesized cooling rates. Conversely, studies dealing with heat transfer models to predict cooling rates in meat products do not address microbial growth. Integration of heat transfer relationships with C. perfringens growth relationships during cooling of meat products has been very limited. Therefore, a computer simulation scheme was developed to analyze heat transfer phenomena and temperature-dependent C. perfringens growth during cooling of cooked boneless cured ham. The temperature history of ham was predicted using a finite element heat diffusion model. Validation of heat transfer predictions used experimental data collected in commercial meat-processing facilities. For C. perfringens growth, a dynamic model was developed using Baranyi's nonautonomous differential equation. The bacterium's growth model was integrated into the computer program using predicted temperature histories as input values. For cooling cooked hams from 66.6 degrees C to 4.4 degrees C using forced air, the maximum deviation between predicted and experimental core temperature data was 2.54 degrees C. Predicted C. perfringens growth curves obtained from dynamic modeling showed good agreement with validated results for three different cooling scenarios. Mean absolute values of relative errors were below 6%, and deviations between predicted and experimental cell counts were within 0.37 log10 CFU/g. For a cooling process which was in exact compliance with the FSIS stabilization performance standards, a mean net growth of 1.37 log10 CFU/g was predicted. This study introduced the combination of engineering modeling and microbiological modeling as a useful quantitative tool for general food safety applications, such as risk assessment and hazard analysis and critical control points (HACCP) plans.

Development of a model to predict growth of Clostridium perfringens in cooked beef during cooling

The objective of this work was to develop a new model to predict the growth of Clostridium perfringens in cooked meat during cooling. All data were collected under changing temperature conditions. Individual growth curves were fit using DMFit. Germination outgrowth and lag (GOL) time was modeled versus temperature at the end of GOL using conservative assumptions. Each growth curve was used to estimate a series of exponential growth rates at a series of temperatures. The squareroot model was used to describe the relationship between the square root of the average exponential growth rate and effective temperature. Predictions from the new model were in close agreement with the data used to create the model. When predictions from the model were compared with new observations, fail-dangerous predictions were made a majority of the time. When GOL time was predicted exactly, many fail-dangerous predictions shifted toward the fail-safe direction. Two important facts regarding C. perfringens should impact future modeling research with this organism and may have broader food safety policy implications: (i) the normal variability in the response of the organism from replicate to replicate may be quite large (1 log CFU) and may exceed the current U.S. Food Safety Inspection Service performance standard, and (ii) the accuracy of the GOL time model has a profound influence upon the overall prediction, with small differences in GOL time prediction (approximately 1 h) having a very large effect on the predicted final concentration of C. perfringens.

Modeling growth of Clostridium perfringens in pea soup during cooling

Clostridium perfringens is a pathogen that mainly causes food poisoning outbreaks when large quantities of food are prepared. Therefore, a model was developed to predict the effect of different cooling procedures on the growth of this pathogen during cooling of food: Dutch pea soup. First, a growth rate model based on interpretable parameters was used to predict growth during linear cooling of pea soup. Second, a temperature model for cooling pea soup was constructed by fitting the model to experimental data published earlier. This cooling model was used to estimate the effect of various cooling environments on average cooling times, taking into account the effect of stirring and product volume. The growth model systematically overestimated growth of C. perfringens during cooling in air, but this effect was limited to less than 0.5 log N/ml and this was considered to be acceptable for practical purposes. It was demonstrated that the growth model for C. perfringens combined with the cooling model for pea soup could be used to sufficiently predict growth of C. perfringens in different volume sizes of pea soup during cooling in air as well as the effect of stirring, different cooling temperatures, and various cooling environments on the growth of C. perfringens in pea soup. Although fine-tuning may be needed to eliminate inaccuracies, it was concluded that the combined model could be a useful tool for designing good manufacturing practices (GMP) procedures.

Growth potential of Clostridium perfringens during cooling of cooked meats

Many meat-based food products are cooked to temperatures sufficient to inactivate vegetative cells of Clostridium perfringens, but spores of this bacterium can survive, germinate, and grow in these products if sufficient time, temperature, and other variables exist. Because ingestion of large numbers of vegetative cells can lead to concomitant sporulation, enterotoxin release in the gastrointestinal tract, and diarrhea-like illness, a necessary food safety objective is to ensure that not more than acceptable levels of C. perfringens are in finished products. As cooked meat items cool they will pass through the growth temperature range of C. perfringens (50 to 15 degrees C). Therefore, an important step in determining the likely level of C. perfringens in the final product is the estimation of growth of the pathogen during cooling of the cooked product. Numerous studies exist dealing with just such estimations, yet consensual methodologies, results, and conclusions are lacking. There is a need to consider the bulk of C. perfringens work relating to cooling of cooked meat-based products and attempt to move toward a better understanding of the true growth potential of the organism. This review attempts to summarize observations made by researchers and highlight variations in experimental approach as possible explanations for different outcomes. An attempt is also made here to identify and justify optimal procedures for conducting C. perfringens growth estimation in meat-based cooked food products during cooling.

Effect of cooling on Clostridium perfringens in pea soup

Foods associated with Clostridium perfringens outbreaks are usually abused after cooking. Because of their short generation times, C. perfringens spores and cells can grow out to high levels during improper cooling. Therefore, the potential of C. perfringens to multiply in Dutch pea soup during different cooling times was investigated. Tubes of preheated pea soup (50 degrees C) were inoculated with cocktails of cells or heat-activated spores of this pathogen. The tubes were linearly cooled to 15 degrees C in time spans of 3, 5, 7.5, and 10 h and were subsequently stored in a refrigerator at 3 or 7 degrees C for up to 84 h. Cell numbers increased by 1-log cycle during the 3-h cooling period and reached their maximum after 10 h of cooling. Subsequent refrigeration hardly reduced cell numbers. Cooling of 3.75 liters of pea soup in an open pan showed that this amount of pea soup cooled from 50 to 15 degrees C in 5 h, which will allow a more than 10-fold increase in cell numbers. These findings emphasize the need of good hygienic practices and quick cooling of heated foods after preparation.

A probabilistic analysis of Clostridium perfringens growth during food service operations

The purpose of this study was threefold: first, the study was designed to illustrate the use of data and information collected in food safety surveys in a quantitative risk assessment. In this case, the focus was on the food service industry; however, similar data from other parts of the food chain could be similarly incorporated. The second objective was to quantitatively describe and better understand the role that the food service industry plays in the safety of food. The third objective was to illustrate the additional decision-making information that is available when uncertainty and variability are incorporated into the modelling of systems.

Survival and growth of enterotoxin-positive and enterotoxin-negative Clostridium perfringens in laboratory media

The survival and growth characteristics of enterotoxin-positive and enterotoxin-negative Clostridium perfringens were compared. Spores of C. perfringens were heated and incubated in laboratory media to simulate the cooking and inadequate storage of cooked food. In our experiment, enterotoxin-positive and enterotoxin-negative spores were heated and incubated individually and it was found that spores of enterotoxin-positive strains were more heat-resistant than spores of the enterotoxin-negative strains. In another experiment, cocktails of enterotoxin-positive and enterotoxin-negative spores were heated and incubated. At the time of inoculation, the ratio of enterotoxin-positive spores to enterotoxin-negative spores was about 1:100. In the case of high-temperature heat treatment, the number of enterotoxin-negative spores decreased to below that of enterotoxin-positive spores after heating, and enterotoxin-positive strains grew to high levels during incubation. In the case of low-temperature heat treatment, the number of enterotoxin-negative spores remained almost unchanged after heating and enterotoxin-positive strains did not grow to high CFU levels during incubation.

Shelf life prediction: status and future possibilities

Although there is rapid progress in the field of chemical detection technology, little of this technology appears to have found application in estimation of the remaining shelf life of foods and early detection of spoilage. Predictive microbiology aims to summarise the probable behaviour of specific spoilage organisms and the progression of spoilage processes in foods. The quantitative knowledge generated in the field of predictive microbiology provides a sound basis for the rational development of devices with which to monitor loss of product shelf life during storage, distribution and retail sale. To predict remaining shelf life accurately it is necessary, however, to consider the microbial ecology of the food system. Aspects of microbial ecology and physiology relevant to the spoilage of foods are briefly reviewed and the potential benefits of the use of predictive microbiology in shelf life estimation are described. These points are exemplified by reference to a modelling program undertaken to develop, validate and 'package' in an easily useable from, models of the effect of temperature, water activity and pH on the growth rate of psychrotrophic spoilage pseudomonads. Necessary properties of devices to monitor loss of shelf life are discussed. 'Bioindicators' are identified as potential monitors of spoilage and suggestions made for their development based on the concept of 'upper limiting bacterial growth' rates, for which preliminary evidence is presented.