A simulation of microbial competition in the human colonic ecosystem

Probiotics as cheater cells: parameter space clustering for individualized prescription

Clinicians often perform infection management administering probiotics along with antibiotics. Such probiotics added to an infecting population showing antibiotic resistance can be compared to a dynamical system composed of cheaters and workers. The presence of cheater strains is known to modulate the fitness of the infecting population. We propose a model where probiotics as cheater strain re-establishes the susceptibility of a resistant population towards an antibiotic. Control parameters must assume optimal values in order to attain minimum worker number within a finite time-scale feasible in a clinical set-up. The problem is made non-trivial by the complicated interplay between parameters. The model is an extension of a logistic framework, where a pay-off function has been included to account for the effect of instantaneous worker number on death rates of each species. The outcomes for a randomized set of parameter values and initial conditions are utilized in partitioning the set and desired clusters were identified. For a test case, one can take random combinations of controllable parameters and combine them with fixed parameters and find out the closeness of the points to the desired cluster centroids. This process leads to the identification of optimum antibiotic versus probiotic dosage range leading to elimination or limited existence of the genetically resistant population.

Salmonella pathogenicity and host adaptation in chicken-associated serovars

Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.

Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium

Background

In this report we have explored the genomic and microbiological basis for a sustained increase in bloodstream infections at a major Australian hospital caused by Enterococcus faecium multi-locus sequence type (ST) 203, an outbreak strain that has largely replaced a predecessor ST17 sequence type.

Results

To establish a ST203 reference sequence we fully assembled and annotated the genome of Aus0085, a 2009 vancomycin-resistant Enterococcus faecium (VREfm) bloodstream isolate, and the first example of a completed ST203 genome. Aus0085 has a 3.2 Mb genome, comprising a 2.9 Mb circular chromosome and six circular plasmids (2 kb–130 kb). Twelve percent of the 3222 coding sequences (CDS) in Aus0085 are not present in ST17 E. faecium Aus0004 and ST18 E. faecium TX16. Extending this comparison to an additional 12 ST17 and 14 ST203 E. faecium hospital isolate genomes revealed only six genomic regions spanning 41 kb that were present in all ST203 and absent from all ST17 genomes. The 40 CDS have predicted functions that include ion transport, riboflavin metabolism and two phosphotransferase systems. Comparison of the vancomycin resistance-conferring Tn1549 transposon between Aus0004 and Aus0085 revealed differences in transposon length and insertion site, and van locus sequence variation that correlated with a higher vancomycin MIC in Aus0085. Additional phenotype comparisons between ST17 and ST203 isolates showed that while there were no differences in biofilm-formation and killing of Galleria mellonella, ST203 isolates grew significantly faster and out-competed ST17 isolates in growth assays.

Conclusions

Here we have fully assembled and annotated the first ST203 genome, and then characterized the genomic differences between ST17 and ST203 E. faecium. We also show that ST203 E. faecium are faster growing and can out-compete ST17 E. faecium. While a causal genetic basis for these phenotype differences is not provided here, this study revealed conserved genetic differences between the two clones, differences that can now be tested to explain the molecular basis for the success and emergence of ST203 E. faecium.

Bayesian analysis of non-linear differential equation models with application to a gut microbial ecosystem

Process models specified by non-linear dynamic differential equations contain many parameters, which often must be inferred from a limited amount of data. We discuss a hierarchical Bayesian approach combining data from multiple related experiments in a meaningful way, which permits more powerful inference than treating each experiment as independent. The approach is illustrated with a simulation study and example data from experiments replicating the aspects of the human gut microbial ecosystem. A predictive model is obtained that contains prediction uncertainty caused by uncertainty in the parameters, and we extend the model to capture situations of interest that cannot easily be studied experimentally.

Cell yields and fermentation responses of a Salmonella Typhimurium poultry isolate at different dilution rates in an anaerobic steady state continuous culture

The objectives of these studies were to determine cell yield and fermentation responses of a Salmonella enterica serovar Typhimurium poultry isolate using various dilution rates in steady state continuous culture incubations. S. enterica Typhimurium cells were propagated in continuous cultures with a total volume of 0.50 l of Luria Bertani medium containing 0.1% glucose. Dilution rates from 0.0125 to 1.44/h were used. Cell protein concentration generally increased linearly with increased dilution rate up to a rate of 0.54/h and declined at the higher dilution rates. Glucose consumption gave a similar pattern to cell protein concentration by declining at the three highest dilution rates. Short chain fatty acid production was inconsistently influenced by dilution rate. Acetate, the most predominant fatty acid produced, declined at the higher dilution rates, as did propionate. Ammonia production remained stable at the lowest dilution rates, but increased significantly at a dilution rates above 0.27/h.

Foodborne Salmonella ecology in the avian gastrointestinal tract

Foodborne Salmonella continues to be a major cause of salmonellosis with Salmonella Enteritidis and S. Typhimurium considered to be responsible for most of the infections. Investigation of outbreaks and sporadic cases has indicated that food vehicles such as poultry and poultry by-products including raw and uncooked eggs are among the most common sources of Salmonella infections. The dissemination and infection of the avian intestinal tract remain somewhat unclear. In vitro incubation of Salmonella with mammalian tissue culture cells has shown that invasion into epithelial cells is complex and involves several genetic loci and host factors. Several genes are required for the intestinal phase of Salmonella invasion and are located on Salmonella pathogenicity island 1 (SPI 1). Salmonella pathogenesis in the gastrointestinal (GI) tract and the effects of environmental stimuli on gene expression influence bacterial colonization and invasion. Furthermore, significant parameters of Salmonella including growth physiology, nutrient availability, pH, and energy status are considered contributing factors in the GI tract ecology. Approaches for limiting Salmonella colonization have been primarily based on the microbial ecology of the intestinal tract. In vitro studies have shown that the toxic effects of short chain fatty acids (SCFA) to some Enterobacteriaceae, including Salmonella, have resulted in a reduction in population. In addition, it has been established that native intestinal microorganisms such as Lactobacilli provide protective mechanisms against Salmonella in the ceca. A clear understanding of the key factors involved in Salmonella colonization in the avian GI tract has the potential to lead to better approach for more effective control of this foodborne pathogen.

Growth and genetic responses of Salmonella Typhimurium to pH-shifts in an anaerobic continuous culture

Salmonella infection of chickens that leads to potential human foodborne salmonellosis continues to be a concern. Changes in the pH of poultry gastrointestinal tract could influence Salmonella growth and virulence response. In the current study, growth responses of a chicken isolate Salmonella enterica serovar Typhimurium (ST) to three incremental pH-shifts (6.17-7.35) in continuous cultures (CC) were evaluated. The expression of rpoS and hilA was determined by real time-polymerase chain reaction (RT-PCR) as well. Increases in pH resulted in higher cell protein concentrations, glucose disappearance, and glucose and ATP yields. Although with some inconsistency between the two trials, the data indicated that the ammonia release into media was favored by low pH. The pH shifts did not significantly affect acetate biosynthesis. No consistent trends of pH influence on propionate and butyrate production could be detected. In all three pH shifts, relative expression of hilA was dominant at 0h which represented CC steady state. In pH shift 7.35-6.86 (Trial 1), the relative expression of rpoS at time 0 and 1h were over five-fold higher than after 3 and 6h of growth. Overall, the results suggest that ST physiology is altered by changes in pH, which could be determinant factors for ST survival in the poultry gastrointestinal ecosystems.

Proteomic investigation of glucose metabolism in the butyrate-producing gut anaerobeFusobacterium varium

A proteome survey and MS analysis were conducted to investigate glucose metabolism in Fusobacterium varium, a butyrate-producing constituent of the indigenous human gut microflora. The bacterium was capable of catabolizing glucose as the main energy source via the Embden-Meyerhof-Parnas pathway. 2-DE analyses revealed that the apparent concentrations of the six identified glycolytic enzymes (pyruvate kinase, enolase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase, and glyceraldehyde-3-phosphate dehydrogenase) were specifically increased in response to the presence of glucose in the chemically defined minimal growth medium, and did not diminish when the medium was additionally supplemented with L-glutamate, an amino acid readily fermented by members of the Fusobacterium genus. A substrate pool depletion study revealed that the sugar, and not the amino acid, is the more efficient growth substrate. Both proteomics and substrate pool depletion studies revealed that F. varium can simultaneously utilize both glucose and L-glutamate as energy sources. Enzymes involved in L-glutamate metabolism were also identified, including an NAD-dependent glutamate dehydrogenase and two enzymes of the methylaspartate pathway of L-glutamate catabolism (glutamate mutase and methylaspartate ammonia-lyase). Their apparent intracellular concentrations were elevated when the bacterium was cultured in media supplemented with excess L-glutamate. Our observation that the apparent concentrations of specific proteins were elevated in response to a particular growth substrate supplied as an energy source provides the first evidence for the presence of a nutrient-responsive mechanism governing intracellular protein concentration in F. varium.

In vitro anaerobic incubation of Salmonella enterica serotype Typhimurium and laying hen cecal bacteria in poultry feed substrates and a fructooligosaccharide prebiotic

The objective of this study was to investigate the effect of combining a prebiotic with poultry feeds on the growth of Salmonella enterica serotype Typhimurium (ST) in an in vitro cecal fermentation system. Cecal contents from three laying hens were pooled and diluted to a 1:3000 concentration in an anaerobic dilution solution. The cecal dilution was added to sterile test tubes filled with alfalfa and layer ration with and without fructooligosaccharide (FOS). Two controls containing cecal dilutions and anaerobic dilution solution were used. The samples were processed in the anaerobic hood and incubated at 37 degrees C. Samples were inoculated with Salmonella at 0 and 24h after in vitro cecal fermentation and plated at 0 and 24h after inoculation with ST. Plates were incubated for 24h and colony forming units (CFU) enumerated. The samples immediately inoculated with ST without prior cecal fermentation did not significantly lower ST counts 24h later. However, samples pre-incubated for 24h with cecal microflora prior to ST inoculation exhibited reduced ST CFU by approximately 2 logarithms, with the most dramatic decreases seen in alfalfa and layer ration combined with FOS. The addition of FOS to feed substrate diets in combination with cecal contents acted in a synergistic manner to decrease ST growth only after ST was introduced to 24h cecal incubations.

L-Sorbose utilization by virulent Escherichia coli and Shigella: different metabolic adaptation of pathotypes

The frequency of L-Sorbose utilization differs significantly between pathotypes of Escherichia coli and Shigella from 93% to 0%. Among 266 strains tested, this frequency increased in the order Shigella, enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli, enteropathogenic E. coli (EPEC), and neonatal bacterial meningitis (NBM) E. coli. This suggests an association of pathomechanism with the capability to degrade L-Sorbose. The use of a selective agar, containing L-Sorbose and antibiotics, facilitated the isolation of L-Sorbose-non-utilizing ETEC from stool specimens of patients. The sor operon, comprising seven genes in the order sorCDFBAME, confers L-Sorbose utilization. Surprisingly, L-Sorbose-non-degrading Shigella harbored all genes of the sor operon indicating L-Sorbose-utilizing E. coli as ancestor. Additionally, strains of several EIEC and STEC serotypes harbored an inactivated sor operon. These L-Sorbose-non-utilizing Shigella, EIEC, and STEC showed significantly reduced amounts of transcripts as examined for sorC and sorD. Common surface antigens, types of intimin gene, and hemolysin gene as well as use of L-Sorbose suggested the relatedness of attaching and effacing O26:H11 and O55:H7 EPEC and STEC, respectively. pepE and yibC genes flank the sor operon of E. coli and Shigella strains. Surprisingly, one O7:K1:H- NBM E. coli harbored an aroE-homologous gene between its sor operon and pepE as in Klebsiella pneumoniae suggesting a horizontal gene transfer. In conclusion, L-Sorbose utilization of virulent E. coli and Shigella is characterized by different adaptation that represents a valuable tool for evolutionary and diagnostic analysis of related patho- and serotypes.

Effect of refrigerating delayed shipments of raw ground beef on the detection of Salmonella Typhimurium

In eight separate trials, four groups of raw ground beef samples were inoculated with 0.04 to 0.3 CFU/g of Salmonella Typhimurium (DT 104). Each group consisted of four 25-g samples (three inoculated and one uninoculated). After inoculation, these samples were shipped by overnight courier in Shipping containers with ice packs from the U.S. Department of Agriculture (USDA), Eastern Regional Research Center, in Wyndmoor, Pa., to the U.S. Food Safety and Inspection Service (FSIS), Eastern Laboratory, in Athens, Ga. A total of 128 samples (32 in each of four groups) were shipped. A temperature data logger was placed inside each shipping container to record the temperature during shipping and storage. The first group of ground beef samples was analyzed within approximately 1 h of arrival. The second group of samples was left in the original containers, with a gel ice pack, for 24 h before processing. The third and fourth groups of samples were removed from the original shipping containers and stored at room temperature (21 +/- 2 degrees C) for 6 h and then in a refrigerator at 4 +/- 2 degrees C for 24 and 48 h, respectively, before analysis. The samples were analyzed for the presence of Salmonella according to the USDA/FSIS Microbiological Laboratory Guidebook, chapter 4.02. There was no significant difference in the presence and levels of Salmonella in ground beef among the four test groups. These data show that it is acceptable to process the late-arriving ground beef samples for the detection of Salmonella if they are kept in a refrigerator (4 +/- 2 degrees C) for 24 to 48 h or when the shipments arrive late (24 h in the container with ice pack).

Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria

Most types of anaerobic respiration are able to outcompete methanogenic consortia for common substrates if the respective electron acceptors are present in sufficient amounts. Furthermore, several products or intermediate compounds formed by anaerobic respiring bacteria are toxic to methanogenic consortia. Despite the potentially adverse effects, only few inorganic electron acceptors potentially utilizable for anaerobic respiration have been investigated with respect to negative interactions in anaerobic digesters. In this chapter we review competitive and inhibitory interactions between anaerobic respiring populations and methanogenic consortia in bioreactors. Due to the few studies in anaerobic digesters, many of our discussions are based upon studies of defined cultures or natural ecosystems.

Impact of microbial ecology of meat and poultry products on predictions from exposure assessment scenarios for refrigerated storage

A novel extension of traditional growth models for exposure assessment of food-borne microbial pathogens was developed to address the complex interactions of competing microbial populations in foods. Scenarios were designed for baseline refrigeration and mild abuse of servings of chicken broiler and ground beef Our approach employed high-quality data for microbiology of foods at production, refrigerated storage temperatures, and growth kinetics of microbial populations in culture media. Simple parallel models were developed for exponential growth of multiple pathogens and the abundant and ubiquitous nonpathogenic indigenous microbiota. Monte Carlo simulations were run for unconstrained growth and growth with the density-dependent constraint based on the "Jameson effect," inhibition of pathogen growth when the indigenous microbiota reached 10(9) counts per serving. The modes for unconstrained growth of the indigenous microbiota were 10(8), 10(10), and 10(11) counts per serving for chicken broilers, and 10(7), 10(9) and 10(11) counts per serving for ground beef at respective sites for backroom, meat case, and home refrigeration. Contamination rates and likelihoods of reaching temperatures supporting growth of the pathogens in the baseline refrigeration scenario were rare events. The unconstrained exponential growth models appeared to overestimate L. monocytogenes growth maxima for the baseline refrigeration scenario by 1500-7233% (10(6)-10(7) counts/serving) when the inhibitory effects of the indigenous microbiota are ignored. The extreme tails of the distributions for the constrained models appeared to overestimate growth maxima 110% (10(4)-10(5) counts/serving) for Salmonella spp. and 108% (6 x 10(3) counts/serving) for E. coli O157:H7 relative to the extremes of the unconstrained models. The approach of incorporating parallel models for pathogens and the indigenous microbiota into exposure assessment modeling motivates the design of validation studies to test the modeling assumptions, consistent with the analytical-deliberative process of risk analysis.

Model intestinal microflora in computer simulation: a simulation and modeling package for host-microflora interactions

The ecology of the human intestinal microflora and its interaction with the host are poorly understood. Though more and more data are being acquired, in part using modern molecular methods, development of a quantitative theory has not kept pace with this increase in observing power. This is in part due to the complexity of the system and to the lack of simulation environments in which to test what the ecological effect of a hypothetical mechanism of interaction would be, before resorting to laboratory experiments. The MIMICS project attempts to address this through the development of a cellular automaton for simulation of the intestinal microflora. In this paper, the design and evaluation of this simulator is discussed.

Predation in the presence of decoys: an inhibitory factor on pathogen control by bacteriophages or bdellovibrios in dense and diverse ecosystems

Several attempts have been made at the removal of specific pathogens from the intestinal microflora using either bacteriophages or "predatory" bacteria such as Bdellovibrio spp. To date these attempts have had mixed success. A mechanism explaining these findings based on competitive hindrance by non-prey, or decoy species is put forward. It is shown that this hindrance tends to damp out predator-prey oscillations, and therefore reduces the probability of prey extinction. Possible experiments to verify this theory are discussed. The decoy effect may play a role in any system with high densities of bacteria or other particulate matter, such as activated sludge or biofilms.

Predictive food microbiology for the meat industry: a review

Predictive food microbiology (PFM) is an emerging multidisciplinary area of food microbiology. It encompasses such disciplines as mathematics, microbiology, engineering and chemistry to develop and apply mathematical models to predict the responses of microorganisms to specified environmental variables. This paper provides a critical review on the development of mathematical modelling with emphasis on modelling techniques, descriptions, classifications and their recent advances. It is concluded that the role and accuracy of predictive food microbiology will increase as understanding of the complex interactions between microorganisms and food becomes clearer. However the reliance of food microbiology on laboratory techniques and skilled personnel to determine process and food safety is still necessary.

Conventional and molecular methods for understanding probiotic bacteria functionality in gastrointestinal tracts

The recent successes of probiotic application to limit colonization of foodborne pathogens in the gastrointestinal tracts of food animals ensures continued commercialization and widespread use of such cultures. Given that the the fermentation response and ecological balance of the probiotic consortium appears to be essential for the effectiveness of the cultures, it is essential to develop a methodology to accurately identify and quantitate these organisms during commercial production as well as successful in vivo colonization after administration. However, if further optimization of the effectiveness of defined cultures is to be achieved, methods to assess expression of key metabolic processes occurring during establishment of the probiotic culture as well as its subsequent ability to limit foodborne pathogen colonization are needed. Conventional methods to study individual probiotic gastrointestinal organisms include selective plating to identify specific nutritional groups, but the requirement of strict anaerobiosis for the obligate anaerobic members of these cultures can confound sample handling and preparation. Immunological methods can circumvent some of these problems but are somewhat limited for assessing functionality. The main advantage of using molecular tools is that the genetic diversity of the microflora, as well as their gene activity data are obtainable, both at the community level and at the single species level. Methods are currently available that permit studying individual members of microbial consortia, fluxes in community diversity, spatial distribution of consortia members, and the expression of specific microbial genes within communities. These methods involve the utilization of both DNA- and RNA-targeted probes, gene amplification protocols, and mRNA analysis. The study of mechanisms and functionality can only enhance the potential of probiotic cultures for limiting foodborne pathogen colonization.