Chawalit Kocharunchitt

Use of bacteriophages as biocontrol agents to control Salmonella associated with seed sprouts

Two Salmonella bacteriophages (SSP5 and SSP6) were isolated and characterized based on their morphology and host range, and evaluated for their potential to control Salmonella Oranienburg in vitro and on experimentally contaminated alfalfa seeds. Phages SSP5 and SSP6 were classified as members of the Myoviridae and Siphoviridae families, respectively. Both phages had a broad host range of over 65% of the 41 Salmonella strains tested. During in vitro trials, the phages resulted in incomplete lysis of Salmonella cultures, in spite of high levels of phage remaining in the system. Phage SSP5 was more effective in reducing Salmonella populations. Addition of phage SSP6 to alfalfa seeds previously contaminated with S. Oranienburg caused an approximately 1 log(10) CFU g(-1) reduction of viable Salmonella, which was achieved 3 h after phage application. Thereafter the phage had no inhibitory effect on Salmonella population growth. A second addition of the same (SSP6) or different (SSP5) phage to a Salmonella culture treated with phage SSP6, did not affect Salmonella populations. It was further shown that development of Salmonella permanently resistant to phage was not evident in either seed or in vitro challenge trials, suggesting the existence of a temporary, acquired, non-specific phage resistance phenomenon. These factors may complicate the use of phages for biocontrol.

Integrated Transcriptomic and Proteomic Analysis of the Physiological Response of Escherichia coli O157:H7 Sakai to Steady-state Conditions of Cold and Water Activity Stress

An integrated transcriptomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcass chilling in cold air. The response of E. coli during exponential growth at 25 °C aw 0.985, 14 °C aw 0.985, 25 °C aw 0.967, and 14 °C aw 0.967 was compared with that of a reference culture (35 °C aw 0.993). Gene and protein expression profiles of E. coli were more strongly affected by low water activity (aw 0.967) than by low temperature (14 °C). Predefined group enrichment analysis revealed that a universal response of E. coli to all test conditions included activation of the master stress response regulator RpoS and the Rcs phosphorelay system involved in the biosynthesis of the exopolysaccharide colanic acid, as well as down-regulation of elements involved in chemotaxis and motility. However, colanic acid-deficient mutants were shown to achieve comparable growth rates to their wild-type parents under all conditions, indicating that colanic acid is not required for growth. In contrast to the transcriptomic data, the proteomic data revealed that several processes involved in protein synthesis were down-regulated in overall expression at 14 °C aw 0.985, 25 °C aw 0.967, and 14 °C aw 0.967. This result suggests that during growth under these conditions, E. coli, although able to transcribe the required mRNA, may lack the cellular resources required for translation. Elucidating the global adaptive response of E. coli O157:H7 during exposure to chilling and water activity stress has provided a baseline of knowledge of the physiology of this pathogen.

Investigation of the Listeria monocytogenes Scott A Acid Tolerance Response and Associated Physiological and Phenotypic Features via Whole Proteome Analysis

The global proteomic responses of the foodborne pathogen Listeria monocytogenes strain Scott A, during active growth and transition to the stationary growth phase under progressively more acidic conditions, created by addition of lactic acid and HCl, were investigated using label-free liquid chromatography/tandem mass spectrometry. Approximately 56% of the Scott A proteome was quantitatively assessable, and the data provides insight into its acquired acid tolerance response (ATR) as well as the relation of the ATR to the growth phase transition. Alterations in protein abundance due to acid stress were focused in proteins belonging to the L. monocytogenes common genome, with few strain-dependent proteins involved. However, one of the two complete prophage genomes appeared to enter lysogeny. During progressive acidification, the growth rate and yield were reduced 55% and 98%, respectively, in comparison to nonacidified control cultures. The maintenance of the growth rate was determined to be connected to activation of cytoplasmic pH homeostatic mechanisms while cellular reproductive-related and cell component turnover proteins were markedly more abundant in acid stressed cultures. Cell biomass accumulation was impeded predominantly due to repression of phosphodonor-linked enzymes involved with sugar phosphotransfer, glycolysis, and cell wall polymer biosynthesis. Acidification caused a shift from heterofermentation to an oxidatively stressed state in which ATP appears to be generated mainly through the pyruvate dehydrogenase/pyruvate oxidase/phosphotransacetylase/acetate kinase and branched chain acid dehydrogenase pathways. Analysis of regulons indicated energy conservation occurs due to repression by the GTP/isoleucine sensor CodY and also the RelA mediated stringent response. Whole proteome analysis proved to be an effective way to highlight proteins involved with the acquisition of the ATR.

Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Downshift in Water Activity

The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw). Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.

Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms

This review will examine the current situation with label-free, quantitative, shotgun-oriented proteomics technology and discuss the advantages and limitations associated with its capability in capturing and quantifying large portions of proteomes of microorganisms. Such an approach allows (1) comparisons between physiological or genetic states of organisms at the protein level, (2) ‘painting’ of proteomic data onto genome data-based metabolic maps, (3) enhancement of the utility of genomic data and finally (4) surveying of non-genome sequenced microorganisms by taking advantage of available inferred protein data in order to gain new insights into strain-dependent metabolic or physiological capacities. The technology essentially is a powerful addition to systems biology with a capacity to be used to ask hypothesis-driven ‘top-down’ questions or for more empirical ‘bottom-up’ exploration.

Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Temperature Downshift

Escherichia coli O157∶H7 is a mesophilic food-borne pathogen. We investigated the growth kinetics of E. coli O157∶H7 Sakai during an abrupt temperature downshift from 35°C to either 20°C, 17°C, 14°C or 10°C; as well as the molecular mechanisms enabling growth after cold stress upon an abrupt downshift from 35°C to 14°C in an integrated transcriptomic and proteomic analysis. All downshifts caused a lag period of growth before growth resumed at a rate typical of the post-shift temperature. Lag and generation time increased with the magnitude of the shift or with the final temperature, while relative lag time displayed little variation across the test range. Analysis of time-dependent molecular changes revealed, in keeping with a decreased growth rate at lower temperature, repression of genes and proteins involved in DNA replication, protein synthesis and carbohydrate catabolism. Consistent with cold-induced remodelling of the bacterial cell envelope, alterations occurred in the expression of genes and proteins involved in transport and binding. The RpoS regulon exhibited sustained induction confirming its importance in adaptation and growth at 14°C. The RpoE regulon was transiently induced, indicating a potential role for this extracytoplasmic stress response system in the early phase of low temperature adaptation during lag phase. Interestingly, genes previously reported to be amongst the most highly up-regulated under oxidative stress were consistently down-regulated. This comprehensive analysis provides insight into the molecular mechanisms operating during adaptation of E. coli to growth at low temperature and is relevant to its physiological state during chilling in foods, such as carcasses.

Combined effect of chilling and desiccation on survival of Escherichia coli suggests a transient loss of culturability

Dry air carcass chilling regimes used in some Australian meat works, which not only rapidly reduce the temperature of the carcasses but also dry the meat surface initially, are reported to cause reductions in the number of Escherichia coli present on carcasses after processing. This study used a laboratory broth model system to systematically investigate the basis of such reductions by simulating chilling and desiccation profiles observed on carcasses separately and, finally, in combination. Observed growth was compared to the predictions generated by a strain-specific modification of a validated E. coli growth model (Mellefont et al., 2003; Performance evaluation of a model describing the effects of temperature, water activity, pH and lactic acid concentration on the growth of E. coli). Good agreement between observed and predicted growth was evident when chilling or desiccation profiles were simulated individually. However, when chilling and desiccation profiles were applied simultaneously the observed population kinetics deviated from those predicted by the model. An initial reduction in cell numbers, not predicted by the model, was observed followed by an anomalously rapid increase in population density before growth resumed at a rate expected for the conditions imposed. From our analysis of the kinetics of the population changes, we suggest that the initial decrease in cell numbers was unlikely due to cell death, because conditions were growth permissive. Considering all possible explanations from the observed population kinetics, we propose that a temporary loss of the ability to produce colonies on agar plates may occur. These results may explain reports of increases in E. coli numbers two to three days after commencement of chilling, compared to those observed after 16-24h, despite the imposition of growth-preventing temperatures.

Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling

Enterohemeorrhagic Escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. Currently, no completely effective method for controlling this pathogen during carcass processing exists. Understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. Therefore, we studied the growth kinetics and physiological response of exponential phase E. coli O157:H7 Sakai cultures upon an abrupt downshift in temperature and water activity (from 35 °C aw 0.993 to 14 °C aw 0.967). A parallel Biolog study was conducted to follow the phenotypic responses to 190 carbon sources. Exposure of E. coli to combined cold and water activity stresses resulted in a complex pattern of population changes. This pattern could be divided into two main phases, including adaptation and regrowth phases, based on growth kinetics and clustering analyses. The transcriptomic and proteomic studies revealed that E. coli exhibited a “window” of cell susceptibility (i.e. weaknesses) during adaptation phase. This included apparent DNA damage, the downregulation of molecular chaperones and proteins associated with responses to oxidative damage. However, E. coli also displayed a transient induction in the RpoE-controlled envelope stress response and activation of the master stress regulator RpoS and the Rcs phosphorelay system involved in colanic acid biosynthesis. Increased expression was observed for several genes and/or proteins involved in DNA repair, protein and peptide degradation, amino acid biosynthesis, and carbohydrate catabolism and energy generation. Furthermore, the Biolog study revealed reduced carbon source utilization during adaptation phase, indicating the disruption of energy-generating processes. This study provides insight into the physiological response of E. coli during exposure to combined cold and water activity stress, which could be exploited to enhance the microbiological safety of carcasses and related foods.

Listeria monocytogenes: illuminating adaptation with proteomics

With increased consumption of minimally processed ready-to-eat foods the potential for exposure to Listeria monocytogenes has potentially increased thus there is a need to maintain a balance between food convenience and safety. L. monocytogenes is not a homogenous species, certain strains are more resilient to stressful conditions while others are potentially more virulent. To understand the basis of these differences we are applying proteomics to determine the mechanistic aspects of environmental adaptations of L. monocytogenes in food-relevant scenarios. The goal is to define how this species grows, behaves and survives thus allowing us to fine tune food safety risk management, especially when developing new minimal food processing guidelines or allowing introduction of unpasteurised food-types such as raw milk cheeses.