Methods for the detection and isolation of Shiga toxin-producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) are an important cause of haemorrhagic colitis and the diarrhoea-associated form of the haemolytic uraemic syndrome. Of the numerous serotypes of E. coli that have been shown to produce Shiga toxin (Stx), E. coli O157:H7 and E. coli O157:NM (non-motile) are most frequently implicated in human disease. Early recognition of STEC infections is critical for effective treatment of patients. Furthermore, rapid microbiological diagnosis of individual patients enables the prompt notification of outbreaks and implementation of control measures to prevent more cases. Most human infections caused by STEC have been acquired by the consumption of contaminated foods, especially those of bovine origin such as undercooked ground beef and unpasteurized cows' milk, and by person-to-person contacts. To identify the reservoirs of STEC and the routes of transmission to man, sensitive methods are needed as these pathogens may only be present in food, environmental and faecal samples in small numbers. In addition, sensitive and rapid detection methods are necessary for the food industry to ensure a safe supply of foods. Sensitive methods are also needed for surveillance programmes in risk assessment studies, and for studies on survival and growth of STEC strains. Cultural methods for the enrichment, isolation and confirmation of O157 STEC are still evolving. Several selective enrichment media have been described, of which modified tryptone soy broth with novobiocin and modified E. coli broth with novobiocin, seem to be the most appropriate. These media are minimally-selective broths that give a somewhat limited differential specificity favouring isolation of O157 STEC, as opposed to other Gram-negative bacteria, in the sample. An incubation temperature of 41-42 degrees C further enhances selectivity. The occurrence of heat-, freeze-, acid- or salt-stressed STEC in foods means that it is important to be able to detect cells that are in a stressed state, as STEC generally have a very low infectious dose, and injured cells mostly retain their pathogenic properties. For the isolation of stressed O157 STEC, pre-enrichment in a non-selective broth is necessary. The most widely used plating medium for the isolation of typical sorbitol-non-fermenting strains of STEC of serogroup O157 is sorbitol MacConkey agar with cefixime and tellurite (CT-SMAC). As some STEC strains are sensitive for tellurite and/or are sorbitol-fermenting, the use of a second isolation medium, such as one of the newer chromogenic media, is recommended. Immunomagnetic separation (IMS) following selective enrichment, and subsequent spread-plating of the concentrated target cells onto CT-SMAC agar, appears to be the most sensitive and cost-effective method for the isolation of E. coli O157 from raw foods. IMS increases sensitivity by concentrating E. coli O157 relative to background microflora, which may overgrow or mimic O157 STEC cells on selective agars. While cultural isolation of O157 STEC from foods and faeces is time-consuming, labour-intensive and hence, costly, rapid immunological detection systems have been developed which significantly reduce the analysis time. These methods include enzyme-linked immunosorbent assays (ELISAs), colony immunoblot assays, direct immunofluorescent filter techniques, and several immunocapture techniques. Both polyclonal and monoclonal antibodies specific for the O and H antigens are used for these methods. Many of these test systems are able to detect less than one O157 STEC cell g(-1) of raw meat after overnight enrichment. Presumptive results are available after just one day, but need to be completed with the isolation of the organisms. The primary use of these procedures is therefore to identify food and faecal samples that possibly contain O157 STEC.     

SoilGrids1km — Global Soil Information Based on Automated Mapping

BackgroundSoils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited spatial detail.Conclusions/SignificanceSoilGrids1km provide an initial set of examples of soil spatial data for input into global models at a resolution and consistency not previously available. Some of the main limitations of the current version of SoilGrids1km are: (1) weak relationships between soil properties/classes and explanatory variables due to scale mismatches, (2) difficulty to obtain covariates that capture soil forming factors, (3) low sampling density and spatial clustering of soil profile locations. However, as the SoilGrids system is highly automated and flexible, increasingly accurate predictions can be generated as new input data become available. SoilGrids1km are available for download via http://soilgrids.org under a Creative Commons Non Commercial license.     

Avoiding high relative air humidity during critical stages of leaf ontogeny is decisive for stomatal functioning

Plants of several species, if grown at high relative air humidity (RH ≥85%), develop stomata that fail to close fully in case of low leaf water potential. We studied the effect of a reciprocal change in RH, at different stages of leaf expansion of Rosa hybrida grown at moderate (60%) or high (95%) RH, on the stomatal closing ability. This was assessed by measuring the leaf transpiration rate in response to desiccation once the leaves had fully expanded. For leaves that started expanding at high RH but completed their expansion after transfer to moderate RH, the earlier this switch took place the better the stomatal functioning. Leaves initially expanding at moderate RH and transferred to high RH exhibited poor stomatal functioning, even when this transfer occurred very late during leaf expansion. Applying a daily abscisic acid (ABA) solution to the leaves of plants grown at continuous high RH was effective in inducing stomatal closure at low water potential, if done before full leaf expansion (FLE). After FLE, stomatal functioning was no longer affected either by the RH or ABA level. The results indicate that the degree of stomatal adaptation depends on both the timing and duration of exposure to high RH. It is concluded that stomatal functionality is strongly dependent on the humidity at which the leaf completed its expansion. The data also show that the effect of ambient RH and the alleviating role of ABA are restricted to the period of leaf expansion.     

Heterotrophic bacterial production on solid fish waste: TAN and nitrate as nitrogen source under practical RAS conditions

The drumfilter effluent from a recirculation aquaculture system (RAS) can be used as substrate for heterotrophic bacteria production. This biomass can be re-used as aquatic feed. RAS effluents are rich in nitrate and low in total ammonia nitrogen (TAN). This might result in 20% lower bacteria yields, because nitrate conversion into bacteria is less energy efficient than TAN conversion. In this study the influence of TAN concentrations (1, 12, 98, 193, 257mgTAN/l) and stable nitrate-N concentrations (174+/-29mg/l) on bacteria yields and nitrogen conversions was investigated in a RAS under practical conditions. The effluent slurry was supplemented with 1.7gC/l sodium acetate, due to carbon deficiency, and was converted continuously in a suspended bacteria growth reactor (hydraulic retention time 6h). TAN utilization did not result in significantly different observed yields than nitrate (0.24-0.32gVSS/gC, p=0.763). However, TAN was preferred compared to nitrate and was converted to nearly 100%, independently of TAN concentrations. TAN and nitrate conversions rates were differing significantly for increasing TAN levels (p<0.000 and p=0.012), and were negatively correlated. It seems, therefore, equally possible to supply the nitrogenous substrate for bacteria conversion as nitrate and not as TAN. The bacteria reactor can, as a result, be integrated into an existing RAS as end of pipe treatment.     

Prevalence and Genetic Characterization of Shiga Toxin-Producing Escherichia coli Isolates from Slaughtered Animals in Bangladesh

To determine the prevalence of Shiga toxin (Stx)-producing Escherichia coli (STEC) in slaughter animals in Dhaka, Bangladesh, we collected rectal contents immediately after animals were slaughtered. Of the samples collected from buffalo (n = 174), cows (n = 139), and goats (n = 110), 82.2%, 72.7%, and 11.8% tested positive for stx₁ and/or stx₂, respectively. STEC could be isolated from 37.9%, 20.1%, and 10.0% of the buffalo, cows, and goats, respectively. STEC O157 samples were isolated from 14.4% of the buffalo, 7.2% of the cows, and 9.1% of the goats. More than 93% (n = 42) of the STEC O157 isolates were positive for the stx₂, eae, katP, etpD, and enterohemorrhagic E. coli hly (hly_EHEC) virulence genes. STEC O157 isolates were characterized by seven recognized phage types, of which types 14 (24.4%) and 31 (24.4%) were predominant. Subtyping of the 45 STEC O157 isolates by pulsed-field gel electrophoresis showed 37 distinct restriction patterns, suggesting a heterogeneous clonal diversity. In addition to STEC O157, 71 STEC non-O157 strains were isolated from 60 stx-positive samples from 23.6% of the buffalo, 12.9% of the cows, and 0.9% of the goats. The STEC non-O157 isolates belonged to 36 different O groups and 52 O:H serotypes. Unlike STEC O157, most of the STEC non-O157 isolates (78.9%) were positive for stx₁. Only 7.0% (n = 5) of the isolates were positive for hly_EHEC, and none was positive for eae, katP, and etpD. None of the isolates was positive for the iha, toxB, and efa1 putative adhesion genes. However, 35.2% (n = 25), 11.3% (n = 8), 12.7% (n = 9), and 12.7% (n = 9) of the isolates were positive for the lpf_O113, saa, lpfA_O157/01-141, and lpfA_O157/OI-154 genes, respectively. The results of this study provide the first evidence that slaughtered animals like buffalo, cows, and goats in Bangladesh are reservoirs for STEC, including the potentially virulent STEC strain O157.     

Role of sink–source relationships in chrysanthemum flower size and total biomass production

The present work was aimed at understanding and quantifying the effect of sink–source relationships on flower size, using chrysanthemum as a model system. Sink/source ratio was manipulated by flower bud removal (leaving one, two or four flowers, and a control), axillary shoot removal, and varying daily light integral. Furthermore, the influence of flower position within the stem on the flower size was investigated. All means applied to reduce sink/source ratio resulted in a significantly higher individual flower dry mass and area in plants with a fixed number of flowers. Nevertheless, control plants responded to supplementary assimilation light with an increased number of flowers rather than producing larger flowers. Flower position had a negligible effect on flower size in both disbudded and control plants, except that the second-order lateral flowers were significantly smaller than the first-order ones. Singly flowered plants without side shoots represented the greatest potential flower size; they had flowers up to 2.4 times heavier than the control plants. Total aerial plant dry mass was only reduced at very low sink strength treatments, whereas flower mass ratio showed a saturating response to the number of flowers per plant. The results indicate that individual flower size is very sensitive to total plant sink strength, but it does not change with plant source strength when the number of flowers is not manipulated.     

Plant development controls leaf area expansion in alfalfa plants competing for light

Background and Aims

The growth of crops in a mixture is more variable and difficult to predict than that in pure stands. Light partitioning and crop leaf area expansion play prominent roles in explaining this variability. However, in many crops commonly grown in mixtures, including the forage species alfalfa, the sensitivity and relative importance of the physiological responses involved in the light modulation of leaf area expansion are still to be established. This study was designed to assess the relative sensitivity of primary shoot development, branching and individual leaf expansion in alfalfa in response to light availability.

Methods

Two experiments were carried out. The first studied isolated plants to assess the potential development of different shoot types and growth periods. The second consisted of manipulating the intensity of competition for light using a range of canopies in pure and mixed stands at two densities so as to evaluate the relative effects on shoot development, leaf growth, and plant and shoot demography.

Key Results

Shoot development in the absence of light competition was deterministic (constant phyllochrons of 32·5 °Cd and 48·2 °Cd for primary axes and branches, branching probability of 1, constant delay of 1·75 phyllochron before axillary bud burst) and identical irrespective of shoot type and growth/regrowth periods. During light competition experiments, changes in plant development explained most of the plant leaf area variations, with average leaf size contributing to a lesser extent. Branch development and the number of shoots per plant were the leaf area components most affected by light availability. Primary axis development and plant demography were only affected in situations of severe light competition.

Conclusions

Plant leaf area components differed with regard to their sensitivity to light competition. The potential shoot development model presented in this study could serve as a framework to integrate light responses in alfalfa crop models.     

Flower and fruit abortion in sweet pepper in relation to source and sink strength

Source strength (assimilate supply) and sink strength (assimilate demand) of the plant were varied in different ways to investigate to what extent flower/fruit abortion in sweet pepper (Capsicum annuum L.) is determined by the availability of assimilates. Source strength was varied by changing the light level, plant density, and leaf pruning. Sink strength was varied by changing the temperature and the number and position of earlier formed fruits. Shading as well as heating for short periods showed that flowers/fruits were the most susceptible to abortion during the first week after anthesis. The different experiments where source strength was varied all showed that when source strength decreased, the rate of abortion increased linearly, whether source strength was decreased by shading, high plant density, or leaf pruning. That flower and fruit abortion not only depends on the source strength but also on the sink strength of competing organs is shown by varying the number or the position of earlier formed fruits. With the same source strength, the rate of abortion showed a close relationship with the growth rate of the earlier formed competing fruits, suggesting that the induction of abortion by earlier formed fruits is due to their sink strength. Most of the variation in abortion could be related to differences in vegetative growth rate, the latter being an indicator of the source-sink ratio. However, with the same vegetative growth rate, the rate of abortion was lower for the leaf pruning treatments where no competing fruits were retained than for the fruit load treatments. This indicates that although most of the variation in abortion can be related to the source and sink strength of the plant, some effects of competing fruits can only be explained by a combination of competition and dominance.     

Jacques Le Magnen (1916-2002)

View larger version (162K): [in this window] [in a new window]   Jacques Le Magnen with his wife Régine on July 14, 1976, the eve of ISOT VI, which he organized at Gif-sur-Yvette.   One of the pioneers in research on olfaction and taste, andon the regulation of water and food intake left us on Thursday,May 23, 2002, at the age of 85. Jacques Le Magnen was a discipleof the famous French physiologist Henri Piéron at theCollège de France, and from 1949 till 1989 developedhis own laboratory of sensory     

Incorporating DEM Uncertainty in Coastal Inundation Mapping

Coastal managers require reliable spatial data on the extent and timing of potential coastal inundation, particularly in a changing climate. Most sea level rise (SLR) vulnerability assessments are undertaken using the easily implemented bathtub approach, where areas adjacent to the sea and below a given elevation are mapped using a deterministic line dividing potentially inundated from dry areas. This method only requires elevation data usually in the form of a digital elevation model (DEM). However, inherent errors in the DEM and spatial analysis of the bathtub model propagate into the inundation mapping. The aim of this study was to assess the impacts of spatially variable and spatially correlated elevation errors in high-spatial resolution DEMs for mapping coastal inundation. Elevation errors were best modelled using regression-kriging. This geostatistical model takes the spatial correlation in elevation errors into account, which has a significant impact on analyses that include spatial interactions, such as inundation modelling. The spatial variability of elevation errors was partially explained by land cover and terrain variables. Elevation errors were simulated using sequential Gaussian simulation, a Monte Carlo probabilistic approach. 1,000 error simulations were added to the original DEM and reclassified using a hydrologically correct bathtub method. The probability of inundation to a scenario combining a 1 in 100 year storm event over a 1 m SLR was calculated by counting the proportion of times from the 1,000 simulations that a location was inundated. This probabilistic approach can be used in a risk-aversive decision making process by planning for scenarios with different probabilities of occurrence. For example, results showed that when considering a 1% probability exceedance, the inundated area was approximately 11% larger than mapped using the deterministic bathtub approach. The probabilistic approach provides visually intuitive maps that convey uncertainties inherent to spatial data and analysis.