High prevalence of multidrug-tolerant bacteria and associated antimicrobial resistance genes isolated from ornamental fish and their carriage water

Background: Antimicrobials are used to directly control bacterial infections in pet (ornamental) fish and are routinely added to the water these fish are shipped in to suppress the growth of potential pathogens during transport. Methodology/Principal Findings: To assess the potential effects of this sustained selection pressure, 127 Aeromonas spp. isolated from warm and cold water ornamental fish species were screened for tolerance to 34 antimicrobials. Representative isolates were also examined for the presence of 54 resistance genes by a combination of miniaturized microarray and conventional PCR. Forty-seven of 94 Aeromonas spp. isolates recovered from tropical ornamental fish and their carriage water were tolerant to >= 15 antibiotics, representing seven or more different classes of antimicrobial. The quinolone and fluoroquinolone resistance gene, qnrS2, was detected at high frequency (37% tested recent isolates were positive by PCR). Class 1 integrons, IncA/C broad host range plasmids and a range of other antibiotic resistance genes, including floR, blaTEM21, tet(A), tet(D), tet(E), qacE2, sul1, and a number of different dihydrofolate reductase and aminoglycoside transferase coding genes were also detected in carriage water samples and bacterial isolates. Conclusions: These data suggest that ornamental fish and their carriage water act as a reservoir for both multi-resistant bacteria and resistance genes.

An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157: H7 with bovine intestinal epithelium

Enterohaemorrhagic Escherichia coli O157 : H7 is a bacterial pathogen that can cause haemorrhagic colitis and haemolytic uremic syndrome. In the primary reservoir host, cattle, the terminal rectum is the principal site of E. coli O157 colonization. In this study, bovine terminal rectal primary epithelial cells were used to examine the role of H7 flagella in epithelial adherence. Binding of a fliC(H7) mutant O157 strain to rectal epithelium was significantly reduced as was binding of the flagellated wild-type strain following incubation with H7-specific antibodies. Complementation of fliC(H7) mutant O157 strain with fliC(H7) restored the adherence to wild-type levels; however, complementation with fliC(H6) did not restore it. High-resolution ultrastructural and imunofluorescence studies demonstrated the presence of abundant flagella forming physical contact points with the rectal epithelium. Binding to terminal rectal epithelium was specific to H7 by comparison with other flagellin types tested. In-cell Western assays confirmed temporal expression of flagella during O157 interaction with epithelium, early expression was suppressed during the later stages of microcolony and attaching and effacing lesion formation. H7 flagella are expressed in vivo by individual bacteria in contact with rectal mucosa. Our data demonstrate that the H7 flagellum acts as an adhesin to bovine intestinal epithelium and its involvement in this crucial initiating step for colonization indicates that H7 flagella could be an important target in intervention strategies.

Catchment phosphorous losses: an export coefficient modelling approach with scenario analysis for water management

This paper presents the development of an export coefficient model to characterise the rates and sources of P export from land to water in four reservoir systems located in a semi-arid rural region in southern of Portugal. The model was developed to enable effective management of these important water resource systems under the EU Water Framework Directive. This is the first time such an approach has been fully adapted for the semi-arid systems typical of Mediterranean Europe. The sources of P loading delivered to each reservoir from its catchment were determined and scenario analysis was undertaken to predict the likely impact of catchment management strategies on the scale of rate of P loading delivered to each water body from its catchment. The results indicate the importance of farming and sewage treatment works/collective septic tanks discharges as the main contributors to the total diffuse and point source P loading delivered to the reservoirs, respectively. A reduction in the total P loading for all study areas would require control of farming practices and more efficient removal of P from human wastes prior to discharge to surface waters. The scenario analysis indicates a strategy based solely on reducing the agricultural P surplus may result in only a slow improvement in water quality, which would be unlikely to support the generation of good ecological status in reservoirs. The model application indicates that a reduction of P-inputs to the reservoirs should first focus on reducing P loading from sewage effluent discharges through the introduction of tertiary treatment (P-stripping) in all major residential areas. The fully calibrated export coefficient modelling approach transferred well to semi-arid regions, with the only significant limitation being the availability of suitable input data to drive the model. Further studies using this approach in semi-arid catchments are now needed to increase the knowledge of nutrient export behaviours in semi-arid regions.

Progressive palaeoenvironmental change during the Late Barremian-Early Aptian as prelude to Oceanic Anoxic Event 1a: Evidence from the Gorgo a Cerbara section (Umbria-Marche basin, central Italy)

During Oceanic Anoxic Event 1a (OAE 1a, 120 Ma; Li et al., 2008), organic carbon-rich layers were deposited in marine environments under anoxic conditions on a global scale. In this study, palaeoenvironmental conditions leading to this event are characterised by studying the Upper Barremian to the Lower Aptian succession of the Gorgo a Cerbara section (central Italy). For this, an integrated multi-proxy approach (δ13Ccarb; δ13Corg; δ18O; phosphorus; Total Organic Carbon, TOC; bulk-rock mineralogy, as well as redox-sensitive trace elements — RSTEs) has been applied. During the LateBarremian, thin organic-rich layers occur episodically, and associated Corg:Ptot ratios indicate the presence of intermittent dysoxic to anoxic conditions. Coarse correlations are observed between TOC, P and biogenic silica contents, indicating links between P availability, productivity, and TOC preservation. However, the corresponding δ13Ccarb and δ18O records remain quite stable, indicating that these brief periods of enhanced TOC preservation did not have sufficient impact on the marine carbon reservoir to deviate δ13C records. Around the Barremian–Aptian boundary, TOC-enriched layers become more frequent. These layers correlate with negative excursions in the δ13Ccarb and δ13Corg records, possibly due to a warming period as indicated by the δ18O record. During the earliest Aptian, this warming trend is reverted into a cooling trend, which is then followed by an important warming step near the onset of Oceanic Anoxic Event 1a (OAE 1a). During this time period, organic-rich intervals occur, which are characterised by the progressive increase in RSTE. The warming step prior the onset of OAE 1a is associated with the well-known negative spike in δ13Ccarb and δ13Corg records, an important peak in P accumulation, RSTE enrichments and Corg:Ptot ratios indicating the prevalence of anoxic conditions. The Selli Level itself may document a cooling phase. RSTE enrichments and Corg:Ptot ratios confirm the importance of anoxic conditions during OAE 1a at this site. The Gorgo a Cerbara section is interpreted to reflect the progressive impact of palaeoenvironmental change related to the formation of the Ontong-Java plate-basalt plateau, which started already around the Barremian–Aptian boundary and culminated into OAE 1a.

Lyme borreliosis in the UK: ecology and risks to domestic animals and man

The different associations of Borrelia burgdorferi sensu lato spirochaetes with their natural reservoir hosts and tick vectors are slowly being unravelled. This review discusses the interactions of different genospecies of Lyme borreliosis spirochaetes and their differing tick vectors, vertebrate reservoirs and 'accidental hosts'. Particular reference is made to spirochaete-host interactions and occurrence of pathological consequences. Attention is focused on the unique prevalence of enzoonotic cycles in operation within the UK. Risk factors for acquiring Lyme borreliosis in man are discussed. (C) 2001 Lippincott Williams & Wilkins.

Production of attaching-effacing lesions in ligated large intestine loops of 6-month-old sheep by Escherichia coli O157:H7

Shiga-toxigenic Escherichia coli O157:H7 (STEC O157:H7) is associated with potentially fatal human disease, and a persistent reservoir of the organism is present in some farm animal species, especially cattle and sheep. The mechanisms of persistent colonisation of the ruminant intestine by STEC O157:H7 are poorly understood but may be associated with intimate adherence to eukaryotic cells. Intimate adherence, as evidenced by induction of attaching-effacing (AE) lesions by STEC O157, has been observed in 6-day-old conventional lambs after deliberate oral infection but not in older animals. Thus, the present study used a ligated intestinal loop technique to investigate whether STEC O157:H7 and other attaching-effacing E. coli may adhere intimately to the sheep large intestinal mucosa. To do this, four STEC O157:H7 strains, one STEC 026:K60:H11 and one Shiga toxin-negative E. coli O157:H7 strain, suspended in either phosphate-buffered saline or Dulbecco's modified Eagle's medium, were inoculated into ligated spiral colon loops of each of two lambs. The loops were removed 6 h after inoculation, fixed and examined by light and electron microscopy. AE lesions on the intestinal mucosa were produced by all the inoculated strains. However, the lesions were sparse and small, typically comprising bacterial cells intimately adhered to a single enterocyte, or a few adjacent enterocytes. There was little correlation between the extent of intimate adherence in this model and the bacterial cell density, pre-inoculation growth conditions of the bacteria or the strain tested.

Non-toxigenic Escherichia coli O157:H7 strain NCTC12900 causes attaching-effacing lesions and eae-dependent persistence in weaned sheep

Ruminants are regarded as a primary reservoir for Escherichia coli O157:H7, an important human pathogen. Intimin, encoded by the Locus of Enterocyte Effacement by E. coli O157:H7 organisms, has been cited as one bacterial mechanism of colonisation of the gastrointestinal tract. To confirm this and to test whether a non-toxigenic E. coli O157:H7 strain would colonise and persist in a sheep model, E. coli O157:H7 strain NCTC12900, that lacks Shiga toxin (stx) genes, was evaluated for use in a sheep model of persistence. Following oral inoculation of six-week-old sheep, persistent excretion of NCTC12900 was observed for up to 48 days. E. coli O157-associated attaching-effacing (AE) lesions were detected in the caecum and rectum of one six-week-old lamb, one day after inoculation. This is the first recorded observation of AE lesions in orally inoculated weaned sheep. Also, mean faecal excretion scores of NCTC12900 and an isogenic intimin (eae)-deficient mutant were determined from twenty-four six-week-old orally inoculated sheep. The eae mutant was cleared within 20 days and had lower mean excretion scores at all time points after day one post inoculation compared with the parental strain that was still being excreted at 48 days. Tissues were collected post mortem from animals selected at random from the study groups over the time course of the experiment. The eae mutant was detected in only 1/43 samples but the parental strain was recovered from 64/140 samples primarily from the large bowel although rumen, duodenum, jejunum, and ileum were culture positive especially from animals that were still excreting at and beyond 27 days after inoculation.

Simple and effective technical procedures for the packing and application of nanospray PicoFrit HPLC columns for proteomic analyses

A simple procedure was developed for packing PicoFrit HPLC columns with chromatographic stationary phase using a reservoir fabricated from standard laboratory HPLC fittings. Packed columns were mounted onto a stainless steel ultra-low volume precolumn filter assembly containing a 0.5-mu m pore size steel frit. This format provided a conduit for the application of the nanospray voltage and protected the column from obstruction by sample material. The system was characterised and operational performance assessed by analysis of a range of peptide standards (n = 9).

Role of intimin-Tir interactions and the Tir-cytoskeleton coupling protein in the colonization of calves and lambs by Escherichia coli O157:H7

Intimin facilitates intestinal colonization by enterohemorrhagic Escherichia coli O157:H7; however, the importance of intimin binding to its translocated receptor (Tir) as opposed to cellular coreceptors is unknown. The intimin-Tir interaction is needed for optimal actin assembly under adherent bacteria in vitro, a process which requires the Tir-cytoskeleton coupling protein (TccP/EspF(U)) in E. coli O157:H7. Here we report that E. coli O157:H7 tir mutants are at least as attenuated as isogenic eae mutants in calves and lambs, implying that the role of intimin in the colonization of reservoir hosts can be explained largely by its binding to Tir. Mutation of tccP uncoupled actin assembly from the intimin-Tir-mediated adherence of E. coli O157:H7 in vitro but did not impair intestinal colonization in calves and lambs, implying that pedestal formation may not be necessary for persistence. However, an E. coli O157:H7 tccP mutant induced typical attaching and effacing lesions in a bovine ligated ileal loop model of infection, suggesting that TccP-independent mechanisms of actin assembly may operate in vivo.

The unsteady flow of a weakly compressible fluid in a thin porous layer II: three-dimensional theory

We consider the problem of determining the pressure and velocity fields for a weakly compressible fluid flowing in a three-dimensional layer, composed of an inhomogeneous, anisotropic porous medium, with vertical side walls and variable upper and lower boundaries, in the presence of vertical wells injecting and/or extracting fluid. Numerical solution of this three-dimensional evolution problem may be expensive, particularly in the case that the depth scale of the layer h is small compared to the horizontal length scale l, a situation which occurs frequently in the application to oil and gas reservoir recovery and which leads to significant stiffness in the numerical problem. Under the assumption that $\epsilon\propto h/l\ll 1$, we show that, to leading order in $\epsilon$, the pressure field varies only in the horizontal directions away from the wells (the outer region). We construct asymptotic expansions in $\epsilon$ in both the inner (near the wells) and outer regions and use the asymptotic matching principle to derive expressions for all significant process quantities. The only computations required are for the solution of non-stiff linear, elliptic, two-dimensional boundary-value, and eigenvalue problems. This approach, via the method of matched asymptotic expansions, takes advantage of the small aspect ratio of the layer, $\epsilon$, at precisely the stage where full numerical computations become stiff, and also reveals the detailed structure of the dynamics of the flow, both in the neighbourhood of wells and away from wells.

Associating spontaneous with evoked activity in a neural mass model of cat visual cortex

Spontaneous activity of the brain at rest frequently has been considered a mere backdrop to the salient activity evoked by external stimuli or tasks. However, the resting state of the brain consumes most of its energy budget, which suggests a far more important role. An intriguing hint comes from experimental observations of spontaneous activity patterns, which closely resemble those evoked by visual stimulation with oriented gratings, except that cortex appeared to cycle between different orientation maps. Moreover, patterns similar to those evoked by the behaviorally most relevant horizontal and vertical orientations occurred more often than those corresponding to oblique angles. We hypothesize that this kind of spontaneous activity develops at least to some degree autonomously, providing a dynamical reservoir of cortical states, which are then associated with visual stimuli through learning. To test this hypothesis, we use a biologically inspired neural mass model to simulate a patch of cat visual cortex. Spontaneous transitions between orientation states were induced by modest modifications of the neural connectivity, establishing a stable heteroclinic channel. Significantly, the experimentally observed greater frequency of states representing the behaviorally important horizontal and vertical orientations emerged spontaneously from these simulations. We then applied bar-shaped inputs to the model cortex and used Hebbian learning rules to modify the corresponding synaptic strengths. After unsupervised learning, different bar inputs reliably and exclusively evoked their associated orientation state; whereas in the absence of input, the model cortex resumed its spontaneous cycling. We conclude that the experimentally observed similarities between spontaneous and evoked activity in visual cortex can be explained as the outcome of a learning process that associates external stimuli with a preexisting reservoir of autonomous neural activity states. Our findings hence demonstrate how cortical connectivity can link the maintenance of spontaneous activity in the brain mechanistically to its core cognitive functions.

The interactive responses of water quality and hydrology to changes in multiple stressors, and implications for the long-term effective management of phosphorus

Soluble reactive phosphorus (SRP) plays a key role in eutrophication, a global problem decreasing habitat quality and in-stream biodiversity. Mitigation strategies are required to prevent SRP fluxes from exceeding critical levels, and must be robust in the face of potential changes in climate, land use and a myriad of other influences. To establish the longevity of these strategies it is therefore crucial to consider the sensitivity of catchments to multiple future stressors. This study evaluates how the water quality and hydrology of a major river system in the UK (the River Thames) respond to alterations in climate, land use and water resource allocations, and investigates how these changes impact the relative performance of management strategies over an 80-year period. In the River Thames, the relative contributions of SRP from diffuse and point sources vary seasonally. Diffuse sources of SRP from agriculture dominate during periods of high runoff, and point sources during low flow periods. SRP concentrations rose under any future scenario which either increased a) surface runoff or b) the area of cultivated land. Under these conditions, SRP was sourced from agriculture, and the most effective single mitigation measures were those which addressed diffuse SRP sources. Conversely, where future scenarios reduced flow e.g. during winters of reservoir construction, the significance of point source inputs increased, and mitigation measures addressing these issues became more effective. In catchments with multiple point and diffuse sources of SRP, an all-encompassing effective mitigation approach is difficult to achieve with a single strategy. In order to attain maximum efficiency, multiple strategies might therefore be employed at different times and locations, to target the variable nature of dominant SRP sources and pathways.

Human microbiota in health and disease

Each human body plays host to a microbial population which is both numerically vast (at around 1014 microbial cells) and phenomenally diverse (over 1,000 species). The majority of the microbial species in the gut have not been cultured but the application of culture-independent approaches for high throughput diversity and functionality analysis has allowed characterisation of the diverse microbial phylotypes present in health and disease. Studies in monozygotic twins, showing that these retain highly similar microbiota decades after birth and initial colonisation, are strongly indicative that diversity of the microbiome is host-specific and affected by the genotype. Microbial diversity in the human body is reflected in both richness and evenness. Diversity increases steeply from birth reaching its highest point in early adulthood, before declining in older age. However, in healthy subjects there appears to be a core of microbial phylotypes which remains relatively stable over time. Studies of individuals from diverse geopraphies suggest that clusters of intestinal bacterial groups tend to occur together, constituting ‘enterotypes’. So variation in intestinal microbiota is stratified rather than continuous and there may be a limited number of host/microbial states which respond differently to environmental influences. Exploration of enterotypes and functional groups may provide biomarkers for disease and insights into the potential for new treatments based on manipulation of the microbiome. In health, the microbiota interact with host defences and exist in harmonious homeostasis which can then be disturbed by invading organisms or when ‘carpet bombing’ by antibiotics occurs. In a portion of individuals with infections, the disease will resolve itself without the need for antibiotics and microbial homeostasis with the host’s defences is restored. The administration of probiotics (live microorganisms which when administered in adequate amounts confer a health benefit on the host) represents an artificial way to enhance or stimulate these natural processes. The study of innate mechanisms of antimicrobial defence on the skin, including the production of numerous antimicrobial peptides (AMPs), has shown an important role for skin commensal organisms. These organisms may produce AMPs, and also amplify the innate immune responses to pathogens by activating signalling pathways and processing host produced AMPs. Research continues into how to enhance and manipulate the role of commensal organisms on the skin. The challenges of skin infection (including diseases caused by multiply resistant organisms) and infestations remain considerable. The potential to re-colonise the skin to replace or reduce pathogens, and exploring the relationship between microbiota elsewhere and skin diseases are among a growing list of research targets. Lactobacillus species are among the best known ‘beneficial’ bacterial members of the human microbiota. Of the approximately 120 species known, about 15 are known to occur in the human vagina. These organisms have multiple properties, including the production of lactic acid, hydrogen peroxide and bacteriocins, which render the vagina inhospitable to potential pathogens. Depletion of the of the normal Lactobacillus population and overgrowth of vaginal anaerobes, accompanied by the loss of normal vaginal acidity can lead to bacterial vaginosis – the commonest cause of abnormal vaginal discharge in women. Some vaginal anaerobes are associated with the formation of vaginal biofilms which serve to act as a reservoir of organisms which persists after standard antibiotic therapy of bacterial vaginosis and may help to account for the characteristically high relapse rate in the condition. Administration of Lactobacillus species both vaginally and orally have shown beneficial effects in the treatment of bacterial vaginosis and such treatments have an excellent overall safety record. Candida albicans is a frequent coloniser of human skin and mucosal membranes, and is a normal part of the microbiota in the mouth, gut and vagina. Nevertheless Candida albicans is the most common fungal pathogen worldwide and is a leading cause of serious and often fatal nosocomial infections. What turns this organism from a commensal to a pathogen is a combination of increasing virulence in the organism and predisposing host factors that compromise immunity. There has been considerable research into the use of probiotic Lactobacillus spp. in vaginal candidiasis. Studies in reconstituted human epithelium and monolayer cell cultures have shown that L. rhamnosus GG can protect mucosa from damage caused by Candida albicans, and enhance the immune responses of mucosal surfaces. Such findings offer the promise that the use of such probiotic bacteria could provide new options for antifungal therapy. Studies of changes of the human intestinal microbiota in health and disease are complicated by its size and diversity. The Alimentary Pharmabiotic Centre in Cork (Republic of Ireland) has the mission to ‘mine microbes for mankind’ and its work illustrates the potential benefits of understanding the gut microbiota. Work undertaken at the centre includes: mapping changes in the microbiota with age; studies of the interaction between the microbiota and the gut; potential interactions between the gut microbiota and the central nervous system; the potential for probiotics to act as anti-infectives including through the production of bacteriocins; and the characterisation of interactions between gut microbiota and bile acids which have important roles as signalling molecules and in immunity. The important disease entity where the role of the gut microbiota appears to be central is the Irritable Bowel Syndrome (IBS). IBS patients show evidence of immune activation, impaired gut barrier function and abnormal gut microbiota. Studies with probiotics have shown that these organisms can exert anti-inflammatory effects in inflammatory bowel disease and may strengthen the gut barrier in IBS of the diarrhoea-predominant type. Formal randomised trials of probiotics in IBS show mixed results with limited benefit for some but not all. Studies confirm that administered probiotics can survive and temporarily colonise the gut. They can also stimulate the numbers of other lactic acid bacilli in the gut, and reduce the numbers of pathogens. However consuming live organisms is not the only way to influence gut microbiota. Dietary prebiotics are selectively fermented ingredients that can change the composition and/or activity of the gastrointestinal microbiota in beneficial ways. Dietary components that reach the colon, and are available to influence the microbiota include poorly digestible carbohydrates, such as non-starch polysaccharides, resistant starch, non-digestible oligosaccharides (NDOs) and polyphenols. Mixtures of probiotic and prebiotic ingredients that can selectively stimulate growth or activity of health promoting bacteria have been termed ‘synbiotics’. All of these approaches can influence gut microbial ecology, mainly to increase bifidobacteria and lactobacilli, but metagenomic approaches may reveal wider effects. Characterising how these changes produce physiological benefits may enable broader use of these tactics in health and disease in the future. The current status of probiotic products commercially available worldwide is less than ideal. Prevalent problems include misidentification of ingredient organisms and poor viability of probiotic microorganisms leading to inadequate shelf life. On occasions these problems mean that some commercially available products cannot be considered to meet the definition of a probiotic product. Given the potential benefits of manipulating the human microbiota for beneficial effects, there is a clear need for improved regulation of probiotics. The potential importance of the human microbiota cannot be overstated. ‘We feed our microbes, they talk to us and we benefit. We just have to understand and then exploit this.’ (Willem de Vos).

Impact of strong deep ocean stratification on the glacial carbon cycle

During the Last Glacial Maximum, the climate was substantially colder and the carbon cycle was clearly different from the late Holocene. According to proxy data deep oceanic δ13C was very low, and the atmospheric CO2 concentration also reduced. Several mechanisms have been proposed to explain these changes, but none can fully explain the data, especially the very low deep ocean δ13C values. Oceanic core data show that the deep ocean was very cold and salty, which would lead to enhanced deep ocean stratification. We show that such an enhanced stratification in the coupled climate model CLIMBER-2 helps get very low deep oceanic δ13C values. Indeed the simulated δ13C reaches values as low as −0.8‰ in line with proxy data evidences. Moreover it increases the oceanic carbon reservoir leading to a small, yet robust, atmospheric CO2 drop of approximately 10 ppm.

Impact of brine-induced stratification on the glacial carbon cycle

During the cold period of the Last Glacial Maximum (LGM, about 21 000 years ago) atmospheric CO2 was around 190 ppm, much lower than the pre-industrial concentration of 280 ppm. The causes of this substantial drop remain partially unresolved, despite intense research. Understanding the origin of reduced atmospheric CO2 during glacial times is crucial to comprehend the evolution of the different carbon reservoirs within the Earth system (atmosphere, terrestrial biosphere and ocean). In this context, the ocean is believed to play a major role as it can store large amounts of carbon, especially in the abyss, which is a carbon reservoir that is thought to have expanded during glacial times. To create this larger reservoir, one possible mechanism is to produce very dense glacial waters, thereby stratifying the deep ocean and reducing the carbon exchange between the deep and upper ocean. The existence of such very dense waters has been inferred in the LGM deep Atlantic from sediment pore water salinity and δ18O inferred temperature. Based on these observations, we study the impact of a brine mechanism on the glacial carbon cycle. This mechanism relies on the formation and rapid sinking of brines, very salty water released during sea ice formation, which brings salty dense water down to the bottom of the ocean. It provides two major features: a direct link from the surface to the deep ocean along with an efficient way of setting a strong stratification. We show with the CLIMBER-2 carbon-climate model that such a brine mechanism can account for a significant decrease in atmospheric CO2 and contribute to the glacial-interglacial change. This mechanism can be amplified by low vertical diffusion resulting from the brine-induced stratification. The modeled glacial distribution of oceanic δ13C as well as the deep ocean salinity are substantially improved and better agree with reconstructions from sediment cores, suggesting that such a mechanism could have played an important role during glacial times.