Genome scale reconstruction of a Salmonella metabolic model comparison of similarity and differences with a commensal Escherichia coli strain

Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.

In vitro evaluation of single- and multi-strain probiotics: inter-species inhibition between probiotic strains, and inhibition of pathogens

Many studies comparing the effects of single- and multi-strain probiotics on pathogen inhibition compare treatments with different concentrations. They also do not examine the possibility of inhibition between probiotic strains with a mixture. We tested the ability of 14 single-species probiotics to inhibit each other using a cross-streak assay, and agar spot test. We then tested the ability of 15 single-species probiotics and 5 probiotic mixtures to inhibit C. difficile, E. coli and S. Typhimurium, using the agar spot test. Testing was done with mixtures created in two ways: one group contained component species incubated together, the other group of mixtures was made using component species which had been incubated separately, equalised to equal optical density, and then mixed in equal volumes. Inhibition was observed for all combinations of probiotics, suggesting that when used as such there may be inhibition between probiotics, potentially reducing efficacy of the mixture. Significant inter-species variation was seen against each pathogen. When single species were tested against mixtures, the multi-species preparations displayed significantly (p<0.05 or less) greater inhibition of pathogens in 12 out of 24 cases. Despite evidence that probiotic species will inhibit each other when incubated together in vitro, in many cases a probiotic mixture was more effective at inhibiting pathogens than its component species when tested at approximately equal concentrations of biomass. This suggests that using a probiotic mixture might be more effective at reducing gastrointestinal infections, and that creating a mixture using species with different effects against different pathogens may have a broader spectrum of action that a single provided by a single strain.

The variant rpoS allele of S-enteritidis strain 27655R does not affect virulence in a chick model nor constitutive curliation but does generate a cold-sensitive phenotype

Adherence of pathogenic Escherichia coli and Salmonella spp. to host cells is in part mediated by curli fimbriae which, along with other virulence determinants, are positively regulated by RpoS. Interested in the role and regulation of curli (SEF17) fimbriae of Salmonella enteritidis in poultry infection, we tested the virulence of naturally occurring S. enteritidis PT4 strains 27655R and 27655S which displayed constitutive and null expression of curli (SEF17) fimbriae, respectively, in a chick invasion assay and analysed their rpoS alleles. Both strains were shown to be equally invasive and as invasive as a wild-type phage type 4 strain and an isogenic derivative defective for the elaboration of curli. We showed that the rpoS allele of 27655S was intact even though this strain was non-curliated and we confirmed that a S. enteritidis rpoS::str(r) null mutant was unable to express curli, as anticipated. Strain 27655R, constitutively curliated, possessed a frameshift mutation at position 697 of the rpoS coding sequence which resulted in a truncated product and remained curliated even when transduced to rpoS::str(r). Additionally, rpoS mutants are known to be cold-sensitive, a phenotype confirmed for strain 27655R. Collectively, these data indicated that curliation was not a significant factor for pathogenesis of S. enteritidis in this model and that curliation of strains 27655R and 27655S was independent of RpoS. Significantly, strain 27655R possessed a defective rpoS allele and remained virulent. Here was evidence that supported the concept that different naturally occurring rpoS alleles may generate varying virulence phenotypic traits. (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Infection of gnotobiotic calves with Escherichia coli O157 : H7 strain A84

Six colostrum-deprived, hysterotomy-derived calves were maintained under sterile conditions and fed a milk replacer diet. At five days of age, five of the calves were dosed orally with 10(9)cfu of Escherichia coli O157: H7 strain A84. They were killed after, one, two, six, 12 and 24 days, and samples were taken for bacteriological and pathological examination. The sixth uninfected control calf was killed at seven days of age and matched samples were taken for pathological comparison. The animals remained normal throughout the observation period. Bacteriological data indicated a heavy bacterial load of strain A84 throughout the gastrointestinal tract but the bacterium was not found in liver, kidney or muscle. No evidence of attaching and effacing' lesions in the small or large intestine was found although there was a mild inflammatory response in the intestinal tract, consisting mainly of infiltrating eosinophils.

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.

Variable and strain dependent colonisation of chickens by Escherichia coli O157

The prevalence of enterohaemorrhagic Escherichia coli (EHEC) O157 in poultry is considered minimal compared with other species, especially ruminants. However, deliberate inoculation studies have shown that poultry are readily and persistently infected by this organism but that the mechanism of colonisation is independent of intimin, a recognised factor in host-EHEC interactions in mammalian species, and may be dependent upon flagella. Few strains of EHEC O157 have been tested in poultry and here 1-day-old and 6-week-old chicks were inoculated with seven non-toxigenic E. coli O157 strains in separate experiments. Persistence was measured semi-quantitatively by bacteriological assessment of E. coli O157 cultured from cloacal swabs (shedding score). In the 1-day-old chick model that was monitored for 43 days, all seven strains established well after inoculation. In the 6-week-old chicken model, one strain established and gave consistently high shedding for the duration of the experiment (156 days). Whereas of the remaining six strains, two persisted for 113 days, two persisted for 43 days, one persisted for 22 days and one strain was never detected.

Comparative in vitro inhibition of urinary tract pathogens by single- and multi-strain probiotics

PURPOSE: Multi-species probiotic preparations have been suggested as having a wide spectrum of application, although few studies have compared their efficacy with that of individual component strains at equal concentrations. We therefore tested the ability of 4 single probiotics and 4 probiotic mixtures to inhibit the urinary tract pathogens Escherichia coli NCTC 9001 and Enterococcus faecalis NCTC 00775. METHODS: We used an agar spot test to test the ability of viable cells to inhibit pathogens, while a broth inhibition assay was used to assess inhibition by cell-free probiotic supernatants in both pH-neutralised and non-neutralised forms. RESULTS: In the agar spot test, all probiotic treatments showed inhibition, L. acidophilus was the most inhibitory single strain against E. faecalis, L. fermentum the most inhibitory against E. coli. A commercially available mixture of 14 strains (Bio-Kult(®)) was the most effective mixture, against E. faecalis, the 3-lactobacillus mixture the most inhibitory against E. coli. Mixtures were not significantly more inhibitory than single strains. In the broth inhibition assays, all probiotic supernatants inhibited both pathogens when pH was not controlled, with only 2 treatments causing inhibition at a neutral pH. CONCLUSIONS: Both viable cells of probiotics and supernatants of probiotic cultures were able to inhibit growth of two urinary tract pathogens. Probiotic mixtures prevented the growth of urinary tract pathogens but were not significantly more inhibitory than single strains. Probiotics appear to produce metabolites that are inhibitory towards urinary tract pathogens. Probiotics display potential to reduce the incidence of urinary tract infections via inhibition of colonisation.

Microcontroller-based peak current mode control using digital slope compensation

Microcontroller-based peak current mode control of a buck converter is investigated. The new solution uses a discrete time controller with digital slope compensation. This is implemented using only a single-chip microcontroller to achieve desirable cycle-by-cycle peak current limiting. The digital controller is implemented as a two-pole, two-zero linear difference equation designed using a continuous time model of the buck converter and a discrete time transform. Subharmonic oscillations are removed with digital slope compensation using a discrete staircase ramp. A 16 W hardware implementation directly compares analog and digital control. Frequency response measurements are taken and it is shown that the crossover frequency and expected phase margin of the digital control system match that of its analog counterpart.

The stability of a two-dimensional vorticity filament under uniform strain

The quantitative effects of uniform strain and background rotation on the stability of a strip of constant vorticity (a simple shear layer) are examined. The thickness of the strip decreases in time under the strain, so it is necessary to formulate the linear stability analysis for a time-dependent basic flow. The results show that even a strain rate γ (scaled with the vorticity of the strip) as small as 0.25 suppresses the conventional Rayleigh shear instability mechanism, in the sense that the r.m.s. wave steepness cannot amplify by more than a certain factor, and must eventually decay. For γ < 0.25 the amplification factor increases as γ decreases; however, it is only 3 when γ e 0.065. Numerical simulations confirm the predictions of linear theory at small steepness and predict a threshold value necessary for the formation of coherent vortices. The results help to explain the impression from numerous simulations of two-dimensional turbulence reported in the literature that filaments of vorticity infrequently roll up into vortices. The stabilization effect may be expected to extend to two- and three-dimensional quasi-geostrophic flows.

Analysis and compensation of I/Q imbalance in MIMO transmit-receive diversity systems

In wireless communication systems, all in-phase and quadrature-phase (I/Q) signal processing receivers face the problem of I/Q imbalance. In this paper, we investigate the effect of I/Q imbalance on the performance of multiple-input multiple-output (MIMO) maximal ratio combining (MRC) systems that perform the combining at the radio frequency (RF) level, thereby requiring only one RF chain. In order to perform the MIMO MRC, we propose a channel estimation algorithm that accounts for the I/Q imbalance. Moreover, a compensation algorithm for the I/Q imbalance in MIMO MRC systems is proposed, which first employs the least-squares (LS) rule to estimate the coefficients of the channel gain matrix, beamforming and combining weight vectors, and parameters of I/Q imbalance jointly, and then makes use of the received signal together with its conjugation to detect the transmitted signal. The performance of the MIMO MRC system under study is evaluated in terms of average symbol error probability (SEP), outage probability and ergodic capacity, which are derived considering transmission over Rayleigh fading channels. Numerical results are provided and show that the proposed compensation algorithm can efficiently mitigate the effect of I/Q imbalance.

Analysis and compensation of power amplifier nonlinearity in MIMO transmit diversity systems

The nonlinearity of high-power amplifiers (HPAs) has a crucial effect on the performance of multiple-input-multiple-output (MIMO) systems. In this paper, we investigate the performance of MIMO orthogonal space-time block coding (OSTBC) systems in the presence of nonlinear HPAs. Specifically, we propose a constellation-based compensation method for HPA nonlinearity in the case with knowledge of the HPA parameters at the transmitter and receiver, where the constellation and decision regions of the distorted transmitted signal are derived in advance. Furthermore, in the scenario without knowledge of the HPA parameters, a sequential Monte Carlo (SMC)-based compensation method for the HPA nonlinearity is proposed, which first estimates the channel-gain matrix by means of the SMC method and then uses the SMC-based algorithm to detect the desired signal. The performance of the MIMO-OSTBC system under study is evaluated in terms of average symbol error probability (SEP), total degradation (TD) and system capacity, in uncorrelated Nakagami-m fading channels. Numerical and simulation results are provided and show the effects on performance of several system parameters, such as the parameters of the HPA model, output back-off (OBO) of nonlinear HPA, numbers of transmit and receive antennas, modulation order of quadrature amplitude modulation (QAM), and number of SMC samples. In particular, it is shown that the constellation-based compensation method can efficiently mitigate the effect of HPA nonlinearity with low complexity and that the SMC-based detection scheme is efficient to compensate for HPA nonlinearity in the case without knowledge of the HPA parameters.

Analysis and compensation of I/Q imbalance in amplify-and-forward cooperative systems

In this paper, dual-hop amplify-and-forward (AF) cooperative systems in the presence of in-phase and quadrature-phase (I/Q) imbalance, which refers to the mismatch between components in I and Q branches, are investigated. First, we analyze the performance of the considered AF cooperative protocol without compensation for I/Q imbalance as the benchmark. Furthermore, a compensation algorithm for I/Q imbalance is proposed, which makes use of the received signals at the destination, from the source and relay nodes, together with their conjugations to detect the transmitted signal. The performance of the AF cooperative system under study is evaluated in terms of average symbol error probability (SEP), which is derived considering transmission over Rayleigh fading channels. Numerical results are provided and show that the proposed compensation algorithm can efficiently mitigate the effect of I/Q imbalance.

Joint compensation of multiple RF impairments in MIMO STBC systems

In this paper, we propose a compensation method for the joint effect of high-power amplifier (HPA) nonlinearity, in-phase/quadrature-phase (I/Q) imbalance and crosstalk in multiple-input multiple-output (MIMO) orthogonal space-time block coding (OSTBC) systems. The performance of the MIMO OSTBC equipped with the proposed compensation mechanism is evaluated in terms of average symbol error probability and system capacity, in Rayleigh fading channels. Numerical results are provided and show the effects on performance of several system parameters, namely, the HPA parameters, image-leakage ratio, crosstalk, numbers of antennas, and phase-shift keying modulation order.

Analysis and compensation for the joint effects of HPA nonlinearity, I/Q imbalance and crosstalk in MIMO beamforming systems

In this paper, we investigate the joint effects of high-power amplifier (HPA) nonlinearity, in-phase/quadrature-phase (I/Q) imbalance and crosstalk, on the performance of multiple-input multiple-output (MIMO) transmit beamforming (TB) systems, and propose a compensation method for the three impairments together. The performance of the MIMO TB system equipped with the proposed compensation scheme is evaluated in terms of average symbol error probability and capacity when transmissions are performed over uncorrelated Rayleigh fading channels. Numerical results are provided and show the effects on performance of several system parameters, namely, the HPA parameters, image-leakage ratio, crosstalk, numbers of antennas, length of pilot symbols and phase-shift keying modulation order.

Compensation for HPA nonlinearity and I/Q imbalance in MIMO beamforming systems

In this paper, we investigate the effects of high-power amplifier (HPA) nonlinearity and in-phase and quadrature-phase (I/Q) imbalance on the performance of multiple-input multiple-output (MIMO) transmit beamforming (TB) systems. Specifically, we propose a compensation method for HPA nonlinearity and I/Q imbalance together in MIMO TB systems. The performance of the MIMO TB system under study is evaluated in terms of the average symbol error probability (SEP) and system capacity, considering transmission over uncorrelated frequency-flat Rayleigh fading channels. Numerical results are provided and show the effects of several system parameters, such as the HPA parameters, image-leakage ratio, numbers of transmit and receive antennas, length of pilot symbols, and modulation order of phase-shift keying (PSK), on performance.