Characterization of natural product inhibitors of quorum sensing in Pseudomonas aeruginosa reveals competitive inhibition of RhlR by ortho-vanillin

Quorum sensing (QS) is a cell-cell signaling system that enables bacteria to coordinate population density-dependent changes in behavior. This chemical communication pathway is mediated by diffusible N-acyl L-homoserine lactone signals and cytoplasmic signal-responsive LuxR-type receptors in Gram-negative bacteria. As many common pathogenic bacteria use QS to regulate virulence, there is significant interest in disrupting QS as a potential therapeutic strategy. Prior studies have implicated the natural products salicylic acid, cinnamaldehyde and other related benzaldehyde derivatives as inhibitors of QS in the opportunistic pathogen Pseudomonas aeruginosa, yet we lack an understanding of the mechanisms by which these compounds function. Herein, we evaluate the activity of a set of benzaldehyde derivatives using heterologous reporters of the P. aeruginosa LasR and RhlR QS signal receptors. We find that most tested benzaldehyde derivatives can antagonize LasR or RhlR reporter activation at micromolar concentrations, although certain molecules also caused mild growth defects and nonspecific reporter antagonism. Notably, several compounds showed promising RhlR or LasR specific inhibitory activities over a range of concentrations below that causing toxicity. Ortho-Vanillin, a previously untested compound, was the most promising within this set. Competition experiments against the native ligands for LasR and RhlR revealed that ortho-vanillin can interact competitively with RhlR but not with LasR. Overall, these studies expand our understanding of benzaldehyde activities in the LasR and RhlR receptors and reveal potentially promising effects of ortho-vanillin as a small molecule QS modulator against RhlR.

An Amino Acid Substitution in Elongation Factor EF-G1A Alters the Antibiotic Susceptibility of Pseudomonas aeruginosa LasR-Null Mutants

The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum-sensing system to increase resistance to the aminoglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism that permits the emergence of lasR-null mutants under tobramycin selection. We hypothesized that some other genetic mutations that emerge in these isolates might modulate the effects of lasR-null mutations on antibiotic resistance. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. In some of these isolates, inactivating lasR further increased resistance, compared with decreasing resistance of the wild-type ancestor. These strain-dependent effects were due to a G61A nucleotide polymorphism in the fusA1 gene encoding amino acid substitution A21T in the translation elongation factor EF-G1A. The EF-G1A mutational effects required the MexXY efflux pump and the MexXY regulator ArmZ. The fusA1 mutation also modulated ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results identify a gene mutation that can reverse the direction of the antibiotic selection of lasR mutants, a phenomenon known as sign epistasis, and provide a possible explanation for the emergence of lasR-null mutants in clinical isolates. IMPORTANCE One of the most common mutations in Pseudomonas aeruginosa clinical isolates is in the quorum sensing lasR gene. In laboratory strains, lasR disruption decreases resistance to the clinical antibiotic tobramycin. To understand how lasR mutations emerge in tobramycin-treated patients, we mutated lasR in highly tobramycin-resistant laboratory strains and determined the effects on resistance. Disrupting lasR enhanced the resistance of some strains. These strains had a single amino acid substitution in the translation factor EF-G1A. The EF-G1A mutation reversed the selective effects of tobramycin on lasR mutants. These results illustrate how adaptive mutations can lead to the emergence of new traits in a population and are relevant to understanding how genetic diversity contributes to the progression of disease during chronic infections.

Tobramycin adaptation alters the antibiotic susceptibility of Pseudomonas aeruginosa quorum sensing-null mutants

The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum sensing system to increase resistance to the aminioglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism allowing the lasR-null mutants to persist under tobramycin selection. We hypothesized that the effects of inactivating lasR on tobramycin resistance might be dependent on the presence or absence of other gene mutations in that strain, a phenomenon known as epistasis. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. We show that the effects of ΔlasR on tobramycin resistance are strain dependent. The effects can be attributed to a point mutation in the gene encoding the translation elongation factor fusA1 (G61A nucleotide substitution), which confers a strong selective advantage to lasR-null PA14 under tobramycin selection. This fusA1 G61A mutation results in increased activity of the MexXY efflux pump and expression of the mexXY regulator ArmZ. The fusA1 mutation can also modulate ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results demonstrate the importance of epistatic gene interactions on antibiotic susceptibility of lasR-null mutants. These results support of the idea that gene interactions might play a significant role in the evolution of quorum sensing in P. aeruginosa.

Unusually high levels of n-6 polyunsaturated fatty acids in whale sharks and reef manta rays

Fatty acid (FA) signature analysis has been increasingly used to assess dietary preferences and trophodynamics in marine animals. We investigated FA signatures of connective tissue of the whale shark Rhincodon typus and muscle tissue of the reef manta ray Manta alfredi. We found high levels of n-6 polyunsaturated fatty acids (PUFA), dominated by arachidonic acid (20:4n-6; 12–17 % of total FA), and comparatively lower levels of the essential n-3 PUFA—eicosapentaenoic acid (20:5n-3; ~1 %) and docosahexaenoic acid (22:6n-3; 3–10 %). Whale sharks and reef manta rays are regularly observed feeding on surface aggregations of coastal crustacean zooplankton during the day, which generally have FA profiles dominated by n-3 PUFA. The high levels of n-6 PUFA in both giant elasmobranchs raise new questions about the origin of their main food source.

Biology, ecology and conservation of the Mobulidae

The Mobulidae are zooplanktivorous elasmobranchs comprising two recognized species of manta rays (Manta spp.) and nine recognized species of devil rays (Mobula spp.). They are found circumglobally in tropical, subtropical and temperate coastal waters. Although mobulids have been recorded for over 400 years, critical knowledge gaps still compromise the ability to assess the status of these species. On the basis of a review of 263 publications, a comparative synthesis of the biology and ecology of mobulids was conducted to examine their evolution, taxonomy, distribution, population trends, movements and aggregation, reproduction, growth and longevity, feeding, natural mortality and direct and indirect anthropogenic threats. There has been a marked increase in the number of published studies on mobulids since c. 1990, particularly for the genus Manta, although the genus Mobula remains poorly understood. Mobulid species have many common biological characteristics although their ecologies appear to be species-specific, and sometimes region-specific. Movement studies suggest that mobulids are highly mobile and have the potential to rapidly travel large distances. Fishing pressure is the major threat to many mobulid populations, with current levels of exploitation in target fisheries unlikely to be sustainable. Advances in the fields of population genetics, acoustic and satellite tracking, and stable-isotope and fatty-acid analyses will provide new insights into the biology and ecology of these species. Future research should focus on the uncertain taxonomy of mobulid species, the degree of overlap between their large-scale movement and human activities such as fisheries and pollution, and the need for management of inter-jurisdictional fisheries in developing nations to ensure their long-term sustainability. Closer collaboration among researchers worldwide is necessary to ensure standardized sampling and modelling methodologies to underpin global population estimates and status.

Community structure of soft sediment pool fishes in Moreton Bay, Australia

A survey of soft sediment tide pools was conducted to assess the occupation and assemblage of fishes on three different intertidal shores in Moreton Bay, Australia, between January and December 2009. Tide-pool volume ranged from 0· 30 to 29· 75 l and varied significantly between months and sites. A total of 1364 individuals representing 15 species and nine families of fishes were observed. At Dunwich, fish assemblages were dominated by the sand goby Favonigobius lentiginosus (89%) and whiting, Sillago spp. (10%). At Manly, the gobies Favonigobius exquisitus (37%), Pseudogobius sp. (31%) and the blenny Omobranchus punctatus (19%) dominated the shores while at Godwin Beach, F. lentiginosus (15%), F. exquisitus (45%) and Sillago spp. (25%) were the most abundant species. The mean ±s.e. density of fishes ranged from 0· 29 ± 0· 13 to 5· 04 ± 1· 74 fishes l(-1) and abundance of fish correlated with pool volume. Juveniles (75%) dominated assemblages suggesting that soft sediment pools may act as nurseries. The persistent and recurrent fish assemblages found in soft sediment tide pools in Moreton Bay suggest that these shores are behaving more like a tropical than a temperate climate shore, as there was no significant difference of fish abundances between seasons.

Scan quality effect on glaucoma discrimination by glaucoma imaging devices

AIM

To evaluate, within ocular imaging scans of acceptable quality as determined by manufacturers' guidelines, the effects of image quality on glaucoma discrimination capabilities.

METHODS

One hundred and four healthy and 75 glaucomatous eyes from the Advanced Imaging in Glaucoma Study (AIGS) were imaged with GDx-VCC, HRT II and StratusOCT. Quality score (QS>/=8), pixel standard deviation (SD</=50) and signal strength (SS>/=5) were used as quality parameter cut-offs, respectively. GDx nerve fibre indicator (NFI) and HRT Moorfields regression analysis (MRA) classifications and OCT mean retinal nerve fibre layer (RNFL) thickness were used as the discriminatory parameters. Logistic regression models were used to model the dichotomous clinical classification (healthy vs glaucoma) as a function of image-quality parameters and discriminatory parameters.

RESULTS

Quality parameter covariates were statistically non-significant for GDx and HRT but had an inverse effect on OCT in predicting disease (a higher SS had a lower probability of glaucoma). Age was a significant covariate for GDx and HRT, but not OCT, while ethnicity and interaction between the image quality and the institute where scans were acquired were significant covariates in the OCT models.

CONCLUSION

Scan quality within the range recommended as acceptable by the manufacturer of each imaging device does not affect the glaucoma discriminating ability of GDx or HRT but does affect Stratus OCT glaucoma discrimination.

Imaging of the retinal nerve fibre layer for glaucoma

BACKGROUND

Glaucoma is a group of diseases characterised by retinal ganglion cell dysfunction and death. Detection of glaucoma and its progression are based on identification of abnormalities or changes in the optic nerve head (ONH) or the retinal nerve fibre layer (RNFL), either functional or structural. This review will focus on the identification of structural abnormalities in the RNFL associated with glaucoma.

DISCUSSION

A variety of new techniques have been created and developed to move beyond photography, which generally requires subjective interpretation, to quantitative retinal imaging to measure RNFL loss. Scanning laser polarimetry uses polarised light to measure the RNFL birefringence to estimate tissue thickness. Optical coherence tomography (OCT) uses low-coherence light to create high-resolution tomographic images of the retina from backscattered light in order to measure the tissue thickness of the retinal layers and intraretinal structures. Segmentation algorithms are used to measure the thickness of the retinal nerve fibre layer directly from the OCT images. In addition to these clinically available technologies, new techniques are in the research stages. Polarisation-sensitive OCT has been developed that combines the strengths of scanning laser polarimetry with those of OCT. Ultra-fast techniques for OCT have been created for research devices. The continued utilisation of imaging devices into the clinic is refining glaucoma assessment. In the past 20 years glaucoma has gone from a disease diagnosed and followed using highly subjective techniques to one measured quantitatively and increasingly objectively.

Heidelberg Retina Tomograph 3 machine learning classifiers for glaucoma detection

AIMS

To assess performance of classifiers trained on Heidelberg Retina Tomograph 3 (HRT3) parameters for discriminating between healthy and glaucomatous eyes.

METHODS

Classifiers were trained using HRT3 parameters from 60 healthy subjects and 140 glaucomatous subjects. The classifiers were trained on all 95 variables and smaller sets created with backward elimination. Seven types of classifiers, including Support Vector Machines with radial basis (SVM-radial), and Recursive Partitioning and Regression Trees (RPART), were trained on the parameters. The area under the ROC curve (AUC) was calculated for classifiers, individual parameters and HRT3 glaucoma probability scores (GPS). Classifier AUCs and leave-one-out accuracy were compared with the highest individual parameter and GPS AUCs and accuracies.

RESULTS

The highest AUC and accuracy for an individual parameter were 0.848 and 0.79, for vertical cup/disc ratio (vC/D). For GPS, global GPS performed best with AUC 0.829 and accuracy 0.78. SVM-radial with all parameters showed significant improvement over global GPS and vC/D with AUC 0.916 and accuracy 0.85. RPART with all parameters provided significant improvement over global GPS with AUC 0.899 and significant improvement over global GPS and vC/D with accuracy 0.875.

CONCLUSIONS

Machine learning classifiers of HRT3 data provide significant enhancement over current methods for detection of glaucoma.

Sources of longitudinal variability in optical coherence tomography nerve-fibre layer measurements

AIMS

The purpose of this study was to compare the day-to-day reproducibility of optical coherence tomography (OCT; StratusOCT, Carl Zeiss Meditec, Dublin, CA) measurements of retinal nerve-fibre layer (RNFL) measurements at time points 1 year apart.

METHODS

One eye in each of 11 healthy subjects was examined using the StratusOCT fast RNFL scan protocol. Three fast RNFL scans with signal strength > or =7 were obtained on each of 3 days within a month. This protocol was repeated after 12 months. A linear mixed effects model fitted to the nested data was used to compute the variance components.

RESULTS

The square root of the variance component that was attributed to the differences between subjects was 7.17 microm in 2005 and 7.28 microm in 2006. The square roots of the variance component due to differences between days within a single subject were 1.95 microm and 1.50 microm, respectively, and for within day within a single subject were 2.51 microm and 2.55 microm, respectively. There were no statistically significant differences for any variance component between the two testing occasions.

CONCLUSIONS

Measurement error variance remains similar from year to year. Day and scan variance component values obtained in a cohort study may be safely applied for prediction of long-term reproducibility.

Pharmacy database for tracking drug costs and utilization

A pharmacy database for tracking drug costs and physician prescribing trends is described. Accuracy problems plagued data systems used to make drug-use-policy decisions at a tertiary care teaching hospital because of structural deficiencies within the systems and their nonclinical orientation. To resolve these problems, a programmer analyst, a clinical supervisor, and a clinical pharmacist developed a hierarchical database of drug costs. The database was designed to be valid for tracking drug costs according to patterns of clinical use. Internal controls were created that could identify and correct cost-tabulation errors arising within the ordering, order-entry, and billing processes. The database was able to tabulate drug costs according to the clinical service on which the patient was being treated at the time so that reports could compare aggregate prescribing trends from one time period to another for the same service. Similarly, the database could track and report drug use by disease or financial classification. Flagging elements were introduced to the database for cancer chemotherapy and antimicrobial drug products to enable reporting by these categories and by therapeutic subcategories within the antimicrobial category. Routine monthly reports were distributed to end users. Development of a database for tracking drug costs and utilization allowed a teaching hospital to derive the cost of medications from billing-charge information and to report data to health care professionals on the basis of important factors like clinical services.

Drug therapy during cardiac arrest in two hospitals

The results of a study evaluating the appropriateness of drug and defibrillation therapy given during cardiac arrest at two hospitals are reported. A retrospective study was performed to evaluate and compare the appropriateness of therapy given during adult cardiac arrest at a large teaching hospital (hospital 1) and at a smaller nonteaching hospital (hospital 2) as measured by conformance to advanced cardiac life support (ACLS) guidelines and by less stringent alternative criteria based on published data and clinical judgment. Patients included in the study were older than 18 years and had experienced at least one of five types of cardiac arrest: ventricular fibrillation, asystole, ventricular tachycardia, electromechanical dissociation, or bradycardia. The type of drug administered, the drug dosage, and the timing of dosages were evaluated, as were the timing of defibrillation attempts and the energy used for such attempts. Treatment decisions were considered inappropriate if they did not conform to standard (ACLS) or alternative criteria. In hospital 1, there were 1137 assessable decisions recorded for 75 cardiac arrests; of these, 205 (18%) were inappropriate according to standard criteria, and 96 (8.4%) were inappropriate according to alternative criteria. In hospital 2, there were 827 assessable decisions recorded for 57 cardiac arrests; of these, 173 (21%) were inappropriate according to standard criteria, and 98 (11.2%) were inappropriate according to alternative criteria. Inappropriate therapy during cardiac arrest occurred with a similar frequency in a large teaching hospital and in a smaller, nonteaching hospital. The number of inappropriate treatments was smaller when more liberal standards of therapy were used.

The use of norfloxacin in a university hospital

Because of increasing norfloxacin use and the development of resistant organisms, an evaluation was undertaken in a University Hospital to assess the appropriateness of norfloxacin for the treatment of urinary tract infections and to calculate the potential cost savings associated with more cost-effective antibiotic therapy. Medical records of 64 patients receiving norfloxacin for a 31-day period were concurrently reviewed. Of these, 58 patients were treated for urinary tract infections and four patients received urinary tract infection prophylaxis. Fourteen patients were prescribed solely empiric therapy whereas an additional 44 patients received definitive treatment confirmed by culture results. Based on the predetermined criteria, norfloxacin use for the definitive treatment of urinary tract infections was deemed to be appropriate in 34 of the 44 patients. Three additional courses of therapy were also judged to be appropriate due to documented signs and symptoms associated with urinary tract infections, despite cultures with less than 10(5) colony forming units per mL urine. Reasons for inappropriate use in the remaining seven patients included isolation of fewer bacteria than required by the criteria in asymptomatic patients (3 cases), isolation of organisms not sensitive to norfloxacin (1 case) and lack of dosage adjustment for renal insufficiency (3 cases). Nineteen of 32 evaluable inpatients (59%) received norfloxacin when a less expensive, equally effective agent was available. Although savings from more cost-effective therapy of urinary tract infections are minimal, due to the potential emergence of resistant organisms, norfloxacin should be reserved for infections not amenable to treatment with other oral antibiotics.