Identification of Risk Loci for Parkinson Disease in Asians and Comparison of Risk Between Asians and Europeans: A Genome-Wide Association Study

Importance

Large-scale genome-wide association studies in the European population have identified 90 risk variants associated with Parkinson disease (PD); however, there are limited studies in the largest population worldwide (ie, Asian).

Objectives

To identify novel genome-wide significant loci for PD in Asian individuals and to compare genetic risk between Asian and European cohorts.

Design Setting, and Participants

Genome-wide association data generated from PD cases and controls in an Asian population (ie, Singapore/Malaysia, Hong Kong, Taiwan, mainland China, and South Korea) were collected from January 1, 2016, to December 31, 2018, as part of an ongoing study. Results were combined with inverse variance meta-analysis, and replication of top loci in European and Japanese samples was performed. Discovery samples of 31 575 individuals passing quality control of 35 994 recruited were used, with a greater than 90% participation rate. A replication cohort of 1 926 361 European-ancestry and 3509 Japanese samples was analyzed. Parkinson disease was diagnosed using UK Parkinson's Disease Society Brain Bank Criteria.

Main Outcomes and Measures

Genotypes of common variants, association with disease status, and polygenic risk scores.

Results

Of 31 575 samples identified, 6724 PD cases (mean [SD] age, 64.3 [10] years; age at onset, 58.8 [10.6] years; 3472 [53.2%] men) and 24 851 controls (age, 59.4 [11.4] years; 11 030 [45.0%] men) were analyzed in the discovery study. Eleven genome-wide significant loci were identified; 2 of these loci were novel (SV2C and WBSCR17) and 9 were previously found in Europeans. Replication in European-ancestry and Japanese samples showed robust association for SV2C (rs246814; odds ratio, 1.16; 95% CI, 1.11-1.21; P = 1.17 × 10-10 in meta-analysis of discovery and replication samples) but showed potential genetic heterogeneity at WBSCR17 (rs9638616; I2=67.1%; P = 3.40 × 10-3 for hetereogeneity). Polygenic risk score models including variants at these 11 loci were associated with a significant improvement in area under the curve over the model based on 78 European loci alone (63.1% vs 60.2%; P = 6.81 × 10-12).

Conclusions and Relevance

This study identified 2 apparently novel gene loci and found 9 previously identified European loci to be associated with PD in this large, meta-genome-wide association study in a worldwide population of Asian individuals and reports similarities and differences in genetic risk factors between Asian and European individuals in the risk for PD. These findings may lead to improved stratification of Asian patients and controls based on polygenic risk scores. Our findings have potential academic and clinical importance for risk stratification and precision medicine in Asia.

Abstract 485: On the Relative Effectiveness of Machine Learning and Statistical Methods in Predicting Abdominal Aortic Aneurysm Rupture in the Asian Population

Background: Abdominal Aortic Aneurysms (AAA) have a high risk of mortality if they rupture, making it one of the leading causes of death in elderly men. Hence, a better prediction method is necessary to identify high rupture risk patients.

Methods: Retrospective data (clinical and AAA geometric parameters) were collected of 114 Asian AAA patients from an IRB approved database. We applied a novel machine learning algorithm (MLA) to predict AAA rupture by generating a decision tree of rupture risk predictors. For comparative analysis, a binary logistic regression (backward stepwise Wald) was also performed. The rupture status was the dependent variable for both methods; each method provided the highest weighted risk factors and effectiveness of classification as assessed by Receiver Operating Characteristic (ROC) curves.

Results: For the MLA, the most significant risk factors were DAAA (maximum diameter) (> 57 mm), presence of hypertension, D4 (diameter at the iliac bifurcation) (> 23.7 mm), age (> 79 years), and D3 (right common iliac artery diameter) (> 14 mm), as seen in Fig. 1a. Similarly, the backward stepwise logistic regression analysis showed a strong association for rupture with DAAA (O.R. 2.635), L1 (distance between the lowest renal artery and the iliac bifurcation) (O.R. 1.658), D3 (O.R. 1.876), NL (AAA neck length) (O.R. 0.294), and age (O.R. 0.681). The MLA exhibited a lower classification accuracy (80.7% vs. 99.2%) and area under the curve (ROC analysis) (56.3% vs. 98.2%) when compared to the regression analysis, as seen in Fig. 1b.

Conclusions: This is the first known report of predictive rupture risk in the Asian AAA patient population using MLA and statistical methods. Although the MLA did not provide improved classification accuracy compared to a standard statistical method, the risk factors obtained from both methods were similar. Future studies will aim at improving the prediction ability of MLA in a racially diverse AAA patient population.

Abstract WMP53: Vitamin D Levels Are Lower In Acute Ischemic Stroke Patients Compared To Matched Controls

Introduction: Vitamin D deficiency is increasingly recognized as a global pandemic. In longitudinal healthy population studies, vitamin D deficiency is associated with increased incidence of ischemic stroke. We compared serum 25-OH vitamin D levels between Asian ischemic stroke patients within 1 week of stroke onset with age and gender matched healthy individuals.

Methods: We prospectively recruited 133 consecutive Asian acute ischemic stroke patients admitted to the Singapore General Hospital. Blood samples were collected within seven days of stroke onset. Stroke patients were matched for age and gender to individuals with no history of stroke from a database of healthy Asian controls. Serum 25-OH vitamin D was measured using Roche competitive electrochemiluminescence immunoassay for both stroke patients and healthy controls in the same laboratory. Vitamin D deficiency was defined as serum 25-OH vitamin D <20 μg/L and insufficiency as 20-40 μg/L. Matched statistical analyses were performed using Wilcoxon and McNemar tests.

Results: Among the 133 matched pairs of ischemic stroke patients and healthy controls, median age was 60 years and 75% are males. Median serum 25-OH vitamin D level was lower among stroke patients (23.2 IQR 16.65-29.60 μg/L) compared to healthy controls (28.9 IQR 21.75-35.50 μg/L) (p<0.0001). Stroke patients had a higher prevalence of vitamin D deficiency (39%) compared to healthy controls (20%) (p<0.0001). A high proportion of stroke patients had insufficient vitamin D compared to healthy controls (95% vs 84%, p=0.007). Corrected serum calcium was lower in stroke patients (median 2.26 mmol/L IQR 2.21-2.35) than controls (median 2.34 mmol/L IQR 2.28- 2.41) (p<0.0001). There was no difference in serum phosphate (p=0.266) and parathyroid hormone levels (p=0.807).

Conclusion: This cross-sectional study of 25-OH vitamin D levels in Asian patients within 1 week of ischemic stroke onset contributes to the growing evidence that vitamin D insufficiency/ deficiency is a stroke risk factor. Vitamin D measurement within 1 week of stroke onset likely reflects pre-stroke levels and is not influenced by post-stroke effects. Our findings provide impetus for future studies to investigate if vitamin D supplementation reduces stroke incidence.

Effect of blood flow, tumour and cold stress in a female breast: a novel time-accurate computer simulation

Breast cancer is a dreadful disease among women and early detection helps in achieving a cure. The mammogram is presently the standard tool for detecting breast abnormality, but its sensitivity is lower for women with dense breasts. It has been found that women with an abnormal thermogram are at a higher risk and have a poorer prognosis. However, performing and interpreting thermograms requires meticulous training. Computer simulations can be an additional tool to help the clinician in the interpretation. In this paper, a novel and flexible finite element model of a female breast is developed. Both steady state and time-dependent solutions are obtained. Steady state solutions globally match experimental thermographic results with the proper choice of blood perfusion source terms, tissue thickness and geometric scaling factor. Although the simulations may not be useful in providing a unique solution (i.e. exact size and location of the tumour owing to the complex physiological relationship between the tumour and the breast surface temperature), it would nevertheless help in the 'analysis by elimination'. An example of this type of analysis is also presented.

Statistical analysis of healthy and malignant breast thermography

Analysis of thermograms has often been subjective and has resulted in inconsistency in the diagnosis of breast diseases by thermography. The aim of this paper is to study the problem of subjective interpretation of breast thermograms and hence using thermography as an adjunct tool for breast cancer diagnosis. It ws proposed that the thermograms should be taken within the recommended screening period, classified and analysed in conjunction with an artificial neural network (ANN). Qualitative interpretation of thermal images can be carried out using an active contours algorithm. The 256 x 200 pixel image can be segmented as one of the inputs to the ANN. To achieve quantitative analysis of the breast thermograms, firstly the inputs of the ANN should be determined, so that the thermograms could be successfuly classified and based on the suggested inputs.

Numerical uncertainty and perfusion induced instability in bioheat equation: its importance in thermographic interpretation

The use of engineering in biomedical sciences has opened new facets in research. The present paper deals with problems arising from numerical simulation, in order to develop an expert system for the diagnosis of breast cancer using thermography. A female breast is modelled in three dimensions and the surface temperature pattern is obtained by solving the bioheat equation. This solution will be used in conjunction with a database of thermograms to develop an intelligent diagnostic tool. The focus of the present paper is to build and check the confidence level of the numerical scheme before proceeding to model the actual problem. The parametric study is done along with a check for mesh insensitivity and wiggle free isotherm contours. This process yielded a benchmark nodal distance, with which the 3D model is generated and isotherm pattern analysed. It can be seen that this enhances the accuracy of the surface temperature distribution. The use of this is tested in a close-to-actual numerical breast model and the results compared with the thermographic results. The outcome is very encouraging. Finally, a typical clinical protocol in conjunction with the use of numerical prediction for breast thermographic interpretation is outlined.

Unsteady viscous flow model on moving the domain through a stenotic artery

An unsteady Navier-Stokes (N-S) solver based on the method of operator splitting and artificial compressibility has been studied for the moving boundary problem to simulate blood flow through a compliant vessel. Galerkin finite element analysis is used to discretize the governing equations. The model has been applied to a time-varying computational domain (two-dimensional tube) as a test case for validation. Consideration has been given to retaining the space conservation property. The same code is then applied to a hypothetical critical high-pressure gradient over a short length of blood vessel based on the spring and dashpot model. The governing equation for the blood vessel is based on two-dimensional dynamic thin-shell theory that takes into account the curvature of the stenotic portion of the vessel. Progressing the solution towards steady state is considered, as the main objective is to show the viability of the current technique for fluid/structure interactions. Preliminary results of the wall velocity and displacement based on steady state prediction agree well with data in the literature. Results, such as the streamlines, wall pressures and wall shear stress depict the possible progression of arterial disease.

An improved three-dimensional direct numerical modelling and thermal analysis of a female breast with tumour

It is well known that malignant tumour tissue generally has higher metabolic and blood perfusion rates than most normal tissues. The authors aim to show that the tissue temperature profile within the breast and the surface temperature profile can be quantified to develop an expert system or diagnostic tool for breast cancer detection. The surface temperature and tissue temperature profiles are analysed for a three-dimensional numerical model of a normal breast and a breast with a tumour. Tumours of different sizes are placed at various locations. In the model, the tissue temperature profile is distorted at the tumour location and was found to compare well with in vivo tests. It was also found that as the tumour was moved to deeper locations its effect on surface temperature was lower. It was observed that small tumours in deeper regions do not have a significant isolated impact on the surface. The numerical results could also capture a shift in the position of the tumour. For tumours greater than 10 mm in the superficial regions and of significant size in deeper regions, it could be seen that the surface temperature distribution of the breast is directly related to the position and size of the tumour embedded in it. The feasibility of providing a diagnostic tool in conjunction with numerical modelling and high-resolution thermograms is also discussed.

Numerical computation as a tool to aid thermographic interpretation

Thermography is an non-invasive and a painless tool for the detection of breast cancer. However, performing and interpreting thermograms requires meticulous training. It was found that women with an abnormal thermogram are at a higher risk and have a poorer prognosis. One of the main drawbacks of the thermogram is the high incidence of false-positive results. The authors believe that the fault lies in misinterpretation of the thermogram, rather than the thermogram itself. The paper aims to show that computer simulations could be an adjunct tool to help the clinician in the interpretation. This would greatly reduce the false-positive diagnosis.

Parametric optimization for tumour identification: bioheat equation using ANOVA and the Taguchi method

Breast cancer is the number one killer disease among women. It is known that early detection of a tumour ensures better prognosis and higher survival rate. In this paper an intelligent, inexpensive and non-invasive diagnostic tool is developed for aiding breast cancer detection objectively. This tool is based on thermographic scanning of the breast surface in conjunction with numerical simulation of the breast using the bioheat equation. The medical applications of thermographic scanning make use of the skin temperature as an indication of an underlying pathological process. The thermal pattern over a breast tumour reflects the vascular reaction to the abnormality. Hence an abnormal temperature pattern may be an indicator of an underlying tumour. Seven important parameters are identified and analysis of variance (ANOVA) is performed using a 2n design (n = number of parameters, 7). The effect and importance of the various parameters are analysed. Based on the above 2(7) design, the Taguchi method is used to optimize the parameters in order to ensure the signal from the tumour maximized compared with the noise from the other factors. The model predicts that the ideal setting for capturing the signal from the tumour is when the patient is at basal metabolic activity with a correspondingly lower subcutaneous perfusion in a low temperature environment.

Computerized breast thermography: study of image segmentation and temperature cyclic variations

Breast cancer is a common and dreadful disease in women. The surface temperature and the vascularization pattern of the breast could indicate breast diseases. Establishing the surface isotherm pattern of the breast and the normal range of cyclic variations of temperature distribution can assist in identifying the abnormal infrared images of diseased breasts. This paper investigates the cyclic variation of temperature and vascularization of the normal breast thermograms under a controlled environment. More than 50 Asian women, were examined and some of them have been examined continuously for two month. All together, not less than 800 thermograms were obtained. Before these thermograms can be analysed objectively via a computer algorithm, they must be digitized and segmented. The authors present a method to segment thermograms and extract the useful region from the background. After the image processing, these thermograms can be analysed and then the best time to perform an examination can be chosen. All these results are important for establishing a data bank of normal breast thermography, to choose the best time for an examination and as a systematic methodology for evaluating and analysing the abnormal breast thermography in the future.

Comparison of two dosages of recombinant human follicle-stimulating hormone in Chinese women undergoing controlled ovarian stimulation: prospective randomised double-blind study

OBJECTIVE

To compare two dosages of recombinant human follicle-stimulating hormone for controlled ovarian stimulation.

DESIGN

Prospective, randomised double-blind study.

SETTING

Tertiary assisted reproduction unit, Hong Kong.

PARTICIPANTS

Forty subfertile Chinese women aged 24 to 38 years undergoing in vitro fertilisation. Entry criteria included good physical and mental health, and a body mass index between 18 and 29 kg/m2. Exclusion criteria were subfertility caused by an endocrine abnormality, polycystic ovarian syndrome, or absent ovarian function; previous assisted reproduction treatment in which fewer than three oocytes were retrieved; prior hospitalisation due to severe ovarian hyperstimulation syndrome; chronic cardiovascular, hepatic, renal, or pulmonary disease; alcohol or drug abuse; and the administration of investigational drugs within the previous 3 months.

INTERVENTION

Injection of recombinant follicle-stimulating hormone, 100 IU/d or 200 IU/d.

MAIN OUTCOME MEASURES

The number of oocytes, total dose of drug used, and pregnancy rates.

RESULTS

Compared with the 20 women receiving 200 IU/d, the 20 who received 100 IU/d had a significantly lower median number of oocytes retrieved and median total dose of drug used (7.5 versus 15.0 [P<0.001] and 1200 IU versus 2000 IU [P<0.001], respectively). The pregnancy rates in the fresh cycles were similar (20%) in both groups, but the cumulative pregnancy rates in the 100 IU/d and 200 IU/d groups were 20.0% and 45.0% per stimulated cycle, respectively. The incidence of ovarian hyperstimulation syndrome in the 100 IU/d and 200 IU/d groups was 5.0% and 20.0%, respectively.

CONCLUSIONS

Use of 100 IU/d of recombinant follicle-stimulating hormone requires a lower total dose but results in the harvest of half the number of oocytes compared with when a dosage of 200 IU/d is used.

Mesh-independent prediction of skin burns injury

This paper presents a robust finite element model (FEM) with multiple-layers of varying properties for investigation of burn effects on human skin during a burning process resulting from exposure of skin surface to a contact heat source and a hot moving fluid. Henriques' theory of skin burns is used in conjunction with two-dimensional Pennes bioheat transfer equation for determining the spatial and temporal extent of burn injury. The model developed is a two-dimensional axisymmetric model in cylindrical coordinates. The various tissue layers account for changing thermal properties with respect to skin anatomy. A finite element scheme that uses the backward Euler method is used to solve the problem. The injury processes of skin subsequent to the removal of the heat source (post-burn) will also be inspected. The mesh employed in this model consists of a high density of nodes and elements in which a thorough mesh convergence study was done. A comparison of the transient temperature field computed by this model against Diller's results using the FE technique with a comparatively coarse mesh of 125 elements and experimental data by Orgill et al. has been done in the present study. It concluded that improved accurate solutions have been performed using the robust model developed due to the achievement of a mesh-independent solution.

Numerical study of unsteady stenosis flow: parametric evaluation of power-law model

Currently the best indicator for surgical treatment of arterio-sclerosis is the degree of stenosis. Although X-ray angiography is currently the standard, cost and morbidity are distinct disadvantages. By modelling stenosis and studying its biofluid mechanics, one can apply its results in the field of arterial disease research. This formed the motivation for this work. A non-Newtonian (power law) incompressible Navier-Stokes (N-S) solver was developed using the method of operator splitting and artificial compressibility. The vehicle used is the computational fluid dynamics (CFD) numerical library FASTFLO. The power-law model developed is then used to do a parametric study of the effect of 'n' on blood flow mechanics where 'n' is the power index that determines the haematocrit of blood. A pulsatile pressure wave over a cardiac cycle of a second was used to simulate transient flow over a hypothetical two-dimensional stenotic geometry. By comparing the different velocity pressure, wall shear stress and viscosity profiles, it has been found when 'n' increases, the vortex formation and peak wall shear stress decreases (magnitudes of < 1.5 Pa). Since the formation of vortices and low oscillatory wall shear stress on the stenotic wall is detrimental to the well-being of the arterial tract, it can therefore be inferred that there might be a relationship between the diseased state of blood (power law) and early genesis of atherosclerosis. However, the conclusion of this paper marks the advent of new research directions in this field of study.

Unsteady stenosis flow prediction: a comparative study of non-Newtonian models with operator splitting scheme

This paper presents a comparative study of non-Newtonian and Newtonian models of blood. A non-Newtonian incompressible 2-D Navier-Stokes (N-S) solver has been developed using Fasttalk language within the Fastflo environment. It is based on the method of operator splitting with artificial compressibility technique. The Power law and Casson models have been used as the constitutive equations for blood with a hematocrit of approximately 45%. These two non-Newtonian models and the Newtonian model are used to simulate unsteady flow through a hypothetical stenotic geometry over an aperiodic time interval of 1 s. Through comparison of the results of the three models, it was found that the wall shear stress (WSS) distribution over the time interval was comparable for both non-Newtonian models. The peak WSS for the Newtonian model had the lowest value. The peak wall shear stress gradient (WSSG) for the Power law was the highest, followed by the Casson and Newtonian models. Flow characteristics such as higher pressure drop across the stenosis, location and movement of vortex were similar in all three models. Non-Newtonian effects were most significant in the vicinity of the stenosis.

Staphylococcus aureus genetic loci impacting growth and survival in multiple infection environments

The Gram-positive bacterium Staphylococcus aureus infects diverse tissues and causes a wide spectrum of diseases, suggesting that it possesses a repertoire of distinct molecular mechanisms promoting bacterial survival in disparate in vivo environments. Signature-tag transposon mutagenesis screening of a 1520-member library identified numerous S. aureus genetic loci affecting growth and survival in four complementary animal infection models including mouse abscess, bacteraemia and wound and rabbit endocarditis. Of a total of 237 in vivo attenuated mutants identified by the murine models, less than 10% showed attenuation in all three models, emphasizing the advantage of screening in diverse disease environments. The largest gene class identified by these analyses encoded peptide and amino acid transporters, some of which were important for S. aureus survival in all animal infection models tested. The identification of staphylococcal loci affecting growth, persistence and virulence in multiple tissue environments provides insight into the complexities of human infection and on the molecular mechanisms that could be targeted by new antibacterial therapies.

Preferential cytotoxicity of cells transduced with cytosine deaminase compared to bystander cells after treatment with 5-flucytosine

In vitro experiments from our laboratory and others have suggested that herpes simplex virus thymidine kinase (HSV-TK)/ganciclovir (GCV) gene therapy depends on gap junctional intercellular communication (GJIC) to produce a strong bystander effect. Furthermore, we have shown that cells transduced with HSV-TK can be protected from GCV-mediated toxicity by GJIC with bystander cells. We wished to determine whether GJIC affected either the bystander or protective effect of the cytosine deaminase (CD)/5-flucytosine (5-FC) gene therapy approach, in which CD converts 5-FC to 5-fluorouracil (5-FU). To test this, we designed a coculture system using communication-competent WB rat hepatocytes and a noncommunicating subclone (aB1), which were transduced with CD and with antibiotic resistance genes so that we could independently determine the survival of the CD-containing or bystander cells. We found that, compared to the HSV-TK/GCV strategy, bystander killing resulting from treatment with CD/5-FC does not depend on GJIC. However, our most striking finding was that both communication-competent and -incompetent CD-transduced cells were preferentially killed, by a factor of up to 500, compared to bystander cells. The lesser dependence of the CD/5-FC system on GJIC, combined with the finding that most cancer cells lack the capacity for GJIC, suggest that the CD/5-FC system may be superior to the HSV-TK/GCV approach for gene therapy. However, the premature death of the CD-transduced 5-FU "factory" suggests that other strategies may be necessary to produce a sufficient quantity of 5-FU for a duration long enough to produce permanent tumor regression.

Identification and characterization of the PutP proline permease that contributes to in vivo survival of Staphylococcus aureus in animal models

Staphylococcus aureus is an important pathogen of humans and other animals, causing bacteremia, abscesses, endocarditis, and other infectious syndromes. A signature-tagged mutagenesis (STM) system was adapted for use in studying the genes required for in vivo survival of S. aureus. An STM library was ultimately created in S. aureus RN6390, with Tn917 being used to create the transposon mutations. Pools of S. aureus RN6390 mutants were screened in mouse abscess, bacteremia, and wound infection models for growth attenuation after in vivo passage. One of the mutants that was identified displayed marked attenuation following large-pool screening in all three animal models, which was confirmed in bacteremia and endocarditis models of infection with a smaller pool of mutants. Sequence analysis of the entire open reading frame showed a 99% identity to the high-affinity proline permease (putP) gene characterized in another strain of S. aureus. In wound and murine abscess infection models, the putP mutant was approximately 10-fold more attenuated than was wild-type strain RN6390. Another S. aureus strain transduced with the putP mutation also displayed an attenuated phenotype after passage in the wound model. A [3H]proline uptake assay showed that less proline was specifically transported into the putP mutant than into strain RN6390. The reduced viability of the bacteria possessing the mutation in the S. aureus high-affinity proline permease suggests that proline scavenging by the bacteria is important for in vivo growth and proliferation and that analogs of proline may serve as potential antistaphylococcal therapeutic agents.

Increased expression of fibronectin-binding proteins by fluoroquinolone-resistant Staphylococcus aureus exposed to subinhibitory levels of ciprofloxacin

Bacterial adhesion, which plays an important role in Staphylococcus aureus colonization and infection, may be altered by the presence of antibiotics or/and antibiotic resistance determinants. This study evaluated the effect of fluoroquinolone resistance determinants on S. aureus adhesion to solid-phase fibronectin, which is specifically mediated by two surface-located fibronectin-binding proteins. Five isogenic mutants, derived from strain NCTC 8325 and expressing various levels of quinolone resistance, were tested in an in vitro bacterial adhesion assay with polymethylmethacrylate coverslips coated with increasing amounts of fibronectin. These strains contained single or combined mutations in the three major loci contributing to fluoroquinolone resistance, namely, grlA, gyrA, and flqB, which code for altered topoisomerase IV, DNA gyrase, and increased norA-mediated efflux of fluoroquinolones, respectively. Adhesion characteristics of the different quinolone-resistant mutants grown in the absence of fluoroquinolone showed only minor differences from those of parental strains. However, more important changes in adhesion were exhibited by mutants highly resistant to quinolones following their exponential growth in the presence of one-quarter MIC of ciprofloxacin. Increased bacterial adhesion of the highly quinolone-resistant mutants, which contained combined mutations in grlA and gyrA, was associated with and explained by the overexpression of their fibronectin-binding proteins as assessed by Western ligand affinity blotting. These findings contradict the notion that subinhibitory concentrations of antibiotics generally decrease the expression of virulence factors by S. aureus. Perhaps the increased adhesion of S. aureus strains highly resistant to fluoroquinolones contributes in part to that emergence in clinical settings.

Quinolone resistance locus nfxD of Escherichia coli is a mutant allele of the parE gene encoding a subunit of topoisomerase IV

The locus nfxD, which contributes to high-level quinolone resistance in Escherichia coli KF111b (gyrAr nfxB nfxD), is only expressed in the presence of a gyrA mutation, and maps to the region of the parC and parE genes, was outcrossed into strain KF130, creating strain DH161 (gyrAr nfxD). DNA sequence analysis of DH161 revealed no changes in the topoisomerase IV parC quinolone resistance-determining region but did identify a single T-to-A mutation in parE at codon 445, leading to a change from Leu to His. Full-length cloned parE+ partially complemented the resistance phenotype in KF111b and DH161, but did not complement the resistance phenotype in strain KF130 (gyrAr). No complementation was seen with cloned, truncated parE+. To confirm these findings, gyrAr was first outcrossed from KF130 into E. coli W3110parE10 [parE temperature sensitive(Ts)] and KL16. The transduced strains KL16 and W3110parE10 were subsequently transformed with plasmids containing cloned parE from DH161 or KL16. Cloned parE from DH161 increased norfloxacin resistance in the parE(Ts) background twofold at 30 degrees C and fourfold at 42 degrees C compared to those for cloned parE from KL16. The same experiment with a non-Ts background revealed a twofold increase in the norfloxacin MIC at both 30 and 42 degrees C. These data identify the nfxD conditional resistance locus as a mutant allele of parE. This report is the first of a quinolone-resistant parE mutant and confirms the role of topoisomerase IV as a secondary target of norfloxacin in E. coli.

Quinolone resistance mutations in topoisomerase IV: relationship to the flqA locus and genetic evidence that topoisomerase IV is the primary target and DNA gyrase is the secondary target of fluoroquinolones in Staphylococcus aureus

Mutations in the flqA (formerly ofx/cfx) resistance locus of Staphylococcus aureus were previously shown to be common after first-step selections for resistance to ciprofloxacin and ofloxacin and to map on the S. aureus chromosome distinctly from gyrA, gyrB, and norA.grlA and grlB, the genes for the topoisomerase IV of S. aureus, were identified from a genomic lambda library on a common KpnI fragment, and grlB hybridized specifically with the chromosomal SmaI A fragment, which contains the flqA locus. Amplification of grlA sequences (codons 1 to 251) by PCRs from nine independent single-step flqA mutants, one multistep mutant, and the parent strain identified mutations encoding a change from Ser to Phe at position 80 in four mutants, a novel change from Ala to either Glu or Pro at position 116 in three mutants, and no change in three mutants. In the multistep mutant, another resistance locus, flqC, was mapped by transformation to the chromosomal SmaI G fragment by linkage to omega(ch::Tn551)1051 (58%) and nov (97.9%), which encodes resistance to novobiocin. This fragment contains the gyrA gene, and flqC mutants had a mutation in gyrA encoding a change from Ser to Leu at position 84, a change previously found in resistant clinical isolates. In genetic outcrosses, the flqC (gyrA) mutation expressed resistance only in flqA mutants, including those with both types of grla mutations. The silent mutant allele of gyrA was present in a flqA background and expressed resistance only upon introduction of a grlA mutation. At fourfold the MIC of ciprofloxacin, the bactericidal activity of ciprofloxacin was reduced in a grlA mutant and was abolished in gyrA grlA double mutants. These findings provide direct genetic evidence that topoisomerase IV is the primary target of current fluoroquinolones in S. aureus and that this effect may result from the greater sensitivity of topoisomerase IV relative to that of DNA gyrase to these agents. Furthermore, resistance from an altered DNA gyrase requires resistant topoisomerase IV for its expression.

Quinolone resistance mediated by norA: physiologic characterization and relationship to flqB, a quinolone resistance locus on the Staphylococcus aureus chromosome

We identified a quinolone resistance locus, flqB, linked to transposon insertion omega 1108 and fus on the SmaI D fragment of the Staphylococcus aureus NCTC 8325 chromosome, the same fragment that contains the norA gene. S. aureus norA cloned from flqB and flqB+ strains in Escherichia coli differed only in a single nucleotide in the putative promoter region. There was no detectable change in the number of copies of norA on the chromosomes of flqB strains, but they had increased levels of norA transcripts. Cloned norA produced resistance to norfloxacin and other hydrophilic quinolones and reduced norfloxacin accumulation in intact cells that was energy dependent, suggesting active drug efflux as the mechanism of resistance. Drug efflux was studied by measurement of norfloxacin uptake into everted inner membrane vesicles prepared from norA-containing E. coli cells. Vesicles exhibited norfloxacin uptake after the addition of lactate or NADH, and this uptake was abolished by carbonyl cyanide m-chlorophenylhydrazone and nigericin but not valinomycin, indicating that it was linked to the pH gradient across the cell membrane. Norfloxacin uptake into vesicles was also saturable, with an apparent Km of 6 microM, a concentration between those that inhibit the growth of flqB and flqB+ S. aureus cells, indicating that drug uptake is mediated by a carrier with a high apparent affinity for norfloxacin. Ciprofloxacin and ofloxacin competitively inhibited norfloxacin uptake into vesicles. Reserpine, which inhibits the multidrug efflux mediated by the bmr gene of bacillus subtilis, which is similar to norA, abolished norfloxacin uptake into vesicles as well as the norfloxacin resistance of an flqB mutant, suggesting a potential means for circumventing quinolone resistance as a result of drug efflux in S. aureus. These findings indicate that the chromosomal flqB resistance locus is associated with increased levels of expression of norA and strongly suggest that the NorA protein itself functions as a drug transporter that is coupled to the proton gradient across the cell membrane.

Limitations of plasmid complementation test for determination of quinolone resistance due to changes in the gyrase A protein and identification of conditional quinolone resistance locus

Plasmid pJSW101 derived from pUC19 and carrying the wild-type gyrA gene was found to be unstable in HM72, a quinolone-resistant (QR) clinical isolate of Escherichia coli, and resulted in no change in quinolone MICs. MICs determined in the presence of ampicillin to ensure plasmid presence, however, resulted in complementation. HM72 was proved to have a gyrA mutation based on the DNA sequence of a 418-bp fragment of gyrA. DNA sequencing identified a common mutation encoding Leu-83 as the cause of QR. To identify loci other than gyrA and nfxB contributing to QR in KF111b, zgh-3075::Tn10 (67 min) in CAG12152 was transduced into KF111b. Sixteen percent of the transductants had a fourfold decrease in norfloxacin MIC, indicating the presence of a locus, nfxD, which contributes to QR. Outcross of nfxD from DH151 (gyrA nfxB nfxD zgh-3075::Tn10) resulted in 8% of the KF130 gyrA, 2% of the EN226-3 gyrA, and none of the KL16 (wild-type) transductants, with a four- to eightfold increase in norfloxacin MIC. In the presence of ampicillin, the resistance of a gyrA nfxD double mutant, DH161 nfxD gyrA (from EN226-3), was fully complemented by gyrA+. Thus, gyrA+ plasmid complementation tests for QR may be falsely negative with plasmid instability, a difficulty which may be circumvented by maintenance of plasmid selection. In addition, if nfxD-like mutations occur in gyrA clinical isolates, a positive test may overestimate the level of resistance attributable to gyrA alone.

Histone H2A.F/Z mRNA is stored in the egg cytoplasm and basally regulated in the sea urchin embryo

The sea urchin H2A.F/Z histone is a member of a subclass of highly conserved H2A variants. Sequence analysis confirms that H2A.F/Z mRNA is polyadenylated. In situ hybridization studies demonstrate that maternal H2A.F/Z message is stored in the egg cytoplasm and present at equal levels in all cells of the mesenchyme blastula-stage embryo, suggesting that H2A.F/Z is not coordinately regulated with DNA synthesis. When blastula-stage embryos were exposed to DNA synthesis inhibitors, no effect on the steady-state level of H2A.F/Z mRNA was observed, while the level of late class H2B mRNA decreased substantially. These results provide evidence that the basal mode of regulation of this unusual histone variant is conserved evolutionarily.

Genetics and regulation of outer membrane protein expression by quinolone resistance loci nfxB, nfxC, and cfxB

Quinolone resistance mutations (cfxB1, marA1, and soxQ1) that reduce porin outer membrane protein OmpF map near 34 min on the Escherichia coli chromosome. Another such mutation, nfxC1, was found in strain KF131 (nfxB, 19 min). nfxC1 and cfxB1 mutants (selected with quinolones) differed slightly but reproducibly from marA1 (selected with tetracycline) and soxQ1 (selected with menadione) mutants in quinolone resistance and linkage to zdd2208::Tn10kan (33.7 min). For nfxB nfxC1 and cfxB1 mutants, as previously shown for marA mutants, resistance and reduced OmpF required the micF locus encoding an antisense RNA complementary to ompF mRNA and were associated with increased micF expression.

Mechanisms of quinolone resistance in Escherichia coli: characterization of nfxB and cfxB, two mutant resistance loci decreasing norfloxacin accumulation

Two genetic loci selected for norfloxacin (nfxB) and ciprofloxacin (cfxB) resistance were characterized. Both mutations have previously been shown to confer pleiotropic resistance to quinolones, chloramphenicol, and tetracycline and to decrease expression of porin outer-membrane protein OmpF. nfxB was shown to map at about 19 min and thus to be genetically distinct from ompF (21 min), and cfxB was shown to be very closely linked to marA (34 min). cfxB was dominant over cfxB+ in merodiploids, in contrast to other quinolone resistance mutations. The two loci appear to interact functionally, because nfxB was not expressed in the presence of marA::Tn5. Both nfxB and cfxB decreased the expression of ompF up to 50-fold at the posttranscriptional level as determined in strains containing ompF-lacZ operon and protein fusions. Both mutations also decreased norfloxacin accumulation in intact cells. This decrease in accumulation was abolished by energy inhibitors and by removal of the outer membrane. These findings, in conjunction with those of Cohen et al. (S. P. Cohen, D. C. Hooper, J. S. Wolfson, K. S. Souza, L. M. McMurry, and S. B. Levy, Antimicrob. Agents Chemother. 32:1187-1191, 1988), suggest a model for quinolone resistance by decreased permeation in which decreased diffusion through porin channels in the outer membrane interacts with a saturable drug efflux system at the inner membrane.

Antagonism of wild-type and resistant Escherichia coli and its DNA gyrase by the tricyclic 4-quinolone analogs ofloxacin and S-25930 stereoisomers

The mechanism of action of the quinolone analogs ofloxacin and S-25930, which are unusual because of the presence of a third ring with an asymmetric carbon, was studied. Drug-resistant strains of Escherichia coli were selected by serial passage in the presence of ofloxacin, and a mutation was mapped near the gyrA gene of DNA gyrase. DNA gyrase containing the A subunit purified from this strain as compared with the isogenic wild-type strain exhibited increased resistance to ofloxacin, proving that the mutation was located in the gyrA gene. For S-25930, the S stereoisomer was more potent than the R isomer in inhibiting wild-type E. coli and DNA gyrase containing an A subunit isolated from this strain. Both isomers had decreased potency against the isogenic ofloxacin-resistant (gyrA) strain and its purified enzyme, but the S isomer remained more potent than the R isomer. These studies, using a combined genetic and biochemical approach, demonstrate (i) that DNA gyrase is a target of the tricyclics ofloxacin and S-25930, (ii) that serial exposure to ofloxacin can select resistance to tricyclic quinolone agents by mutation in the gyrA gene, and (iii) that the more potent antibacterial activity of S relative to R S-25930 correlates with increased activity against DNA gyrase for both wild-type and ofloxacin-resistant (gyrA) isogenic strains.

Mechanisms of action of and resistance to ciprofloxacin

Ciprofloxacin and other newer quinolone antimicrobial agents exhibit increased potency and decreased frequency of spontaneous bacterial resistance in comparison with older analogues such as nalidixic acid. New and published observations on the mechanisms of action of and resistance to ciprofloxacin in Escherichia coli are presented and discussed. Genetic and biochemical studies have identified the A subunit of the essential bacterial enzyme DNA gyrase as a target of ciprofloxacin and other quinolones. For a series of quinolones, inhibition of purified DNA gyrase correlated with antibacterial activity. The bactericidal activity of ciprofloxacin and ofloxacin is, in contrast to that of certain other quinolones, somewhat less affected by rifampin and cell starvation, suggesting the existence of a site of drug action in addition to DNA gyrase. The frequency of selection of spontaneous single-step resistance mutants of E. coli was more than 100-fold lower with ciprofloxacin than with nalidixic acid. Strains highly resistant to ciprofloxacin could, nevertheless, be selected by serial passage on drug-containing agar. Two mutations contributing to this high level of resistance were analyzed. One, designated cfxA, conferred a 16-fold increase in drug resistance and mapped in a location consistent with a gyrA mutation; similar increases in resistance to ciprofloxacin were seen with gyrA mutations selected for resistance to other quinolones. The other mutation, cfxB, conferred pleiotropic resistance to ciprofloxacin, tetracycline, and chloramphenicol and appeared to be an allele of the multiple antibiotic resistance gene marA. The mutation cfxB was associated with a decreased amount of porin outer membrane protein OmpF, suggesting that drug permeation may occur in part through this channel. In summary, the A subunit of DNA gyrase is a target of ciprofloxacin and other quinolones. Ciprofloxacin resistance appears to occur both by mutation in this target and by alteration of drug permeation through the outer membrane of the cell.