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Biomedical subjects

A J Fox

Publications and source records attributed to A J Fox.

At least 19 recordsLinked to original sources
PubMed2006

Specific detection of Campylobacter jejuni from faeces using single nucleotide polymorphisms.

Specimens of human faeces were tested by a rapid strategy for detection of Campylobacter jejuni lineages by the presence of specific single nucleotide polymorphisms (SNPs) based on the C. jejuni multi locus sequence typing (MLST) scheme. This strategy was derived from analysis of the MLST databases to identify clonal complex specific SNPs followed by the design of real-time PCR assays to enable identification of six major C. jejuni clonal complexes associated with cases of human infection. The objective was to use the MLST SNP-based assays for the direct detection of C. jejuni by clonal complex from specimens of human faeces, and then confirm the accuracy of the clonal complex designation from the SNP-based assays by performing MLST on the cultured faecal material, this targeted at determining the validity of direct molecular specimen identification. Results showed it was possible to identify 38% of the isolates to one of the six major MLST clonal complexes using a rapid DNA extraction method directly from faeces in under 3 h. This method provides a novel strategy for the use of real-time PCR for detection and characterization beyond species level, supplying real-time epidemiological data, which is comparable with MLST results.

Campylobacter jejuni↗
PubMed2006

Identification of penumbra and infarct in acute ischemic stroke using computed tomography perfusion-derived blood flow and blood volume measurements.

BACKGROUND AND PURPOSE: We investigated whether computed tomography (CT) perfusion-derived cerebral blood flow (CBF) and cerebral blood volume (CBV) could be used to differentiate between penumbra and infarcted gray matter in a limited, exploratory sample of acute stroke patients. METHODS: Thirty patients underwent a noncontrast CT (NCCT), CT angiography (CTA), and CT perfusion (CTP) scan within 7 hours of stroke onset, NCCT and CTA at 24 hours, and NCCT at 5 to 7 days. Twenty-five patients met the criteria for inclusion and were subsequently divided into 2 groups: those with recanalization at 24 hours (n=16) and those without (n=9). Penumbra was operationally defined as tissue with an admission CBF <25 mL x 100 g(-1) x min(-1) that was not infarcted on the 5- to 7-day NCCT. Logistic regression was applied to differentiate between infarct and penumbra data points. RESULTS: For recanalized patients, CBF was significantly lower (P<0.05) for infarct (13.3+/-3.75 mL x 100 g(-1) x min(-1)) than penumbra (25.0+/-3.82 mL x 100 g(-1) x min(-1)). CBV in the penumbra (2.15+/-0.43 mL x 100 g(-1)) was significantly higher than contralateral (1.78+/-0.30 mL x 100 g(-1)) and infarcted tissue (1.12+/-0.37 mL x 100 g(-1)). Logistic regression using an interaction term (CBFxCBV) resulted in sensitivity, specificity, and accuracy of 97.0%, 97.2%, and 97.1%, respectively. The interaction term resulted in a significantly better (P<0.05) fit than CBF or CBV alone, suggesting that the CBV threshold for infarction varies with CBF. For patients without recanalization, CBF and CBV for infarcted regions were 15.1+/-5.67 mL x 100 g(-1) x min(-1) and 1.17+/-0.41 mL x 100 g(-1), respectively. CONCLUSIONS: We have shown in a limited sample of patients that CBF and CBV obtained from CTP can be sensitive and specific for infarction and should be investigated further in a prospective trial to assess their utility for differentiating between infarct and penumbra.

Acute Disease↗
PubMed2006

Quantification of carotid stenosis on CT angiography.

PURPOSE: Carotid artery stenosis quantification uses percent diameter ratios from conventional angiography. Multidetector high-speed CT angiography (CTA) allows direct millimeter measurement of carotid stenosis. We hypothesize a linear relationship between millimeter stenosis measurements and derived percent, alleviating cumbersome ratio calculations. METHODS: Two neuroradiologists separately reviewed CTAs of 268 carotid arteries, blinded to other information. The narrowest portion of each carotid stenosis was measured in millimeters from axial source images. Distal internal carotid arteries (ICAs) were measured beyond the bulb, where walls are parallel. North American Symptomatic Carotid Endarterectomy Trial (NASCET)-style ratios were calculated for each ICA, except for suspected near-occlusions. Interobserver agreement was calculated for all measurements. Correlation coefficients were calculated comparing millimeter and derived percent stenosis, followed by regression analysis. Sensitivity and specificity values tested validity. RESULTS: Interobserver agreement correlations were excellent, from 0.78 to 0.89 (2-tailed P </= .01). Excellent reader correlation permitted averaging of millimeter stenosis and distal ICA measurements, which were then used to calculate mean percent stenosis. Stenosis assessment was confidently performed from source images even with calcification. Regression analysis of mean percent as a function of mean millimeter stenosis shows a linear relationship, correlating 1.3 mm to 70% and 2.2 mm to 50% NASCET-style stenosis (Pearson's correlation of -0.95; n = 136). Direct millimeter measurement defining severe stenosis (70% or greater) has sensitivity of 88.2%, specificity of 92.4%, and negative predicted value of 98.2%. CONCLUSION: There is a linear relationship between millimeter carotid stenosis diameter and derived percent stenosis. This allows prediction of NASCET-type percent from millimeter stenosis.

Carotid Artery, Internal↗
PubMed2006

Association between calcification of the cervical carotid artery bifurcation and white matter ischemia.

BACKGROUND AND PURPOSE: The association of cervical carotid artery bifurcation calcification to future stroke risk is unknown, though coronary artery calcification is a proven indicator of heart disease risk. Severity of white matter change has been correlated with future stroke risk. We sought to use white matter severity grade on CT as a surrogate predictor of relative future stroke risk and thus correlate white matter and future stroke risk with carotid calcification grade. METHODS: We retrospectively reviewed unenhanced neck and brain CTs in 209 patients. Carotid calcification degree was scored by the Agatston method, adapted from that commonly used to quantify coronary artery calcification. White matter change severity was scored by the European Task Force for Age-Related White Matter Change scale. Both scores were measured blinded to each other, and to age and sex covariables. Association was tested by univariate and multivariate analyses. RESULTS: Both carotid calcification and white matter scores were strongly, and independently, associated with increasing age (r = 0.61, P < .001; and r = 0.67, P < .001, respectively). Despite apparent association between carotid calcification and white matter scores on univariate analysis, there was no independent effect evident after adjusting for age as a covariant (r = 0.07, P = .14). Sex had no independent effect on white matter scores, though men had a marginally higher mean calcified carotid plaque load than women after controlling for age (P = .008). CONCLUSIONS: Carotid calcification scores do not independently predict severity of white matter ischemia. Future stroke risk, assessed by white matter severity scores, cannot be predicted from carotid calcium scores.

Adult↗
PubMed2006

Diagnosing carotid stenosis near-occlusion by using CT angiography.

BACKGROUND/PURPOSE: Identification of carotid near-occlusion is essential before calculation of percent stenosis because stroke risk is lower than other severe stenosis and the treatment benefit is less. Calculations with reduced distal diameters are fallacious. CT angiography (CTA) is convenient and accurately quantifies internal carotid artery (ICA) stenosis. METHODS: In a blinded protocol, 268 carotid artery CTAs for known or suspected carotid disease were independently evaluated by 2 neuroradiologists. All carotid arteries were measured in millimeters at the narrowest diameter of the stenotic bulb, distal ICA well beyond the tapering bulb, and distal external carotid artery (ECA). Near-occlusions were independently identified, with disagreements settled by consensus meeting. Receiver operating characteristic (ROC) curve analysis defined the threshold values that best predicted near-occlusion according to (1) ICA stenosis, (2) distal ICA, (3) distal ICA: contralateral distal ICA, and (4) distal ICA: ECA. Paired permutations of variables were evaluated. RESULTS: Forty-two near-occlusion distal ICAs were identified. The ROC-derived threshold values determined near-occlusion carotid stenosis with a sensitivity range, 90.2-97.3; specificity, 84.1-89.9; positive predictive value (PPV), 61.3-66.7; and negative predictive value (NPV), 96.7-99.4. Ranges for paired permutations were also determined: sensitivity, 82.9-91.9; specificity, 95.4-96.8; PPV, 78.6-85.7; and NPV, 96.3-98.4. CONCLUSIONS: Threshold values provide guidelines for CTA interpretation when assessing carotid artery disease and the presence of near-occlusion. Ultimate identification of near-occlusion requires the interpreter's judgment, with attention to the following criteria: (1) notable stenosis of the ICA bulb and (2) distal ICA caliber reduction compared with (A) expected size, (B) contralateral ICA, and (C) ipsilateral ECA. Near-occlusion distal ICAs can be reliably identified on CTA.

Angiography↗
PubMed2006

Correlation of carotid stenosis diameter and cross-sectional areas with CT angiography.

PURPOSE: Carotid stenosis quantification traditionally uses measurements of narrowest stenosis diameter. The stenotic carotid lumen, however, is often irregularly shaped. New PACS workstation tools allow for more precise calculation of carotid geometry. We compare the narrowest stenosis diameter with 2D area stenosis measurements, with the hypothesis that the narrowest diameter is a good predictor of the more precise area measurement. METHODS: Two neuroradiologists evaluated 178 stenosed carotids in a blinded protocol. Carotid artery bulb stenosis was identified on axial CT angiography and measured in millimeters at its narrowest diameter. An AGFA Impax 4.5 Volume Tool (VT) using Hounsfield units was used to estimate the cross-sectional area of the contrast luminogram. Pearson correlation coefficients were calculated between the millimeter stenosis and the VT area, as well as between the VT area and the calculated area (radius based on narrowest diameter). Regression analysis was performed with the VT area and narrowest diameter datasets. RESULTS: Excellent interobserver correlation (correlation coefficients, 0.71-0.85; 2-tailed significance = .01) permitted averaging of measurement data. There is excellent correlation between the VT area and the narrowest diameter (correlation coefficient, 0.88; n = 176). The VT area was generally greater than the calculated area by an average of 2.77 mm2. There was excellent correlation between the VT area and the calculated area (correlation coefficient, 0.87; n = 176). Regression analysis shows the ability of the diameter measurements to predict corresponding area stenosis. CONCLUSION: Although some carotid stenoses are irregularly shaped and noncircular, measurement of the narrowest stenosis is a reasonably reliable predictor of the cross-sectional area.

Angiography↗
PubMed2005

Retreating glacier fronts on the Antarctic Peninsula over the past half-century.

The continued retreat of ice shelves on the Antarctic Peninsula has been widely attributed to recent atmospheric warming, but there is little published work describing changes in glacier margin positions. We present trends in 244 marine glacier fronts on the peninsula and associated islands over the past 61 years. Of these glaciers, 87% have retreated and a clear boundary between mean advance and retreat has migrated progressively southward. The pattern is broadly compatible with retreat driven by atmospheric warming, but the rapidity of the migration suggests that this may not be the sole driver of glacier retreat in this region.

Journal Article↗
PubMed2005

Optimisation of intact cell MALDI method for fingerprinting of methicillin-resistant Staphylococcus aureus.

The use of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry on intact cell microorganisms, Intact Cell MALDI (ICM), has been shown by numerous workers to yield effective species level identification. Early work highlighted the significant effect that variation in culture media, incubation conditions and length of incubation had on the spectra produced. Therefore, in order to achieve reliable and reproducible species level identification and sub-typing of microorganisms from ICM fingerprints, it has been essential to develop standardised methods. For methicillin-resistant Staphylococcus aureus (MRSA), a major nosocomial pathogen, we have developed such a standardised method. In this paper we present the experimental parameters, namely, the incubation period, the number of passages required from lyophilised or stored isolates, the method of deposition of the bacterial cells, the concentration of matrix solution, the drying time of bacterial cells prior to the addition of the matrix solution, the time between preparation of the bacterial/matrix sample and analysis and the MALDI pulsed extraction setting, which were considered during the development of defined methods.

Bacterial Proteins↗
PubMed2005

Real-time single-nucleotide polymorphism profiling using Taqman technology for rapid recognition of Campylobacter jejuni clonal complexes.

The rapid identification of Campylobacter jejuni isolates to strain level would significantly inform the public health investigation of C. jejuni infection. Conceptual advances provided by multilocus sequence typing (MLST) have established the clonal complex as an important epidemiological group at the strain level, enabling accurate and phylogenetically valid strain identification for C. jejuni. The development of real-time PCR assays for allelic discrimination of strain-associated single-nucleotide polymorphisms (SNPs) based upon MLST locus alleles offers one possible approach for rapid strain detection. SNPs defining key alleles diagnostic for the most prevalent clonal complexes were identified following a detailed analysis of the available MLST data. Real-time Taqman allelic discrimination assays designed to detect the SNPs specific for six major clonal complexes, ST-21, ST-45, ST-48, ST-61, ST-206 and ST-257, were developed, allowing the rapid detection of C. jejuni isolates and preliminary strain identification. This will provide an important complementary technique to sequence typing for rapid detection and strain characterization to inform in real-time the public health management and investigation of C. jejuni infections.

Alleles↗
PubMed2004

Identification of Campylobacter jejuni multilocus sequence type ST-21 clonal complex by single-nucleotide polymorphism analysis.

Conserved single-nucleotide polymorphisms (SNPs) which characterize the allelic profile of the major epidemiological lineage ST-21 were identified from the alleles within the current Campylobacter jejuni multilocus sequence typing (MLST) database. Allelic discrimination assays were designed for the detection of SNPs, enabling rapid strain profiling for clonal complex ST-21. This method is suitable for epidemiological investigations and is complementary to full MLST.

Alleles↗
PubMed2003

Analysis of pooled data from the randomised controlled trials of endarterectomy for symptomatic carotid stenosis.

BACKGROUND: Endarterectomy reduces risk of stroke in certain patients with recently symptomatic internal carotid stenosis. However, investigators have made different recommendations about the degree of stenosis above which surgery is effective, partly because of differences between trials in the methods of measurement of stenosis. To accurately assess the overall effect of surgery, and to increase power for secondary analyses, we pooled trial data and reassessed carotid angiograms. METHODS: We pooled data from the European Carotid Surgery Trial (ECST), North American Symptomatic Carotid Endarterectomy Trial, and Veterans Affairs trial 309 from the original electronic data files. Outcome events were re-defined, if necessary, to achieve comparability. Pre-randomisation carotid angiograms from ECST were re-measured by the method used in the other two trials. RESULTS: Risks of main outcomes in both treatment groups and effects of surgery did not differ between trials. Data for 6092 patients, with 35000 patient-years of follow-up, were therefore pooled. Surgery increased the 5-year risk of ipsilateral ischaemic stroke in patients with less than 30% stenosis (n=1746, absolute risk reduction -2.2%, p=0.05), had no effect in patients with 30-49% stenosis (1429, 3.2%, p=0.6), was of marginal benefit in those with 50-69% stenosis (1549, 4.6%, p=0.04), and was highly beneficial in those with 70% stenosis or greater without near-occlusion (1095, 16.0%, p<0.001). There was a trend towards benefit from surgery in patients with near-occlusion at 2 years' follow-up (262, 5.6%, p=0.19), but no benefit at 5 years (-1.7%, p=0.9). INTERPRETATION: Re-analysis of the trials with the same measurements and definitions yielded highly consistent results. Surgery is of some benefit for patients with 50-69% symptomatic stenosis, and highly beneficial for those with 70% symptomatic stenosis or greater but without near-occlusion. Benefit in patients with carotid near-occlusion is marginal in the short-term and uncertain in the long-term.

Aged↗
PubMed2003

In vivo and in vitro effects of peripheral galanin on nociceptive transmission in naive and neuropathic states.

Galanin is widely distributed in the nervous system and is consistently upregulated in both dorsal root ganglion and spinal neurones by peripheral nerve injury. This study investigates the peripheral effects of galanin on nociceptive neurones using in vitro and in vivo electrophysiological techniques in naive and neuropathic rats. Using an in vitro skin-nerve preparation recording from single nociceptive fibres, galanin (1 microM) significantly inhibited firing induced by noxious heat in 65% of fibres examined. In the remaining 35% of fibres, galanin (1 microM) induced a facilitation of the responses to noxious heat. To examine the effect of peripheral galanin in vivo, extracellular recordings from convergent dorsal horn neurones were made in anaesthetised naive sham-operated and spinal nerve-ligated (SNL) rats. Injection of galanin (0.1-10 microg) into hindpaw receptive fields inhibited responses to innocuous mechanical, noxious mechanical and noxious heat stimuli in a proportion of neurones in each animal group and facilitated the remaining neurones. However, a higher proportion of neurones (80-90%) was inhibited by peripheral galanin administration in SNL rats compared with naive (45-55%) and sham (70-80%) rats. These results show that galanin can have both excitatory and inhibitory effects on peripheral sensory neurones, perhaps reflecting differential receptor activation, and that the proportion of these receptors may change following peripheral neuropathy.

Action Potentials↗
PubMed2003

Employment of broad-range 16S rRNA PCR to detect aetiological agents of infection from clinical specimens in patients with acute meningitis--rapid separation of 16S rRNA PCR amplicons without the need for cloning.

AIMS: The aim of this study was to develop a polyacrylamide gel electrophoresis (PAGE) method for the rapid separation of 16S rRNA PCR amplicons from aetiological agents of acute meningitis. METHODS AND RESULTS: Blood samples from 40 patients with suspected acute meningococcal meningitis were examined for the presence of causal agents, including Neisseria meningitidis employing two methods: (i) broad-range 16S rRNA PCR in conjunction with PAGE and automated sequencing and (ii) species-specific PCR employing ABI TaqMan technology for N. meningitidis. Analysis of clinical specimens employing 16S rRNA PCR yielded 33/40 (82.5%) positive for the presence of bacterial DNA. Species-specific PCR yielded 30/40 (75%) clinical specimens positive for N. meningitidis. Prior to separation by PAGE, only 6/33 (18.2%) amplicons were able to be identified by sequence analysis, the remaining amplicons (n=27) did not yield an identification due to the presence of mixed 16S rRNA PCR amplicons. Following separation, amplicons were re-amplified and sequenced, yielding 24/27 (88.9%) positive for N. meningitidis and three specimens positive for Acinetobacter sp., Staphylococcus aureus and Streptococcus pneumoniae. One specimen was positive for both N. meningitidis and Streptococcus spp. and another specimen was positive for N. meningitidis and Pseudomonas sp., by broad-range PCR. Seven clinical specimens were negative for N. meningitidis and other eubacteria using both detection techniques. CONCLUSIONS: Clinical specimens including blood and cerebrospinal fluid from patients with suspected acute bacterial meningitis, may become contaminated with commensal skin flora, resulting in difficulties in downstream sequencing of pathogen plus contaminant DNA. This study allows for the rapid separation of amplified pathogen from contaminant DNA. SIGNIFICANCE AND IMPACT OF STUDY: This study demonstrated the usefulness of the rapid separation of multiple 16S rRNA PCR amplicons using a combination of PAGE and automated sequencing, without the need of cloning. Adoption of this technique is therefore proposed when trying to rapidly identify pathogens in clinical specimens employing broad-range 16S rRNA PCR.

Acinetobacter↗
PubMed2003

Reference isolates for the clonal complexes of Campylobacter jejuni.

AIMS: To identify and make available through the National Collection of Type Cultures (NCTC) a set of reference isolates for the clonal complexes of Campylobacter jejuni. METHODS AND RESULTS: The development of a multilocus sequence typing scheme for C. jejuni enabled the genetic characterization of a large number of isolates (n = 814) from cases of human disease, animals, birds and their food products. The nucleotide sequence data were used to assign each isolate an allelic profile or sequence type (ST) and examine the C. jejuni population structure in terms of clonal complexes. The clonal complexes consisted of an abundant central or founder genotype (ST), after which the complex was named, together with very closely related, generally less abundant genotypes differing from the founder at one, two or three loci. The clonal complex is an informative unit for the study C. jejuni epidemiology. It provides data which enabled the choice of 13 C. jejuni founder isolates for submission to the NCTC as a representative cross-section of the C. jejuni population. CONCLUSIONS: These 13 isolates provide a defined resource for further research into aspects of C. jejuni biology such as genomic diversity, virulence and adaptation to particular hosts or environmental survival. SIGNIFICANCE AND IMPACT OF STUDY: This isolate collection is available through the NCTC and provides a resource for further research.

Alleles↗
PubMed2002

Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility.

Intact cell mass spectrometry (ICMS) rapidly analyses the surface composition of microorganisms providing rapid, discriminatory fingerprints for identification and subtyping of important nosocomial pathogens such as methicillin resistant Staphylocccus aureus (MRSA). In this study, ICMS using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF/MS) was assessed for the identification and subtyping of MRSA. An intra- and inter-laboratory reproducibility study was carried out and the effects of culture media (an important source of variation for ICMS) were also studied. Several media used for the cultural identification of MRSA were examined using a panel of well-characterised staphylococcal isolates (n=26). Six MRSA isolates were analysed over a 1-month period for intra-laboratory reproducibility on the same instrument and three different culture media. Spectra were consistent for each isolate between the four experiments on the same culture medium. Individual isolates produced different spectral profiles on different culture media. Spectra from organisms grown on Columbia blood agar contained more peaks (approximately 120) compared to Columbia agar (approximately 50) and methicillin mannitol salt agar (approximately 25). All 26 staphylococcal isolates were subjected to an inter-laboratory study on two MALDI instruments. For each isolate, the overall spectral profile was the same for each of the two instruments but the baseline threshold values was adjusted due to instrument differences in detector sensitivities. Differences between certain regions of the spectra reproducibly identified isolates belonging to the two major MRSA strains (EMRSA phage group 15 and 16). These results demonstrate ICMS with appropriate media selection is a rapid and reproducible technique for identification and discrimination of MRSA.

Culture Media↗
PubMed2002

Using the Sustained Attention to Response Test to detect cognitive dysfunction after day case surgery.

BACKGROUND AND OBJECTIVE: Cognitive dysfunction has been reported after general anaesthesia, but its assessment is time consuming and difficult to evaluate. This pilot study assessed the feasibility of using the Sustained Attention to Response Test to assess 35 ASA I-II adults (mean age 31.6 yr) undergoing day case surgery under general anaesthesia, and 25 ASA I-II adults (mean age 47.8 yr) undergoing day case surgery under local anaesthesia. METHODS: The Sustained Attention to Response Test was performed before surgery and repeated 2 h after surgery. RESULTS: When patients repeated the test after surgery under local anaesthesia, the number of incorrect responses increased, but reaction times decreased (P < 0.05). Following general anaesthesia, the number of incorrect responses increased (P < 0.05), but reaction times remained unchanged. CONCLUSIONS: The Sustained Attention to Response Test is simple to administer and may be a useful tool when comparing different anaesthetic techniques and their effects on postoperative deficits in sustained attention.

Adult↗
PubMed2002

Phenotypic diversity of Campylobacter isolates from sporadic cases of human enteritis in the UK.

AIMS: The aim of this study was to identify and subtype a large collection of isolates of Campylobacter spp. to quantify diversity among strains causing human disease from geographically diverse sources in the United Kingdom. METHODS AND RESULTS: Isolates were characterized by the Penner serotyping scheme, Preston phage typing and biotyping methods. The diversity index calculated from the combined results of all three methods was 0.997 and indicated that isolates from sporadic cases of infection are very diverse. Strong associations between common phagetypes (PG52, PG121 and PG55) and the three most common serotypes (HS1, HS2 and HS4) found in the study were evident. CONCLUSIONS: Strains of C. jejuni causing human infections in the United Kingdom are very phenotypically diverse. Individual strains characterized by serotype, phagetype and biotype were detected throughout the 7-month study period and from geographically distinct sources, indicating an unrecognized outbreak or other epidemiologically significant source of human infection. SIGNIFICANCE AND IMPACT OF THE STUDY: The low frequency incidence of most C. jejuni strains should enable easy recognition of outbreaks by strain type surveillance at local, regional and national level in the United Kingdom. The characterization of common strain profiles in this study by simple phenotypic methods could provide the basis for strain specific epidemiological studies for reservoirs of infection and transmission routes for human infection.

Bacterial Typing Techniques↗