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R Urwin

Publications and source records attributed to R Urwin.

17 recordsLinked to original sources
PubMed2001

Multilocus sequence typing system for Campylobacter jejuni.

The gram-negative bacterium Campylobacter jejuni has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in seven housekeeping loci to determine the genetic relationships among isolates. The MLST system was established using 194 C. jejuni isolates of diverse origins, from humans, animals, and the environment. The allelic profiles, or sequence types (STs), of these isolates were deposited on the Internet (http://mlst.zoo.ox.ac.uk), forming a virtual isolate collection which could be continually expanded. These data indicated that C. jejuni is genetically diverse, with a weakly clonal population structure, and that intra- and interspecies horizontal genetic exchange was common. Of the 155 STs observed, 51 (26% of the isolate collection) were unique, with the remainder of the collection being categorized into 11 lineages or clonal complexes of related STs with between 2 and 56 members. In some cases membership in a given lineage or ST correlated with the possession of a particular Penner HS serotype. Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism.

Alleles↗
PubMed2001

Phenotypic and genotypic approaches to characterization of isolates of Neisseria meningitidis from patients and their close family contacts.

Characterization of isolates of Neisseria meningitidis obtained from patients with meningococcal disease or from pharyngeal swabs of asymptomatic carriers can be achieved by several approaches which provide different levels of discrimination. A total of 45 gram negative, oxidase-positive diplococcus strains isolated from 15 individuals with meningococcal disease and 30 of their family contacts were examined by three approaches: serological typing, multilocus enzyme electrophoresis (MLEE), and multilocus sequence typing (MLST). For 10 of the 15 patient and contact groups, all of the isolates were confirmed as meningococci, and the bacteria obtained from the patients and contacts, including their mother or principal caregiver in the case of children, were indistinguishable by all three methods. In the remaining five groups the isolates from the patients were distinct from those recovered from the contacts, and in three examples, in two separate groups, the contacts were shown by MLST to be carrying strains of Neisseria lactamica. The data obtained from the three techniques were consistent, although complete serological typing was possible for only a minority of isolates. Both MLEE and MLST established the genetic relationships of the isolates and identified members of known hypervirulent lineages, but MLST was faster than MLEE and had the additional advantages that it could be performed on noninfective material distributed by mail and that the results from different laboratories could be compared via the internet (http://mlst.zoo.ox.ac.uk).

Adolescent↗
PubMed2000

Carriage of serogroup W-135, ET-37 meningococci in The Gambia: implications for immunisation policy?

We found high levels of symptomless carriage of a hyperinvasive Neisseria meningitidis strain (electrophoretic type 37 [ET-37], serogroup W-135) during a vaccine trial in Gambian children in 1996. Serogroup C, ET-37 complex meningococci cause 30-40% of meningococcal disease in countries such as the UK, and have a point prevalence of 0.5-1.0%. The recent Haj-associated spread of serogroup W-135, ET-37 complex meningococci, which has been accompanied by numerous secondary cases, might be explained by the apparently raised carriage rates reported here.

Bacterial Vaccines↗
PubMed1999

The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis.

The extent to which recombination disrupts the bifurcating treelike phylogeny and clonal structure imposed by binary fission on bacterial populations remains contentious. Here, we address this question with a study of nucleotide sequence data from 107 isolates of the human pathogen Neisseria meningitidis. Gene fragments from 12 house-keeping loci distributed around the meningococcal chromosome were analyzed, showing that (1) identical alleles are disseminated among genetically diverse isolates, with no evidence for linkage disequilibrium; (2) different loci give distinct and incongruent phylogenetic trees; and (3) allele sequences are incompatible with a bifurcating treelike phylogeny at all loci. These observations are consistent with the hypothesis that meningococcal populations comprise organisms assembled from a common gene pool, with alleles and allele fragments spreading independently, together with the occasional importation of genetic material from other species. Further, they support the view that recombination is an important genetic mechanism in the generation new meningococcal clones and alleles. Consequently, for anything other than the short-term evolution of this species, a bifurcating treelike phylogeny is not an appropriate model.

Alleles↗
PubMed1999

Structural and evolutionary inference from molecular variation in Neisseria porins.

The porin proteins of the pathogenic Neisseria species, Neisseria gonorrhoeae and Neisseria meningitidis, are important as serotyping antigens, putative vaccine components, and for their proposed role in the intracellular colonization of humans. A three-dimensional structural homology model for Neisseria porins was generated from Escherichia coli porin structures and N. meningitidis PorA and PorB sequences. The Neisseria sequences were readily assembled into the 16-strand beta-barrel fold characteristic of porins, despite relatively low sequence identity with the Escherichia proteins. The model provided information on the spatial relationships of variable regions of peptide sequences in the PorA and PorB trimers and insights relevant to the use of these proteins in vaccines. The nucleotide sequences of the porin genes from a number of other Neisseria species were obtained by PCR direct sequencing and from GenBank. Alignment and analysis of all available Neisseria porin sequences by use of the structurally conserved regions derived from the PorA and PorB structural models resulted in the recovery of an improved phylogenetic signal. Phylogenetic analyses were consistent with an important role for horizontal genetic exchange in the emergence of different porin classes and confirmed the close evolutionary relationships of the porins from N. meningitidis, N. gonorrhoeae, Neisseria lactamica, and Neisseria polysaccharea. Only members of this group contained three conserved lysine residues which form a potential GTP binding site implicated in pathogenesis. The model placed these residues on the inside of the pore, in close proximity, consistent with their role in regulating pore function when inserted into host cells.

Amino Acid Sequence↗
PubMed1999

Population genetic and evolutionary approaches to analysis of Neisseria meningitidis isolates belonging to the ET-5 complex.

Periodically, new disease-associated variants of the human pathogen Neisseria meningitidis arise. These meningococci diversify during spread, and related isolates recovered from different parts of the world have different genetic and antigenic characteristics. An example is the ET-5 complex, members of which were isolated globally from the mid-1970s onwards. Isolates from a hyperendemic outbreak of meningococcal disease in Worcester, England, during the late 1980s were characterized by multilocus sequence typing and sequence determination of antigen genes. These data established that the Worcester outbreak was caused by ET-5 complex meningococci which were not closely related to the ET-5 complex bacteria responsible for a hyperendemic outbreak in the nearby town of Stroud during the years preceding the Worcester outbreak. A comparison with other ET-5 complex meningococci established that there were at least three distinct globally distributed subpopulations within the ET-5 complex, characterized by particular housekeeping and antigen gene alleles. The Worcester isolates belonged to one of these subpopulations, the Stroud isolates belonged to another, and at least one representative of the third subpopulation identified in this work was isolated elsewhere in the United Kingdom. The sequence data demonstrated that ET-5 variants have arisen by multiple complex pathways involving the recombination of antigen and housekeeping genes and de novo mutation of antigen genes. The data further suggest that either the ET-5 complex has been in existence for many years, evolving and spreading relatively slowly until its disease-causing potential was recognized, or it has evolved and spread rapidly since its first identification in the 1970s, with each of the subpopulations attaining a distribution spanning several continents.

Amino Acid Sequence↗
PubMed1999

Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak.

Multilocus sequence typing and antigen gene sequencing were used to investigate an outbreak of meningococcal disease in a university in the United Kingdom. The data obtained showed that five distinct Neisseria meningitidis strains belonging to the ET-37 complex were present in the student population during the outbreak. Three of these strains were not associated with invasive disease, and two distinct strains caused invasive disease, including several fatalities. The initial case of the disease cluster was caused by a strain distinct from that responsible for at least two subsequent cases and two cases remote from the university, which were epidemiologically linked to the outbreak. These observations were consistent with pulsed-field gel electrophoresis data, but the sequence data alone were sufficient to resolve the strains involved in the disease cluster. Interpretation of the nucleotide sequence data was more straightforward than interpretation of the fingerprint patterns, and the sequence data provided information on the genetic differences among the isolates.

Bacterial Outer Membrane Proteins↗
PubMed1998

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Bacterial Typing Techniques↗
PubMed1998

Amplification of the meningococcal porB gene for non-culture serotype characterization.

Since 1992, the proportion of culture-confirmed meningococcal infections compared with numbers of notified cases of meningococcal disease has decreased in England and Wales. As most meningococcal strain characterization methods depend on a clinical isolate, this has resulted in a loss of epidemiological information. To address this problem, and to aid nonculture diagnosis, a semi-nested PCR protocol for the amplification of the meningococcal porB gene from clinical specimens was developed. This gene encodes the meningococcal serotyping antigen; strain typing data was provided by hybridization of allele-specific oligonucleotide probes to the digoxigenin-labelled porB amplicon in a 'PCR ELISA'. This assay was specific for meningococcal DNA and sensitivities of 0.81 for cerebrospinal fluid (CSF), 0.57 for serum, and 0.62 for whole blood taken from patients with proven meningococcal infection were obtained.

Bacterial Outer Membrane Proteins↗
PubMed1998

Molecular variation of meningococcal serotype 4 antigen genes.

Changes in the frequency of serogroup B non serotypable (B:NT) meningococci isolated in England and Wales were investigated by T-track fingerprint analysis, DNA nucleotide sequence determination, and serotyping by whole cell ELISA and dot blot assay. Seventy-three per cent of the isolates designated as B:NT by the Meningococcal Reference Unit (MRU) dot blot assay during 1993-4, expressed variants of the serotyping antigen, PorB, that were serotype 4 by whole cell ELISA. T-track fingerprint patterns of these and other 'serotype 4' isolates revealed five distinct porB alleles which were shown by nucleotide sequence determination to encode different peptide sequences. Differential binding of the 'serotype 4' mAbs MN14G21 and 5DC4C8G8 in whole cell ELISA and dot blot assays was the result, (i) of differences in the peptide sequence of predicted surface loop I and (ii) an amino acid deletion in predicted loop VI of the PorB protein.

Amino Acid Sequence↗
PubMed1998

Heterogeneity of the PorB protein in serotype 22 Neisseria meningitidis.

The genetic diversity of porB genes from meningococcal isolates characterized as serotype 22 was investigated by gene sequencing. This procedure identified seven distinct porB sequences, demonstrating variation in the PorB protein recognized by the serotype 22 monoclonal antibody. This is consistent with the genetic heterogeneity of serotype 22 meningococci reported previously.

Amino Acid Sequence↗
PubMed1997

Intravascular stent and endovascular coil placement for a ruptured fusiform aneurysm of the basilar artery. Case report and review of the literature.

The authors demonstrate the technical feasibility of using intravascular stents in conjunction with electrolytically detachable coils (Guglielmi detachable coils [GDCs]) for treatment of fusiform, broad-based, acutely ruptured intracranial aneurysms and review the literature on endovascular approaches to ruptured aneurysms and cerebral stent placement. A 77-year-old man presented with an acute subarachnoid hemorrhage of the posterior fossa. A fusiform aneurysm with a broad-based neck measuring 12 mm and involving the distal vertebral artery (VA) and proximal third of the basilar artery (BA) was demonstrated on cerebral angiography. The aneurysm was judged to be inoperable. Six days later a repeated hemorrhage occurred. A 15-mm-long intravascular stent was placed across the base of the aneurysm in the BA and expanded to 4 mm to act as a bridging scaffold to create a neck. A microcatheter was then guided through the interstices of the stent into the body and dome of the aneurysm, and GDCs were deposited for occlusion. The arteriogram obtained after stent placement demonstrated occlusion of the main dome and body of the aneurysm. The coils were stably positioned and held in place by the stent across the distal VA and BA fusiform aneurysm. Excellent blood flow to the distal BA and posterior cerebral artery was maintained through the stent. There were no new brainstem ischemic events attributable to the procedure. No rebleeding from the aneurysm had occurred by the 10.5-month follow-up evaluation, and the patient has experienced significant neurological improvement. Certain types of intracranial fusiform aneurysms may now be treated by combining intravascular stent and GDC placement for aneurysm occlusion via an endovascular approach. This is the first known clinical application of this novel approach in a ruptured cerebral aneurysm.

Acute Disease↗
PubMed1992

Molecular biological approaches to the study of vectors in relation to malaria control.

To a large extent, control of malaria vectors relies on the elimination of breeding sites and the application of chemical agents. There are increasing problems associated with the use of synthetic insecticides for vector control, including the evolution of resistance, the high cost of developing and registering new insecticides and an awareness of pollution from insecticide residues. These factors have stimulated interest in the application of molecular biology to the study of mosquito vectors of malaria; focussing primarily on two aspects. First, the improvement of existing control measures through the development of simplified DNA probe systems suitable for identification of vectors of malaria. The development of synthetic, non-radioactive DNA probes suitable for the identification of species in the Anopheles gambiae complex is described with the aim of defining a simplified methodology which is suitable for entomologist in the field. The second aspect to be considered is the development of completely novel strategies through the genetic manipulation of insect vectors of malaria in order to alter their ability to transmit the disease. The major requirements for producing transgenic mosquitoes are outlined together with the progress which has been made to date and discussed in relation to the prospects which this type of approach has for the future control of malaria.

Animals↗
PubMed1991

Synthetic DNA probes for the identification of sibling species in the Anopheles gambiae complex.

The cloned DNA sequences pAna1, pAnq1 and pAnm14, which may be used to distinguish between at least five of the six species in the Anopheles gambiae Giles complex of Afrotropical malaria vector mosquitoes, have been sequenced. Each clone was found to possess a series of repeated sequences of 41, 30 and 163 bases respectively. In pAnq1 and pAnm14 the repeats were in direct tandem array, whilst in pAna1 the repetitive sequence was found to be interspersed by 15-17 variable bases. A comparison of a number of copies of each of the repetitive sequences within the three clones enabled the definition of the consensus sequence for each repetitive element. Based on these consensus sequences, three oligonucleotides of 21, 23 and 26 bases were derived from pAna1, pAnq1 and pAnm14 respectively. When tested as probes against DNA dot-blots and squash-blots of mosquito specimens, each oligonucleotide retained the same species-specificity as the original clones from which they were derived. The radioactively labelled oligonucleotides were able to detect as little as 5 ng of target genomic DNA in an overnight autoradiographic exposure. The synthetic DNA probes will form the basis of a simplified system for the field identification of Anopheles gambiae sibling species specimens.

Animals↗
PubMed1991

A comparison of non-radioactive labeling and detection systems with synthetic oligonucleotide probes for the species identification of mosquitoes in the Anopheles gambiae complex.

Different non-radioactive probe labeling and detection systems were used with pAnaI, a species-specific oligonucleotide probe that distinguishes male Anopheles gambiae and An. arabiensis mosquitoes. Comparisons have been made between the performance of each technique with respect to sensitivity and specificity against DNA dot-blots and mosquito squashes. Their relative costs, economy, and ease of use were analyzed in an attempt to develop an appropriate non-radioactive system for use in the field. Enzyme-labeled probes that were detected directly by label activity proved more suitable than probes requiring reporter molecules for detection. Binding of reporter molecules to mosquito squashes caused the appearance of false positives and, in addition, their binding to nylon filters caused high background coloration. Chemiluminescent detection provided an attractive alternative to colorimetric detection. Both systems analyzed were rapid, simple, and economic. However, less severe treatment of filters was required for reprobing with chemiluminescence. The greatest sensitivity achieved was with chemiluminescent detection in which the limit of detection was 0.15 ng of target DNA. This study suggests that a synthetic DNA probe coupled to a chemiluminescent detection system should provide a sufficiently simple, sensitive, and reliable technique for insect vector identification in the field.

Animals↗
PubMed1983

Cystic fibrosis screening by dried blood spot trypsin assay: results in 75,000 newborn infants.

Seventy-five thousand 5-day-old babies were screened for cystic fibrosis by blood spot immunoreactive trypsin (IRT) assay as part of a statewide screening program. IRT was elevated in 433 babies; retesting revealed persistent elevation in 38. Sweat testing confirmed cystic fibrosis in 35 babies and was normal in two babies, whose IRT remained elevated at the time of the test. Sweat testing was refused by one mother. Of the 35 babies with cystic fibrosis, 13 had meconium ileus or an already diagnosed affected sibling, but the diagnosis was unsuspected in 22, although all but four had some symptoms suggestive of cystic fibrosis. Stool trypsin activity at the time of the diagnostic screen was normal in nine and reduced in seven of the babies with cystic fibrosis. One baby did not have elevated IRT, and the cystic fibrosis was missed by the screening test. In a retrospective study of blood spot samples from 36 newborn infants, who were later diagnosed as having cystic fibrosis, all had IRT levels greater than in matched controls. Our study confirms that elevated IRT is characteristic of newborn babies with cystic fibrosis, and shows that this test is very specific and sensitive when used as a newborn screening test.

Australia↗