Publications
288 results found
Turner KME, Hanage WP, Fraser C, et al., 2007, Assessing the reliability of eBURST using simulated populations with known ancestry, BMC Microbiology, Vol: 7, ISSN: 1471-2180
Background: The program eBURST uses multilocus sequence typing data to divide bacterialpopulations into groups of closely related strains (clonal complexes), predicts the founding genotype of each group, and displays the patterns of recent evolutionary descent of all other strains in the group from the founder. The reliability of eBURST was evaluated using populations simulated with different levels of recombination in which the ancestry of all strains was known.Results: For strictly clonal simulations, where all allelic change is due to point mutation, the groups of related strains identified by eBURST were very similar to those expected from the true ancestry and most of the true ancestor-descendant relationships (90–98%) were identified by eBURST. Populations simulated with low or moderate levels of recombination showed similarly high performance but the reliability of eBURST declined with increasing recombination to mutationratio. Populations simulated under a high recombination to mutation ratio were dominated by a single large straggly eBURST group, which resulted from the incorrect linking of unrelated groups of strains into the same eBURST group. The reliability of the ancestor-descendant links in eBURST diagrams was related to the proportion of strains in the largest eBURST group, which provides auseful guide to when eBURST is likely to be unreliable.Conclusion: Examination of eBURST groups within populations of a range of bacterial speciesshowed that most were within the range in which eBURST is reliable, and only a small number (e.g. Burkholderia pseudomallei and Enterococcus faecium) appeared to have such high rates of recombination that eBURST is likely to be unrel iable. The study also demonstrates how three simple tests in eBURST v3 can be used to detect unreliable eBURST performance and recognisepopulations in which there appears to be a high rate of recombination relative to mutation.
Fraser C, Hanage WP, Spratt BG, 2007, Recombination and the nature of bacterial speciation, Science, Vol: 315, Pages: 476-480, ISSN: 0036-8075
Glass MB, Gee JE, Steigerwalt AG, et al., 2006, Pneumonia and septicemia caused by <i>Burkholderia thailandensis</i> in the United States, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 44, Pages: 4601-4604, ISSN: 0095-1137
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- Citations: 90
Hanage WP, Spratt BG, Turner KME, et al., 2006, Modelling bacterial speciation, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 361, Pages: 2039-2044, ISSN: 1471-2970
A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we observe a transition between clonal structure and sexual structure as the rate of recombination increases. In the clonal situation, clearly resolved clusters are regularly formed, break up or go extinct. In the sexual situation, the formation of distinct clusters is prevented by the cohesive force of recombination. Where the rate of recombination is a declining log-linear function of the genetic distance between the donor and recipient strain, distinct clusters emerge even with high rates of recombination. These clusters arise in the absence of selection, and have many of the properties of species, with high recombination rates and thus sexual cohesion within clusters and low rates between clusters. Distance-scaled recombination can thus lead to a population splitting into distinct genotypic clusters, a process that mimics sympatric speciation. However, empirical estimates of the relationship between sequence divergence and recombination rate indicate that the decline in recombination is an insufficiently steep function of genetic distance to generate species in nature under neutral drift, and thus that other mechanisms should be invoked to explain speciation in the presence of recombination.
Spratt BG, Staley JT, Fisher MC, 2006, Introduction: species and speciation in micro-organisms, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 361, Pages: 1897-1898, ISSN: 0962-8436
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- Citations: 10
Hanage WP, Fraser C, Spratt BG, 2006, Sequences, sequence clusters and bacterial species, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 361, Pages: 1917-1927, ISSN: 0962-8436
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- Citations: 132
Choudhury B, Risley CL, Ghani AC, et al., 2006, Identification of individuals with gonorrhoea within sexual networks: a population-based study, LANCET, Vol: 368, Pages: 139-146, ISSN: 0140-6736
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- Citations: 64
Vesaratchavest M, Tumapa S, Day NP, et al., 2006, Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence., J Clin Microbiol., Vol: 44, Pages: 2553-2557
Jones N, Oliver KA, Barry J, et al., 2006, Enhanced invasiveness of bovine-derived neonatal sequence type 17 group B <i>Streptococcus</i> is independent of capsular serotype, CLINICAL INFECTIOUS DISEASES, Vol: 42, Pages: 915-924, ISSN: 1058-4838
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- Citations: 85
Hanage WP, Fraser C, Spratt BG, 2006, The impact of homologous recombination on the generation of diversity in bacteria, JOURNAL OF THEORETICAL BIOLOGY, Vol: 239, Pages: 210-219, ISSN: 0022-5193
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- Citations: 85
Bentley SD, Aanensen DM, Mavroidi A, et al., 2006, Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes, PLOS Genetics, Vol: 2, Pages: 262-269, ISSN: 1553-7390
Several major invasive bacterial pathogens are encapsulated. Expression of a polysaccharide capsule is essential forsurvival in the blood, and thus for virulence, but also is a target for host antibodies and the basis for effective vaccines.Encapsulated species typically exhibit antigenic variation and express one of a number of immunochemically distinctcapsular polysaccharides that define serotypes. We provide the sequences of the capsular biosynthetic genes of all 90 serotypes of Streptococcus pneumoniae and relate these to the known polysaccharide structures and patterns of immunological reactivity of typing sera, thereby providing the most complete understanding of the genetics and origins of bacterial polysaccharide diversity, laying the foundations for molecular serotyping. This is the first time, toour knowledge, that a complete repertoire of capsular biosynthetic genes has been available, enabling a holistic analysis of a bacterial polysaccharide biosynthesis system. Remarkably, the total size of alternative coding DNA at thisone locus exceeds 1.8 Mbp, almost equivalent to the entire S. pneumoniaechromosomal complement.
Hanage WP, Kaijalainen T, Saukkoriipi A, et al., 2006, A successful, diverse disease-associated lineage of nontypeable pneumococci that has lost the capsular biosynthesis locus, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 44, Pages: 743-749, ISSN: 0095-1137
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- Citations: 46
Spratt BG, 2006, Health Hazards of Depleted Uranium Munitions: Estimatesof Exposures and Risks in the Gulf War, the Balkans, and Iraq., Depleted Uranium: Properties, Uses, and Health Consequences, Editors: Miller, USA, Publisher: CRC Press, Pages: 121-141, ISBN: 9780849330476
Le Hello S, Currie BJ, Godoy D, et al., 2005, Melioidosis in New Caledonia, Emerging Infectious Diseases, Vol: 11, Pages: 1607-1609, ISSN: 1080-6059
Martin IMC, Ison CA, Aanensen DM, et al., 2005, Changing epidemiologic profile of quinolone-resistant <i>Neisseria gonorrhoeae</i> in London, JOURNAL OF INFECTIOUS DISEASES, Vol: 192, Pages: 1191-1195, ISSN: 1537-6613
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- Citations: 31
Palmer HM, Young H, Martin IMC, et al., 2005, The epidemiology of ciprofloxacin resistant isolates of <i>Neisseria gonorrhoeae</i> in Scotland 2002:: a comparison of phenotypic and genotypic analysis, SEXUALLY TRANSMITTED INFECTIONS, Vol: 81, Pages: 403-407, ISSN: 1368-4973
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- Citations: 22
Abbott JC, Aanensen DM, Rutherford K, et al., 2005, WebACT - an online companion for the artemis comparison tool, BIOINFORMATICS, Vol: 21, Pages: 3665-3666, ISSN: 1367-4803
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- Citations: 72
Gevers D, Cohan FM, Lawrence JG, et al., 2005, Re-evaluating prokaryotic species, NATURE REVIEWS MICROBIOLOGY, Vol: 3, Pages: 733-739, ISSN: 1740-1526
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- Citations: 767
Hanage WP, Kaijalainen T, Herva E, et al., 2005, Using multilocus sequence data to define the pneumococcus, JOURNAL OF BACTERIOLOGY, Vol: 187, Pages: 6223-6230, ISSN: 0021-9193
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- Citations: 80
Luan SL, Granlund M, Sellin M, et al., 2005, Multilocus sequence typing of Swedish invasive group B streptococcus isolates indicates a neonatally associated genetic lineage and capsule switching, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 43, Pages: 3727-3733, ISSN: 0095-1137
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- Citations: 138
Aanensen DM, Spratt BG, 2005, The multilocus sequence typing network: mlst.net, NUCLEIC ACIDS RES, Vol: 33, Pages: W728-W733, ISSN: 0305-1048
The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven housekeeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.
Spratt BG, Bailey MR, Beral V, et al., 2005, Report of the royal society working group on the health hazards of depleted uranium munitions, part II - chemical toxicity and environmental effects, ISBN: 9780854035748
McGregor KF, Spratt BG, 2005, Identity and prevalence of multilocus sequence typing-defined clones of group A streptococci within a hospital setting, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 43, Pages: 1963-1967, ISSN: 0095-1137
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- Citations: 22
Aanensen DM, Spratt BG, 2005, The multilocus sequence typing network: mlst.net, Nucleic Acids Research, Vol: 33, Pages: W728-W733, ISSN: 1362-4962
Hanage WP, Fraser C, Spratt BG, 2005, Fuzzy species among recombinogenic bacteria, BMC Biology, Vol: 3, ISSN: 1741-7007
Background: It is a matter of ongoing debate whether a universal species concept is possible forbacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discretegenotypic clusters that can be assigned as species. The most challenging test of whether species canbe clearly delineated is provided by analysis of large populations of closely-related, highlyrecombinogenic, bacteria that colonise the same body site. We have used concatenated sequencesof seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees,to investigate whether genotypic clusters can be resolved among these recombinogenic bacteriaand, if so, the extent to which they correspond to named species.Results: Alleles at individual loci were widely distributed among the named species but thisdistorting effect of recombination was largely buffered by using concatenated sequences, whichresolved clusters corresponding to the three species most numerous in the sample, N. meningitidis,N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidisfrom N. lactamica leading us to describe these species as 'fuzzy'.Conclusion: A multilocus approach using large samples of closely related isolates delineatesspecies even in the highly recombinogenic human Neisseria where individual loci are inadequate forthe task. This approach should be applied by taxonomists to large samples of other groups ofclosely-related bacteria, and especially to those where species delineation has historically beendifficult, to determine whether genotypic clusters can be delineated, and to guide the definition ofspecies.
Fraser C, Hanage WP, Spratt BG, 2005, Neutral microepidemic evolution of bacterial pathogens, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 102, Pages: 1968-1973, ISSN: 0027-8424
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- Citations: 102
Hanage WP, Kaijalainen TH, Syrjänen RK, et al., 2005, Invasiveness of serotypes and clones of <i>Streptococcus pneumoniae</i> among children in Finland, INFECTION AND IMMUNITY, Vol: 73, Pages: 431-435, ISSN: 0019-9567
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- Citations: 124
Porat N, Arguedas A, Spratt BG, et al., 2004, Emergence of penicillin-nonsusceptible <i>Streptococcus pneumoniae</i> clones expressing serotypes not present in the antipneumococcal conjugate vaccine, JOURNAL OF INFECTIOUS DISEASES, Vol: 190, Pages: 2154-2161, ISSN: 0022-1899
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- Citations: 72
Spratt BG, Hanage WP, Li B, et al., 2004, Displaying the relatedness among isolates of bacterial species - the eBURST approach, FEMS MICROBIOLOGY LETTERS, Vol: 241, Pages: 129-134, ISSN: 0378-1097
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- Citations: 162
Cheng AC, Godoy D, Mayo M, et al., 2004, Isolates of <i>Burkholderia pseudomallei</i> from northern Australia are distinct by multilocus sequence typing, but strain types do not correlate with clinical presentation, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 42, Pages: 5477-5483, ISSN: 0095-1137
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- Citations: 44
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