45 results found
Hanage WP, 2011, Charles Darwin in modern epidemiology and public health: the celebration continues, JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH, Vol: 65, Pages: 6-7, ISSN: 0143-005X
Regev-Yochay G, Hanage WP, Trzcinski K, et al., 2010, Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA, VACCINE, Vol: 28, Pages: 4842-4846, ISSN: 0264-410X
Hanage WP, Finkelstein JA, Huang SS, et al., 2010, Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete, EPIDEMICS, Vol: 2, Pages: 80-84, ISSN: 1755-4365
Hollingsworth TD, Laeyendecker O, Shirreff G, et al., 2010, HIV-1 Transmitting Couples Have Similar Viral Load Set-Points in Rakai, Uganda, PLOS PATHOGENS, Vol: 6, ISSN: 1553-7366
Hanage WP, 2010, The New Foundations of Evolution On the Tree of Life, SCIENCE, Vol: 327, Pages: 645-646, ISSN: 0036-8075
Tang J, Hanage WP, Fraser C, et al., 2009, Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach, PLOS COMPUTATIONAL BIOLOGY, Vol: 5
Lee GM, Huang SS, Rifas-Shiman SL, et al., 2009, Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era, BMC INFECTIOUS DISEASES, Vol: 9, ISSN: 1471-2334
Huang SS, Hinrichsen VL, Stevenson AE, et al., 2009, Continued Impact of Pneumococcal Conjugate Vaccine on Carriage in Young Children, PEDIATRICS, Vol: 124, Pages: E1-E11, ISSN: 0031-4005
Fraser C, Donnelly CA, Cauchemez S, et al., 2009, Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings, SCIENCE, Vol: 324, Pages: 1557-1561, ISSN: 0036-8075
Hanage WP, Fraser C, Tang J, et al., 2009, Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus, SCIENCE, Vol: 324, Pages: 1454-1457, ISSN: 0036-8075
Fraser C, Alm EJ, Polz MF, et al., 2009, The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity, SCIENCE, Vol: 323, Pages: 741-746, ISSN: 0036-8075
Bishop CJ, Aanensen DM, Jordan GE, et al., 2009, Assigning strains to bacterial species via the internet, BMC Biology, Vol: 7, ISSN: 1741-7007
BackgroundMethods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysis; MLSA) is that, for any group of related species, a strain database can be produced and combined with software that allows query strains to be assigned to species via the internet. As an exemplar of this approach, we have studied a group of species, the viridans streptococci, which are very difficult to assign to species using standard taxonomic procedures, and have developed a website that allows species assignment via the internet.ResultsSeven house-keeping gene sequences were obtained from 420 streptococcal strains to produce a viridans group database. The reference tree produced using the concatenated sequences identified sequence clusters which, by examining the position on the tree of the type strain of each viridans group species, could be equated with species clusters. MLSA also identified clusters that may correspond to new species, and previously described species whose status needs to be re-examined. A generic website and software for electronic taxonomy was developed. This site http://www.eMLSA.net allows the sequences of the seven gene fragments of a query strain to be entered and for the species assignment to be returned, according to its position within an assigned species cluster on the reference tree.ConclusionThe MLSA approach resulted in the identification of well-resolved species clusters within this taxonomically challenging group and, using the software we have developed, allows unknown strains to be assigned to viridans species via the internet. Submission of new strains will provide a growing resource for the taxonomy of viridans group streptococci, allowing the recognition of potential new species and taxonomic anomalies. M
Hanage WP, Aanensen DM, 2009, Methods for data analysis., Methods Mol Biol, Vol: 551, Pages: 287-304, ISSN: 1064-3745
The molecular epidemiology of infectious diseases uses a variety of techniques to assay the relatedness of disease-causing organisms to identify strains responsible for outbreaks or associated with particular phenotypes of interest (such as antibiotic resistance) and, it is hoped, provide insights into where and how these strains have emerged. The correct analysis of such data requires that we understand how the assayed variation accumulates. We discuss this with specific reference to three classes of methods: those based on gel electrophoresis of fragments generated by restriction enzymes or polymerase chain reaction (PCR), those based on microsatellites and other repeat elements, and raw sequence data from protein-coding genes. We also provide a simple example of how the likely origin of an apparently novel antibiotic-resistant strain may be identified and conclude with a discussion of some popular analysis packages and the more interesting prospects for the future in this rapidly developing field.
Hyams CJ, Opel S, Yuste J, et al., 2008, INVASIVE CAPSULAR SEROTYPES OF STREPTOCOCCUS PNEUMONIAE ARE RELATIVELY RESISTANT TO COMPLEMENT COMPARED WITH NON-INVASIVE SEROTYPES, Winter Meeting of the British-Thoracic-Society, Publisher: B M J PUBLISHING GROUP, Pages: A52-A52, ISSN: 0040-6376
Marttinen P, Baldwin A, Hanage WP, et al., 2008, Bayesian modeling of recombination events in bacterial populations, BMC BIOINFORMATICS, Vol: 9, ISSN: 1471-2105
Melin MM, Hollingshead SK, Briles DE, et al., 2008, Distribution of pneumococcal surface protein A families 1 and 2 among Streptococcus pneumoniae isolates from children in Finland who had acute otitis media or were nasopharyngeal carriers, CLINICAL AND VACCINE IMMUNOLOGY, Vol: 15, Pages: 1555-1563, ISSN: 1556-6811
Moschioni M, Donati C, Muzzi A, et al., 2008, Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related, JOURNAL OF INFECTIOUS DISEASES, Vol: 197, Pages: 888-896, ISSN: 0022-1899
Moschioni M, Donati C, Muzzi A, et al., 2008, Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related, Symposium on Novel Opportunities to Develop Vaccines to Control Antibiotic Resistant Bacteria: From the Trials Back to the Laboratory, Pages: 888-896
Background. Pilus components of Streptococcus pneumoniae encoded by rlrA were recently shown to elicit protection in an animal model of infection. Limited data are available on the prevalence of the rlrA operon in pneumococci; therefore, we investigated its distribution and its antigenic variation among disease-causing strains.Methods. The prevalence of rlrA and its association with serotype and genotype were evaluated in a global panel of 424 pneumococci isolates (including the 26 drug-resistant clones described by the Pneumococcal Molecular Epidemiology Network).Results. The rlrA islet was found in 130 isolates (30.6%) of the defined collection. Sequence alignment of 15 rlrA islets defined the presence of 3 clade types, with an overall homology of 88%-92%. The presence or absence of a pilus-encoding operon correlated with S. pneumoniae genotype (P < .001), as determined by multilocus sequence typing, and not with serotype. Further investigation identified a positive trend of rlrA occurrence among antimicrobial-resistant pneumococci.Conclusions. On the basis of S. pneumoniae genotype, it is possible to predict the incidence of the rlrA pilus operon in a collection of pneumococcal isolates. This will facilitate the development of a protein vaccine.
Hanage WP, 2008, Serotype-specific problems associated with pneumococcal conjugate vaccination, FUTURE MICROBIOLOGY, Vol: 3, Pages: 23-30, ISSN: 1746-0913
Hanage WP, 2007, Serotype replacement in invasive pneumococcal disease: Where do we go from here?, JOURNAL OF INFECTIOUS DISEASES, Vol: 196, Pages: 1282-1284, ISSN: 0022-1899
Pelton SI, Huot H, Finkelstein AA, et al., 2007, Emergence of 19A as virulent and multidrug resistant pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine, PEDIATRIC INFECTIOUS DISEASE JOURNAL, Vol: 26, Pages: 468-472, ISSN: 0891-3668
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.
Hanage WP, Huang SS, Lipsitch M, et al., 2007, Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era, JOURNAL OF INFECTIOUS DISEASES, Vol: 195, Pages: 347-352, ISSN: 0022-1899
Fraser C, Hanage WP, Spratt BG, 2007, Recombination and the nature of bacterial speciation, Science, Vol: 315, Pages: 476-480, ISSN: 0036-8075
Fraser C, Hollingsworth D, Chapman D, et al., 2007, Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis., Proc Natl Acad Sci USA, Vol: In press
Spratt BG, Fraser C, Hanage WP, 2007, Exploring genetic relatedness, patterns of evolutionary descent, and the population genetics of bacterial pathogens using multilocus sequence typing, Encyclopedia of Infectious Diseases: Modern Methodologies, Editors: Tibayrenc, Publisher: Wiley, ISBN: 978-0-471-65732-3
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.
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
Porat N, Greenberg D, Givon-Lavi N, et al., 2006, The important role of nontypable Streptococcus pneumoniae international clones in acute conjunctivitis, JOURNAL OF INFECTIOUS DISEASES, Vol: 194, Pages: 689-696, ISSN: 0022-1899
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