Publications
60 results found
Cheng L, Connor TR, Aanensen DM, et al., 2011, Bayesian semi-supervised classification of bacterial samples using MLST databases, BMC Bioinformatics, Vol: 12, ISSN: 1471-2105
Background: Worldwide effort on sampling and characterization of molecular variation within a large number ofhuman and animal pathogens has lead to the emergence of multi-locus sequence typing (MLST) databases as animportant tool for studying the epidemiology and evolution of pathogens. Many of these databases are currentlyharboring several thousands of multi-locus DNA sequence types (STs) enriched with metadata over traits such asserotype, antibiotic resistance, host organism etc of the isolates. Curators of the databases have thus the possibilityof dividing the pathogen populations into subsets representing different evolutionary lineages, geographicallyassociated groups, or other subpopulations, which are defined in terms of molecular similarities and dissimilaritiesresiding within a database. When combined with the existing metadata, such subsets may provide invaluableinformation for assessing the position of a new set of isolates in relation to the whole pathogen population.Results: To enable users of MLST schemes to query the databases with sets of new bacterial isolates and toautomatically analyze their relation to existing curated sequences, we introduce here a Bayesian model-based methodfor semi-supervised classification of MLST data. Our method can use an MLST database as a training set and assignsimultaneously any set of query sequences into the earlier discovered lineages/populations, while also allowing some orall of these sequences to form previously undiscovered genetically distinct groups. This tool provides probabilisticquantification of the classification uncertainty and is highly efficient computationally, thus enabling rapid analyses oflarge databases and sets of query sequences. The latter feature is a necessary prerequisite for an automated accessthrough the MLST web interface. We demonstrate the versatility of our approach by anayzing both real and synthesizeddata from MLST databases. The introduced method for semi-supervised classification of
Chaloner GL, Harrison TG, Coyne KP, et al., 2011, Multilocus Sequence Typing of <i>Bartonella</i> <i>henselae</i> in the United Kingdom Indicates that Only a Few, Uncommon Sequence Types Are Associated with Zoonotic Disease, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 49, Pages: 2132-2137, ISSN: 0095-1137
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- Citations: 17
Ogden NH, Margos G, Aanensen DM, et al., 2011, Investigation of Genotypes of <i>Borrelia burgdorferi</i> in <i>Ixodes scapularis</i> Ticks Collected during Surveillance in Canada, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 77, Pages: 3244-3254, ISSN: 0099-2240
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- Citations: 74
Vollmer SA, Bormane A, Dinnis RE, et al., 2011, Host migration impacts on the phylogeography of Lyme Borreliosis spirochaete species in Europe, ENVIRONMENTAL MICROBIOLOGY, Vol: 13, Pages: 184-192, ISSN: 1462-2912
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- Citations: 89
Simwami SP, Khayhan K, Henk DA, et al., 2011, Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin, Plos Pathog, Vol: 7, ISSN: 1553-7366
The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year, causing up to a third of all AIDS-related deaths. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly-virulent emerging lineages are changing patterns of human disease both temporally and spatially. Cryptococcus neoformans variety grubii (Cng, serotype A) constitutes the most ubiquitous cause of cryptococcal meningitis worldwide, however patterns of molecular diversity are understudied across some regions experiencing significant burdens of disease. We compared 183 clinical and environmental isolates of Cng from one such region, Thailand, Southeast Asia, against a global MLST database of 77 Cng isolates. Population genetic analyses showed that Thailand isolates from 11 provinces were highly homogenous, consisting of the same genetic background (globally known as VNI) and exhibiting only ten nearly identical sequence types (STs), with three (STs 44, 45 and 46) dominating our sample. This population contains significantly less diversity when compared against the global population of Cng, specifically Africa. Genetic diversity in Cng was significantly subdivided at the continental level with nearly half (47%) of the global STs unique to a genetically diverse and recombining population in Botswana. These patterns of diversity, when combined with evidence from haplotypic networks and coalescent analyses of global populations, are highly suggestive of an expansion of the Cng VNI clade out of Africa, leading to a limited number of genotypes founding the Asian populations. Divergence time testing estimates the time to the most common ancestor between the African and Asian populations to be 6,920 years ago (95% HPD 122.96 - 27,177.76
Grundmann H, Aanensen DM, van den Wijngaard CC, et al., 2010, Geographic distribution of staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis, PLOS Medicine, Vol: 7, ISSN: 1549-1277
BackgroundStaphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe.Methods and FindingsIn each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA) and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing), and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel.ConclusionsIn contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clo
Margos G, Hojgaard A, Lane RS, et al., 2010, Multilocus sequence analysis of <i>Borrelia bissettii</i> strains from North America reveals a new <i>Borrelia</i> species, <i>Borrelia kurtenbachii</i>, TICKS AND TICK-BORNE DISEASES, Vol: 1, Pages: 151-158, ISSN: 1877-959X
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- Citations: 83
Aanensen DM, Huntley DM, Feil EJ, et al., 2009, EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection, PLOS One, Vol: 4, ISSN: 1932-6203
Background:Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter theirdata into a database for further analysis. The recent introduction of mobile phones that utilise the open source Androidoperating system, and which include (among other features) both GPS and Google Maps, provide new opportunities fordeveloping mobile phone applications, which in conjunction with web applications, allow two-way communicationbetween field workers and their project databases.Methodology:Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a webapplication located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted byphone, together with GPS data, to a common web database and can be displayed and analysed, along with previouslycollected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayedon the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individualfield workers or, for example, those data within certain values of a measured variable or a time period.Conclusions:Data collection frameworks utilising mobile phones with data submission to and from central databases arewidely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would haveif viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection anddisplay, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworksoffer great potential for recruiting ‘citizen scientists’ to contribute data easily to central databases through their mobilephone.
Holden MTG, Heather Z, Paillot R, et al., 2009, Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens, PLOS Pathogens, Vol: 5, ISSN: 1553-7366
The continued evolution of bacterial pathogens has major implications for both human and animal disease, but theexchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S.equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecieszooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the importanthuman pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicusH70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events thathave shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysisprovides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through theacquisition of bacteriophage encoding a phospholipase A2 toxin, and four superantigens, and an integrative conjugativeelement carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We alsohighlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogenevolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchangebetween S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.
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, MOLECULAR EPIDEMIOLOGY OF MICROORGANISMS, Vol: 551, Pages: 287-304, ISSN: 1064-3745
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- Citations: 4
Meyer W, Aanensen DM, Boekhout T, et al., 2009, Consensus multi-locus sequence typing scheme for <i>Cryptococcus neoformans</i> and <i>Cryptococcus gattii</i>, MEDICAL MYCOLOGY, Vol: 47, Pages: 561-570, ISSN: 1369-3786
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- Citations: 355
Margos G, Gatewood AG, Aanensen DM, et al., 2008, MLST of housekeeping genes captures geographic population structure and suggests a European origin of <i>Borrelia burgdorferi</i>, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 8730-8735, ISSN: 0027-8424
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- Citations: 233
Pryce-Miller E, Aanensen D, Vanittanakom N, et al., 2008, Environmental detection of <i>Penicillium marneffei</i> and growth in soil microcosms in competition with <i>Talaromyces stipitatus</i>, FUNGAL ECOLOGY, Vol: 1, Pages: 49-56, ISSN: 1754-5048
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- Citations: 9
Mavroidi A, Aanensen DM, Godoy D, et al., 2007, Genetic relatedness of the <i>Streptococcus pneumoniae</i> capsular Biosynthetic loci, JOURNAL OF BACTERIOLOGY, Vol: 189, Pages: 7841-7855, ISSN: 0021-9193
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- Citations: 99
Aanensen DM, Mavroldi A, Bentley SD, et al., 2007, Predicted functions and linkage Specificities of the products of the <i>Streptococcus pneumoniae</i> capsular biosynthetic loci, JOURNAL OF BACTERIOLOGY, Vol: 189, Pages: 7856-7876, ISSN: 0021-9193
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- Citations: 98
Abbott JC, Aanensen DM, Bentley SD, 2007, Methods in Molecular Biology - Comparative Genomics - WebACT: An Online Genome Comparison Suite, Publisher: Humana Press, ISBN: 978-1-58829-693-1
Abbott JC, Aanensen DM, Bentley SD, 2007, WebACT: an online genome comparison suite., Methods Mol Biol, Vol: 395, Pages: 57-74, ISSN: 1064-3745
Comparison of related genomes is an enormously powerful technique for explaining phenotypic differences and revealing recent evolutionary events. Genomes evolve through a host of mechanisms including long- and short-range intragenomic rearrangements, insertion of laterally acquired DNA, gene loss, and single-nucleotide polymorphisms. The Artemis Comparison Tool (ACT) was developed to enable the intuitive visualization of the consequences of such events in the context of two or more aligned genomes. WebACT is an online resource designed to allow the alignment of up to five genomic sequences within the ACT environment without the need for local software installation. Comparisons can be carried out between uploaded sequences, or those selected from the EMBL or RefSeq databases, using BLASTZ, MUMmer, or Basic Local Alignment Search Tool (BLAST). Precomputed comparisons can be selected from a database covering all the completed bacterial chromosome and plasmid sequences in the Genome Reviews database (1). This allows the rapid visualization of regions of interest, without the need to handle the full genome sequences. Here, we describe the process of using WebACT to prepare comparisons for visualization, and the selection of precomputed comparisons from the database. The use of ACT to view the selected comparison is then explored using examples from bacterial genomes.
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.
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
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
Aanensen DM, Spratt BG, 2005, The multilocus sequence typing network: mlst.net, Nucleic Acids Research, Vol: 33, Pages: W728-W733, ISSN: 1362-4962
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
Mavroidi A, Godoy D, Aanensen DM, et al., 2004, Evolutionary genetics of the capsular locus of serogroup 6 pneumococci, JOURNAL OF BACTERIOLOGY, Vol: 186, Pages: 8181-8192, ISSN: 0021-9193
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- Citations: 86
Fisher MC, Aanensen D, de Hoog S, et al., 2004, Multilocus microsatellite typing system for <i>Penicillium marneffei</i> reveals spatially structured populations, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 42, Pages: 5065-5069, ISSN: 0095-1137
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- Citations: 40
Bougnoux M-E, Aanensen DM, Morand S, et al., 2004, Multilocus sequence typing of <i>Candida albicans</i>: strategies, data exchange and applications, INFECTION GENETICS AND EVOLUTION, Vol: 4, Pages: 243-252, ISSN: 1567-1348
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- Citations: 79
Martin IMC, Ison CA, Aanensen DM, et al., 2004, Rapid sequence-based identification of gonococcal transmission clusters in a large metropolitan area, JOURNAL OF INFECTIOUS DISEASES, Vol: 189, Pages: 1497-1505, ISSN: 1537-6613
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- Citations: 303
Feil EJ, Li BC, Aanensen DM, et al., 2004, eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data, JOURNAL OF BACTERIOLOGY, Vol: 186, Pages: 1518-1530, ISSN: 0021-9193
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- Citations: 1477
Godoy D, Randle G, Simpson AJ, et al., 2003, Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, <i>Burkholderia pseudomallei</i> and <i>Burkholdefia mallei</i> (vol 41, pg 2068, 2003), JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 41, Pages: 4913-4913, ISSN: 0095-1137
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- Citations: 6
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