David M Aanensen

Publications of David M Aanensen

• Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus.

  Authors: Paul R McAdam, Kate E Templeton, Giles F Edwards, Matthew T G Holden, Edward J Feil, David M Aanensen, Hiba J A Bargawi, Brian G Spratt, Stephen D Bentley, Julian Parkhill, Mark C Enright, Anne Holmes, E Kirsty Girvan, Paul A Godfrey, Michael Feldgarden, Angela M Kearns, Andrew Rambaut, D Ashley Robinson, J Ross Fitzgerald

  Proceedings of the National Academy of Sciences of the United States of America. 05/2012;

  Hospital-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a global health burden dominated by a small number of bacterial clones. The pandemic EMRSA-16 cloneHospital-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a global health burden dominated by a small number of bacterial clones. The pandemic EMRSA-16 clone (ST36-II) has been widespread in UK hospitals for 20 y, but its evolutionary origin and the molecular basis for its hospital association are unclear. We carried out a Bayesian phylogenetic reconstruction on the basis of the genome sequences of 87 S. aureus isolates including 60 EMRSA-16 and 27 additional clonal complex 30 (CC30) isolates, collected from patients in three continents over a 53-y period. The three major pandemic clones to originate from the CC30 lineage, including phage type 80/81, Southwest Pacific, and EMRSA-16, shared a most recent common ancestor that existed over 100 y ago, whereas the hospital-associated EMRSA-16 clone is estimated to have emerged about 35 y ago. Our CC30 genome-wide analysis revealed striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements and nonsynonymous mutations affecting antibiotic resistance and virulence. Importantly, phylogeographic analysis indicates that EMRSA-16 spread within the United Kingdom by transmission from hospitals in large population centers in London and Glasgow to regional health-care settings, implicating patient referrals as an important cause of nationwide transmission. Taken together, the high-resolution phylogenomic approach used resulted in a unique understanding of the emergence and transmission of a major MRSA clone and provided molecular correlates of its hospital adaptation. Similar approaches for hospital-associated clones of other bacterial pathogens may inform appropriate measures for controlling their intra- and interhospital spread.

• Comparison of two multilocus sequence based genotyping schemes for Leptospira species.

  Authors: Ahmed Ahmed, Janjira Thaipadungpanit, Siriphan Boonsilp, Vanaporn Wuthiekanun, Kishore Nalam, Brian G Spratt, David M Aanensen, Lee D Smythe, Niyaz Ahmed, Edward J Feil, Rudy A Hartskeerl, Sharon J Peacock

  PLoS neglected tropical diseases. 11/2011; 5(11):e1374.

  Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two mostSeveral sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results. A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence) was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5-96.5) vs. 93.5 (95% CI 88.6-98.4). The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L. This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages.

• Low diversity Cryptococcus neoformans variety grubii multilocus sequence types from Thailand are consistent with an ancestral African origin.

  Authors: Sitali P Simwami, Kantarawee Khayhan, Daniel A Henk, David M Aanensen, Teun Boekhout, Ferry Hagen, Annemarie E Brouwer, Thomas S Harrison, Christl A Donnelly, Matthew C Fisher

  PLoS pathogens. 04/2011; 7(4):e1001343.

  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 theThe 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). Further high-density sampling of global Cng STs is now necessary to resolve the temporal sequence underlying the global emergence of this human pathogen.

• Multilocus sequence typing of Bartonella henselae in the United Kingdom indicates that only a few, uncommon sequence types are associated with zoonotic disease.

  Authors: Gemma L Chaloner, Timothy G Harrison, Karen P Coyne, David M Aanensen, Richard J Birtles

  Journal of clinical microbiology. 04/2011; 49(6):2132-7.

  Bartonella henselae is one of the most common zoonotic agents acquired from companion animals (cats) in industrialized countries. Nonetheless, although the prevalence of infections in cats is high,Bartonella henselae is one of the most common zoonotic agents acquired from companion animals (cats) in industrialized countries. Nonetheless, although the prevalence of infections in cats is high, the number of human cases reported is relatively low. One hypothesis for this discrepancy is that B. henselae strains vary in their zoonotic potential. To test this hypothesis, we employed structured sampling to explore the population structure of B. henselae in the United Kingdom and to determine the distribution of strains associated with zoonotic disease within this structure. A total of 118 B. henselae strains were delineated into 12 sequence types (STs) using multilocus sequence typing. We observed that most (85%) of the zoonosis-associated strains belonged to only three genotypes, i.e., ST2, ST5, and ST8. Conversely, most (74%) of the feline isolates belonged to ST4, ST6, and ST7. The difference in host association of ST2, ST5, and ST8 (zoonosis associated) and ST6 (feline) was statistically significant (P < 0.05), indicating that a few, uncommon STs were responsible for the majority of symptomatic human infections.

• Host migration impacts on the phylogeography of Lyme Borreliosis spirochaete species in Europe.

  Authors: Stephanie A Vollmer, Antra Bormane, Ruth E Dinnis, Frederik Seelig, Andrew D M Dobson, David M Aanensen, Marianne C James, Michael Donaghy, Sarah E Randolph, Edward J Feil, Klaus Kurtenbach, Gabriele Margos

  Environmental microbiology. 01/2011; 13(1):184-92.

  The geographic patterns of transmission opportunities of vector-borne zoonoses are determined by a complex interplay between the migration patterns of the host and the vector. Here we examine theThe geographic patterns of transmission opportunities of vector-borne zoonoses are determined by a complex interplay between the migration patterns of the host and the vector. Here we examine the impact of host migration on the spread of a tick-borne zoonotic disease, using Lyme Borreliosis (LB) spirochaetal species in Europe. We demonstrate that the migration of the LB species is dependent on and limited by the migration of their respective hosts. We note that populations of Borrelia spp. associated with birds (Borrelia garinii and B. valaisiana) show limited geographic structuring between countries compared with those associated with small mammals (Borrelia afzelii), and we argue that this can be explained by higher rates of migration in avian hosts. We also show the presence of B. afzelii strains in England and, through the use of the multi-locus sequence analysis scheme, reveal that the strains are highly structured. This pattern in English sites is very different from that observed at the continental sites, and we propose that these may be recent introductions.

• Bayesian semi-supervised classification of bacterial samples using MLST databases.

  Authors: Lu Cheng, Thomas R Connor, David M Aanensen, Brian G Spratt, Jukka Corander

  BMC bioinformatics. 01/2011; 12:302.

  Worldwide effort on sampling and characterization of molecular variation within a large number of human and animal pathogens has lead to the emergence of multi-locus sequence typing (MLST) databasesWorldwide effort on sampling and characterization of molecular variation within a large number of human and animal pathogens has lead to the emergence of multi-locus sequence typing (MLST) databases as an important tool for studying the epidemiology and evolution of pathogens. Many of these databases are currently harboring several thousands of multi-locus DNA sequence types (STs) enriched with metadata over traits such as serotype, antibiotic resistance, host organism etc of the isolates. Curators of the databases have thus the possibility of dividing the pathogen populations into subsets representing different evolutionary lineages, geographically associated groups, or other subpopulations, which are defined in terms of molecular similarities and dissimilarities residing within a database. When combined with the existing metadata, such subsets may provide invaluable information for assessing the position of a new set of isolates in relation to the whole pathogen population. To enable users of MLST schemes to query the databases with sets of new bacterial isolates and to automatically analyze their relation to existing curated sequences, we introduce here a Bayesian model-based method for semi-supervised classification of MLST data. Our method can use an MLST database as a training set and assign simultaneously any set of query sequences into the earlier discovered lineages/populations, while also allowing some or all of these sequences to form previously undiscovered genetically distinct groups. This tool provides probabilistic quantification of the classification uncertainty and is highly efficient computationally, thus enabling rapid analyses of large databases and sets of query sequences. The latter feature is a necessary prerequisite for an automated access through the MLST web interface. We demonstrate the versatility of our approach by anayzing both real and synthesized data from MLST databases. The introduced method for semi-supervised classification of sets of query STs is freely available for Windows, Mac OS X and Linux operative systems in BAPS 5.4 software which is downloadable at http://web.abo.fi/fak/mnf/mate/jc/software/baps.html. The query functionality is also directly available for the Staphylococcus aureus database at http://www.mlst.net and shortly will be available for other species databases hosted at this web portal. We have introduced a model-based tool for automated semi-supervised classification of new pathogen samples that can be integrated into the web interface of the MLST databases. In particular, when combined with the existing metadata, the semi-supervised labeling may provide invaluable information for assessing the position of a new set of query strains in relation to the particular pathogen population represented by the curated database.Such information will be useful both for clinical and basic research purposes.

• Multilocus sequence analysis of Borrelia bissettii strains from North America reveals a new Borrelia species, Borrelia kurtenbachii.

  Authors: Gabriele Margos, Andrias Hojgaard, Robert S Lane, Muriel Cornet, Volker Fingerle, Nataliia Rudenko, Nicholas Ogden, David M Aanensen, Durland Fish, Joseph Piesman

  Ticks and tick-borne diseases. 12/2010; 1(4):151-8.

  Using multilocus sequence analyses (MLSA), we investigated the phylogenetic relationship of spirochaete strains from North America previously assigned to the genospecies Borrelia bissettii. WeUsing multilocus sequence analyses (MLSA), we investigated the phylogenetic relationship of spirochaete strains from North America previously assigned to the genospecies Borrelia bissettii. We amplified internal fragments of 8 housekeeping genes (clpA, clpX, nifS, pepX, pyrG, recG, rplB, and uvrA) located on the main linear chromosome by polymerase chain reaction. Phylogenetic analysis of concatenated sequences of the 8 loci showed that the B. bissettii clade consisted of 4 closely related clusters which included strains from California (including the type strain DN127-Cl9-2/p7) and Colorado that were isolated from Ixodes pacificus, I. spinipalpis, or infected reservoir hosts. Several strains isolated from I. scapularis clustered distantly from B. bissettii. Genetic distance analyses confirmed that these strains are more distant to B. bissettii than they are to B. carolinensis, a recently described Borrelia species, which suggests that they constitute a new Borrelia genospecies. We propose that it be named Borrelia kurtenbachii sp. nov. in honour of the late Klaus Kurtenbach. The data suggest that ecological differences between B. bissettii and the new Borrelia genospecies reflect different transmission cycles. In view of these findings, the distinct vertebrate host-tick vector associations and the distributions of B. bissettii and B. kurtenbachii require further investigation.

• Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

  Authors: Hajo Grundmann, David M Aanensen, Cees C van den Wijngaard, Brian G Spratt, Dag Harmsen, Alexander W Friedrich

  PLoS medicine. 01/2010; 7(1):e1000215.

  Staphylococcus 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 theStaphylococcus 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. In 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. In 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 clones within health care networks, suggesting that control efforts aimed at interrupting the spread within and between health care institutions may not only be feasible but ultimately successful and should therefore be strongly encouraged.

• Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens.

  Authors: Matthew T G Holden, Zoe Heather, Romain Paillot, Karen F Steward, Katy Webb, Fern Ainslie, Thibaud Jourdan, Nathalie C Bason, Nancy E Holroyd, Karen Mungall [......] Brian G Spratt, Keith A Jolley, Martin C J Maiden, Michael Kehoe, Neil Chanter, Stephen D Bentley, Carl Robinson, Duncan J Maskell, Julian Parkhill, Andrew S Waller

  PLoS pathogens. 04/2009; 5(3):e1000346.

  The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered.The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange 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 subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.

• EpiCollect: linking smartphones to web applications for epidemiology, ecology and community data collection.

  Authors: David M Aanensen, Derek M Huntley, Edward J Feil, Fada'a al-Own, Brian G Spratt

  PloS one. 01/2009; 4(9):e6968.

  BACKGROUND: Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction ofBACKGROUND: Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases. METHODOLOGY: Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field 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 are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting 'citizen scientists' to contribute data easily to central databases through their mobile phone.

• MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi.

  Authors: Gabriele Margos, Anne G Gatewood, David M Aanensen, Klára Hanincová, Darya Terekhova, Stephanie A Vollmer, Muriel Cornet, Joseph Piesman, Michael Donaghy, Antra Bormane, Merrilee A Hurn, Edward J Feil, Durland Fish, Sherwood Casjens, Gary P Wormser, Ira Schwartz, Klaus Kurtenbach

  Proceedings of the National Academy of Sciences of the United States of America. 07/2008; 105(25):8730-5.

  Lyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become the most common vector-borne disease in North America over the last three decades. To understand the dynamics ofLyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become the most common vector-borne disease in North America over the last three decades. To understand the dynamics of the epizootic spread and to predict the evolutionary trajectories of B. burgdorferi, accurate information on the population structure and the evolutionary relationships of the pathogen is crucial. We, therefore, developed a multilocus sequence typing (MLST) scheme for B. burgdorferi based on eight chromosomal housekeeping genes. We validated the MLST scheme on B. burgdorferi specimens from North America and Europe, comprising both cultured isolates and infected ticks. These data were compared with sequences for the commonly used genetic markers rrs-rrlA intergenic spacer (IGS) and the gene encoding the outer surface protein C (ospC). The study demonstrates that the concatenated sequences of the housekeeping genes of B. burgdorferi provide highly resolved phylogenetic signals and that the housekeeping genes evolve differently compared with the IGS locus and ospC. Using sequence data, the study reveals that North American and European populations of B. burgdorferi correspond to genetically distinct populations. Importantly, the MLST data suggest that B. burgdorferi originated in Europe rather than in North America as proposed previously.

• Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci.

  Authors: David M Aanensen, Angeliki Mavroidi, Stephen D Bentley, Peter R Reeves, Brian G Spratt

  Journal of bacteriology. 12/2007; 189(21):7856-76.

  The sequences of the capsular biosynthetic (cps) loci of 90 serotypes of Streptococcus pneumoniae have recently been determined. Bioinformatic procedures were used to predict the general functions ofThe sequences of the capsular biosynthetic (cps) loci of 90 serotypes of Streptococcus pneumoniae have recently been determined. Bioinformatic procedures were used to predict the general functions of 1,973 of the 1,999 gene products and to identify proteins within the same homology group, Pfam family, and CAZy glycosyltransferase family. Correlating cps gene content with the 54 known capsular polysaccharide (CPS) structures provided tentative assignments of the specific functions of the different homology groups of each functional class (regulatory proteins, enzymes for synthesis of CPS constituents, polymerases, flippases, initial sugar transferases, glycosyltransferases [GTs], phosphotransferases, acetyltransferases, and pyruvyltransferases). Assignment of the glycosidic linkages catalyzed by the 342 GTs (92 homology groups) is problematic, but tentative assignments could be made by using this large set of cps loci and CPS structures to correlate the presence of particular GTs with specific glycosidic linkages, by correlating inverting or retaining linkages in CPS repeat units with the inverting or retaining mechanisms of the GTs predicted from their CAZy family membership, and by comparing the CPS structures of serotypes that have very similar cps gene contents. These large-scale comparisons between structure and gene content assigned the linkages catalyzed by 72% of the GTs, and all linkages were assigned in 32 of the serotypes with known repeat unit structures. Clear examples where very similar initial sugar transferases or glycosyltransferases catalyze different linkages in different serotypes were also identified. These assignments should provide a stimulus for biochemical studies to evaluate the reactions that are proposed.

• Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci.

  Authors: Angeliki Mavroidi, David M Aanensen, Daniel Godoy, Ian C Skovsted, Margit S Kaltoft, Peter R Reeves, Stephen D Bentley, Brian G Spratt

  Journal of bacteriology. 12/2007; 189(21):7841-55.

  Streptococcus pneumoniae (the pneumococcus) produces 1 of 91 capsular polysaccharides (CPS) that define the serotype. The cps loci of 88 pneumococcal serotypes whose CPS is synthesized by theStreptococcus pneumoniae (the pneumococcus) produces 1 of 91 capsular polysaccharides (CPS) that define the serotype. The cps loci of 88 pneumococcal serotypes whose CPS is synthesized by the Wzy-dependent pathway were compared with each other and with additional streptococcal polysaccharide biosynthetic loci and were clustered according to the proportion of shared homology groups (HGs), weighted for the sequence similarities between the genes encoding the shared HGs. The cps loci of the 88 pneumococcal serotypes were distributed into eight major clusters and 21 subclusters. All serotypes within the same serogroup fell into the same major cluster, but in six cases, serotypes within the same serogroup were in different subclusters and, conversely, nine subclusters included completely different serotypes. The closely related cps loci within a subcluster were compared to the known CPS structures to relate gene content to structure. The Streptococcus oralis and Streptococcus mitis polysaccharide biosynthetic loci clustered within the pneumococcal cps loci and were in a subcluster that also included the cps locus of pneumococcal serotype 21, whereas the Streptococcus agalactiae cps loci formed a single cluster that was not closely related to any of the pneumococcal cps clusters.

• WebACT: an online genome comparison suite.

  Authors: James C Abbott, David M Aanensen, Stephen D Bentley

  Methods in molecular biology (Clifton, N.J.). 02/2007; 395:57-74.

  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 includingComparison 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.

• Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes.

  Authors: Stephen D Bentley, David M Aanensen, Angeliki Mavroidi, David Saunders, Ester Rabbinowitsch, Matthew Collins, Kathy Donohoe, David Harris, Lee Murphy, Michael A Quail, Gabby Samuel, Ian C Skovsted, Margit Staum Kaltoft, Bart Barrell, Peter R Reeves, Julian Parkhill, Brian G Spratt

  PLoS genetics. 04/2006; 2(3):e31.

  Several major invasive bacterial pathogens are encapsulated. Expression of a polysaccharide capsule is essential for survival in the blood, and thus for virulence, but also is a target for hostSeveral major invasive bacterial pathogens are encapsulated. Expression of a polysaccharide capsule is essential for survival 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 distinct capsular 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, to our 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 this one locus exceeds 1.8 Mbp, almost equivalent to the entire S. pneumoniae chromosomal complement.

• Changing epidemiologic profile of quinolone-resistant Neisseria gonorrhoeae in London.

  Authors: Iona M C Martin, Catherine A Ison, David M Aanensen, Kevin A Fenton, Brian G Spratt

  The Journal of infectious diseases. 11/2005; 192(7):1191-5.

  The percentage of quinolone-resistant Neisseria gonorrhoeae isolated in London increased between 2000 and 2003, from 0.9% to 7.9% of total isolates. This increase was investigated by genotypingThe percentage of quinolone-resistant Neisseria gonorrhoeae isolated in London increased between 2000 and 2003, from 0.9% to 7.9% of total isolates. This increase was investigated by genotyping resistant isolates and comparing demographic and behavioral data. In 2000, resistant isolates predominantly had unique sequence types (STs) that were associated with imported infection, whereas, in 2002 and 2003, large ST clusters of indistinguishable isolates were associated with endemic acquisition. Resistant isolates that belonged to these large clusters were typically from patients who had similar epidemiological characteristics (such as ethnicity and sexual orientation) and behavioral characteristics (such as multiple sex partners and previous gonorrhea). In London, quinolone resistance is no longer associated with importation from areas of high prevalence and is spreading endemically in high-risk groups.

• The multilocus sequence typing network: mlst.net.

  Authors: David M Aanensen, Brian G Spratt

  Nucleic acids research. 08/2005; 33(Web Server issue):W728-33.

  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),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 house-keeping 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.

• Displaying the relatedness among isolates of bacterial species -- the eBURST approach.

  Authors: Brian G Spratt, William P Hanage, Bao Li, David M Aanensen, Edward J Feil

  FEMS microbiology letters. 01/2005; 241(2):129-34.

  Determining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species. In many cases, a bifurcating treeDetermining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species. In many cases, a bifurcating tree can be positively misleading. The recently described program eBURST can be used with multilocus data to define groups or clonal complexes of related isolates derived from a common ancestor, the patterns of descent linking them together, and the ancestral genotype. eBURST has recently been extensively updated to include additional tools for exploring the relationships between isolates. We discuss the advantages of this approach and describe its use to explore patterns of descent within clonal complexes identified using multilocus sequence typing.

• Evolutionary genetics of the capsular locus of serogroup 6 pneumococci.

  Authors: Angeliki Mavroidi, Daniel Godoy, David M Aanensen, D Ashley Robinson, Susan K Hollingshead, Brian G Spratt

  Journal of bacteriology. 01/2005; 186(24):8181-92.

  The evolution of the capsular biosynthetic (cps) locus of serogroup 6 Streptococcus pneumoniae was investigated by analyzing sequence variation within three serotype-specific cps genes from 102The evolution of the capsular biosynthetic (cps) locus of serogroup 6 Streptococcus pneumoniae was investigated by analyzing sequence variation within three serotype-specific cps genes from 102 serotype 6A and 6B isolates. Sequence variation within these cps genes was related to the genetic relatedness of the isolates, determined by multilocus sequence typing, and to the inferred patterns of recent evolutionary descent, explored using the eBURST algorithm. The serotype-specific cps genes had a low percent G+C, and there was a low level of sequence diversity in this region among serotype 6A and 6B isolates. There was also little sequence divergence between these serotypes, suggesting a single introduction of an ancestral cps sequence, followed by slight divergence to create serotypes 6A and 6B. A minority of serotype 6B isolates had cps sequences (class 2 sequences) that were approximately 5% divergent from those of other serotype 6B isolates (class 1 sequences) and which may have arisen by a second, more recent introduction from a related but distinct source. Expression of a serotype 6A or 6B capsule correlated perfectly with a single nonsynonymous polymorphism within wciP, the rhamnosyl transferase gene. In addition to ample evidence of the horizontal transfer of the serotype 6A and 6B cps locus into unrelated lineages, there was evidence for relatively frequent changes from serotype 6A to 6B, and vice versa, among very closely related isolates and examples of recent recombinational events between class 1 and 2 cps serogroup 6 sequences.

• WebACT - an online companion for the Artemis Comparison Tool.

  Authors: J. C. Abbott, David M. Aanensen, Kim Rutherford, S. Butcher, Brian G. Spratt

  Bioinformatics. 01/2005; 21:3665-3666.