Publications
288 results found
Hyams C, Opel S, Hanage W, et al., 2011, Effects of Streptococcus pneumoniae Strain Background on Complement Resistance, PLOS One, Vol: 6, ISSN: 1932-6203
Background: Immunity to infections caused by Streptococcus pneumoniae is dependent on complement. There are widevariations in sensitivity to complement between S. pneumoniae strains that could affect their ability to cause invasiveinfections. Although capsular serotype is one important factor causing differences in complement resistance betweenstrains, there is also considerable other genetic variation between S. pneumoniae strains that may affect complementmediatedimmunity. We have therefore investigated whether genetically distinct S. pneumoniae strains with the samecapsular serotype vary in their sensitivity to complement mediated immunity.Methodology and Principal Findings: C3b/iC3b deposition and neutrophil association were measured using flowcytometry assays for S. pneumoniae strains with different genetic backgrounds for each of eight capsular serotypes. Forsome capsular serotypes there was marked variation in C3b/iC3b deposition between different strains that wasindependent of capsule thickness and correlated closely to susceptibility to neutrophil association. C3b/iC3b depositionresults also correlated weakly with the degree of IgG binding to each strain. However, the binding of C1q (the firstcomponent of the classical pathway) correlated more closely with C3b/iC3b deposition, and large differences remained incomplement sensitivity between strains with the same capsular serotype in sera in which IgG had been cleaved with IdeS.Conclusions: These data demonstrate that bacterial factors independent of the capsule and recognition by IgG have strongeffects on the susceptibility of S. pneumoniae to complement, and could therefore potentially account for some of thedifferences in virulence between strains.
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
Hampton V, Kaestli M, Mayo M, et al., 2011, Melioidosis in Birds and Burkholderia pseudomallei Dispersal, Australia, Emerging Infectious Diseases, Vol: 17, Pages: 1310-1312, ISSN: 1080-6059
Mukhopadhyay C, Kaestli M, Vandana KE, et al., 2011, Short Report: Molecular Characterization of Clinical Burkholderia pseudomallei Isolates from India, American Journal of Tropical Medicine and Hygiene, Vol: 85, Pages: 121-123, ISSN: 1476-1645
Multilocus sequence typing of seven isolates of Burkholderia pseudomallei from India showed considerable diversity, with six different sequence types. Possible dissemination of melioidosis by historical trading routes is supported by links to strains from Southeast Asia, China, and Africa and the presence of the Burkholderia mallei allele of the bimA gene.
Mayo M, Kaestli M, Harrington G, et al., 2011, Burkholderia pseudomallei in Unchlorinated Domestic Bore Water, Tropical Northern Australia, Emerging Infectious Diseases, Vol: 17, Pages: 1283-1285, ISSN: 1080-6059
To determine whether unchlorinated bore water in northern Australia contained Burkholderia pseudomallei organisms, we sampled 55 bores; 18 (33%) were culture positive. Multilocus sequence typing identified 15 sequence types. The B. pseudomallei sequence type from 1 water sample matched a clinical isolate from a resident with melioidosis on the same property.
Mavroidi A, Tzelepi E, Siatravani E, et al., 2011, Analysis of Emergence of Quinolone-Resistant Gonococci in Greece by Combined Use of Neisseria gonorrhoeae Multiantigen Sequence Typing and Multilocus Sequence Typing, Journal of Clinical Microbiology, Vol: 49, Pages: 1196-1201, ISSN: 1098-660X
The prevalence of quinolone-resistant Neisseria gonorrhoeae (QRNG) in Greece remained low from 1997 to 2003 but increased dramatically from 11% to 56% between 2004 and 2007. N. gonorrhoeae multiantigen sequence typing (NG-MAST) and multilocus sequence typing (MLST) were used to investigate trends in quinolone resistance from 1997 to 2007 and explore the origins of the recent increase in QRNG. We characterized 295 QRNG isolates from the study period and 233 quinolone-susceptible (QS) gonococci from 2004 and 2005, when the rapid increase in QRNG occurred. From 1997 to 1999, an outbreak of QRNG was due to the dissemination of isolates of serovar Arst that belonged to two closely related genotypes. Few QRNG isolates, of diverse genotypes, were present between 2001 and 2003, whereas the sharp increase in QRNG from 2004 onwards was due to the appearance of serovar Bropyst isolates of several major NG-MAST sequence type (STs) that previously had not been identified in Greece. These isolates were shown by MLST to be variants of a single multiply antibiotic-resistant QRNG strain (ST1901) that appeared in Greece and rapidly diversified into 31 NG-MAST STs. There were no isolates of MLST ST1901 or any of the 31 NG-MAST STs among QS isolates from 2004 and 2005 or among 8 representatives of multiresistant but quinolone-susceptible serovar Bropyst isolates circulating in Greece during the 1990s, supporting the view that the recent increase in QRNG was due to importation of a QRNG strain(s) of MLST ST1901 into Greece. Recently, multiresistant QRNG isolates of ST1901 with reduced susceptibility to the newer cephalosporins have appeared in Greece.
Dang TNH, Thi PTL, Wolbers M, et al., 2011, Risk Factors of Streptococcus suis Infection in Vietnam. A Case-Control Study, PLOS One, Vol: 6, ISSN: 1932-6203
Background: Streptococcus suis infection, an emerging zoonosis, is an increasing public health problem across South EastAsia and the most common cause of acute bacterial meningitis in adults in Vietnam. Little is known of the risk factorsunderlying the disease.Methods and Findings: A case-control study with appropriate hospital and matched community controls for each patientwas conducted between May 2006 and June 2009. Potential risk factors were assessed using a standardized questionnaireand investigation of throat and rectal S. suis carriage in cases, controls and their pigs, using real-time PCR and culture ofswab samples. We recruited 101 cases of S. suis meningitis, 303 hospital controls and 300 community controls. Bymultivariate analysis, risk factors identified for S. suis infection as compared to either control group included eating ‘‘highrisk’’ dishes, including such dishes as undercooked pig blood and pig intestine (OR1 = 2.22; 95%CI = [1.15–4.28] andOR2 = 4.44; 95%CI = [2.15–9.15]), occupations related to pigs (OR1 = 3.84; 95%CI = [1.32–11.11] and OR2 = 5.52; 95%CI = [1.49–20.39]), and exposures to pigs or pork in the presence of skin injuries (OR1 = 7.48; 95%CI = [1.97–28.44] and OR2 = 15.96;95%CI = [2.97–85.72]). S. suis specific DNA was detected in rectal and throat swabs of 6 patients and was cultured from 2rectal samples, but was not detected in such samples of 1522 healthy individuals or patients without S. suis infection.Conclusions: This case control study, the largest prospective epidemiological assessment of this disease, has identified themost important risk factors associated with S. suis bacterial meningitis to be eating ‘high risk’ dishes popular in parts of Asia,occupational exposure to pigs and pig products, and preparation of pork in the presence of skin lesions. These risk factorscan be addressed in public health campaigns aimed at preventing S. suis infection.
Enright MC, Spratt BG, 2011, The Genomic View of Bacterial Diversification, SCIENCE, Vol: 331, Pages: 407-409, ISSN: 0036-8075
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- Citations: 6
Aanensen D, Huntley D, Powell C, et al., 2011, EpiCollect - A Mobile Phone/Web Application Framework for Epidemiological Data Collection and Visualisation, ECOHEALTH, Vol: 7, Pages: S48-S49, ISSN: 1612-9202
Lima JBT, Ribeiro GS, Cordeiro SM, et al., 2010, Poor Clinical Outcome for Meningitis Caused by <i>Haemophilus influenzae</i> Serotype A Strains Containing the IS<i>1016</i>-<i>bexA</i> Deletion, JOURNAL OF INFECTIOUS DISEASES, Vol: 202, Pages: 1577-1584, ISSN: 0022-1899
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- Citations: 28
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
Parkes HM, Shilton CM, Jerrett IV, et al., 2009, Primary ocular melioidosis due to a single genotype of <i>Burkholderia pseudomallei</i> in two cats from Arnhem Land in the Northern Territory of Australia, JOURNAL OF FELINE MEDICINE AND SURGERY, Vol: 11, Pages: 856-863, ISSN: 1098-612X
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- Citations: 5
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.
Dean D, Bruno WJ, Wan R, et al., 2009, Predicting Phenotype and Emerging Strains among Chlamydia trachomatis Infections, Emerging Infectious Diseases, Vol: 15, Pages: 1385-1394, ISSN: 1080-6059
Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.
Holden MTG, Hauser H, Sanders M, et al., 2009, Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis, PLOS One, Vol: 4, ISSN: 1932-6203
Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections inhumans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has beendescribed in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorlyunderstood.Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides opportunities toinvestigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the samelineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis wasused to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species forwhich genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is unique in comparison toother Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation;virtually all of the genome is common to the S. suis strains. The only exceptions are three ,90 kb regions, present in the twoisolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are codingsequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes inputative virulence and colonization factors.Conclusions/Significance: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts anddiseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer hascontributed to the evolution of drug resistance.
Bilek N, Ison CA, Spratt BG, 2009, Relative Contributions of Recombination and Mutation to the Diversification of the <i>opa</i> Gene Repertoire of <i>Neisseria gonorrhoeae</i>, JOURNAL OF BACTERIOLOGY, Vol: 191, Pages: 1878-1890, ISSN: 0021-9193
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- Citations: 19
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.
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
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- Citations: 287
Currie BJ, Haslem A, Pearson T, et al., 2009, Identification of Melioidosis Outbreak by Multilocus Variable Number Tandem Repeat Analysis, EMERGING INFECTIOUS DISEASES, Vol: 15, Pages: 169-174, ISSN: 1080-6040
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- Citations: 25
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
Reis JN, Palma T, Ribeiro GS, et al., 2008, Transmission of <i>Streptococcus pneumoniae</i> in an urban slum community, JOURNAL OF INFECTION, Vol: 57, Pages: 204-213, ISSN: 0163-4453
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- Citations: 23
Nghia HDT, Hoa NT, Linh LD, et al., 2008, Human case of Streptococcus suis serotype 16 infection, Emerging Infectious Diseases, Vol: 14, Pages: 155-157, ISSN: 1080-6059
Cheng AC, Ward L, Godoy D, et al., 2008, Genetic diversity of <i>Burkholderia pseudomallei</i> isolates in Australia, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 46, Pages: 249-254, ISSN: 0095-1137
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- Citations: 33
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
Bishop EJ, Shilton C, Benedict S, et al., 2007, Necrotizing fasciitis in captive juvenile <i>Crocodylus porosus</i> caused by <i>Streptococcus agalactiae</i>:: an outbreak and review of the animal and human literature, EPIDEMIOLOGY AND INFECTION, Vol: 135, Pages: 1248-1255, ISSN: 0950-2688
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- Citations: 39
Bilek N, Martin IM, Bell G, et al., 2007, Concordance between <i>Neisseria gonorrhoeae</i> genotypes recovered from known sexual contacts, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 45, Pages: 3564-3567, ISSN: 0095-1137
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- Citations: 25
Currie BJ, Thomas AD, Godoy D, et al., 2007, Australian and Thai isolates of <i>Burkholderia pseudomallei</i> are distinct by multilocus sequence typing:: Revision of a case of mistaken identity, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 45, Pages: 3828-3829, ISSN: 0095-1137
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- Citations: 13
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
Risley CL, Ward H, Choudhury B, et al., 2007, Geographical and demographic clustering of gonorrhoea in London, SEXUALLY TRANSMITTED INFECTIONS, Vol: 83, Pages: 481-487, ISSN: 1368-4973
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- Citations: 42
Currie BJ, Gal D, Mayo M, et al., 2007, Using BOX-PCR to exclude a clonal outbreak of melioidosis, BMC Infectious Diseases, Vol: 7, ISSN: 1471-2334
Background: Although melioidosis in endemic regions is usually caused by a diverse range ofBurkholderia pseudomallei strains, clonal outbreaks from contaminated potable water have beendescribed. Furthermore B. pseudomallei is classified as a CDC Group B bioterrorism agent.Ribotyping, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) havebeen used to identify genetically related B. pseudomallei isolates, but they are time consuming andtechnically challenging for many laboratories.Methods: We have adapted repetitive sequence typing using a BOX A1R primer for typing B.pseudomallei and compared BOX-PCR fingerprinting results on a wide range of well-characterizedB. pseudomallei isolates with MLST and PFGE performed on the same isolates.Results: BOX-PCR typing compared favourably with MLST and PFGE performed on the sameisolates, both discriminating between the majority of multilocus sequence types and showingrelatedness between epidemiologically linked isolates from various outbreak clusters.Conclusion: Our results suggest that BOX-PCR can be used to exclude a clonal outbreak ofmelioidosis within 10 hours of receiving the bacterial strains.
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