Publications
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Rhodes JL, Abdolrasouli A, Farrer R, et al., 2018, Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris, Emerging Microbes and Infections, Vol: 7, ISSN: 2222-1751
Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across at least 19 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak within the UK, involving a total of 72 patients. To understand the genetic epidemiology of C. auris infection, both within this hospital and within a global context, we sequenced the outbreak isolate genomes using Oxford Nanopore Technologies and Illumina to detect antifungal resistance alleles and to reannotate the C. auris genome. Phylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin: the outbreak showed similar genetic diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations add to a growing body of research on multiple antifungal drug targets in this organism. Multiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.
Domman D, Quilici M-L, Dorman MJ, et al., 2017, Integrated view of <i>Vibrio cholerae</i> in the Americas, SCIENCE, Vol: 358, Pages: 789-792, ISSN: 0036-8075
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- Citations: 88
Otter JA, Doumith M, Davies F, et al., 2017, Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London, Scientific Reports, Vol: 7, ISSN: 2045-2322
Carbapenemase-producing Enterobacteriaceae (CPE) are emerging worldwide, limiting therapeutic options. Mutational and plasmid-mediated mechanisms of colistin resistance have both been reported. The emergence and clonal spread of colistin resistance was analysed in 40 epidemiologically-related NDM-1 carbapenemase producing Klebsiella pneumoniae isolates identified during an outbreak in a group of London hospitals. Isolates from July 2014 to October 2015 were tested for colistin susceptibility using agar dilution, and characterised by whole genome sequencing (WGS). Colistin resistance was detected in 25/38 (65.8%) cases for which colistin susceptibility was tested. WGS found that three potential mechanisms of colistin resistance had emerged separately, two due to different mutations in mgrB, and one due to a mutation in phoQ, with onward transmission of two distinct colistin-resistant variants, resulting in two sub-clones associated with transmission at separate hospitals. A high rate of colistin resistance (66%) emerged over a 10 month period. WGS demonstrated that mutational colistin resistance emerged three times during the outbreak, with transmission of two colistin-resistant variants.
Hadfield J, Croucher NJ, Goater RJ, et al., 2017, Phandango: an interactive viewer for bacterial population genomics., Bioinformatics, Vol: 34, Pages: 292-293, ISSN: 1367-4803
Summary: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner. Availability: Phandango is a web application freely available for use at www.phandango.net and includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub at https://github.com/jameshadfield/phandango. Contact: jh22@sanger.ac.uk, sh16@sanger.ac.uk.
Reuter S, Torok ME, Holden MTG, et al., 2017, Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland (vol 26, pg 263, 2016), GENOME RESEARCH, Vol: 27, Pages: 1622-1622, ISSN: 1088-9051
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- Citations: 1
Donker T, Reuter S, Scriberras J, et al., 2017, Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns., Microbial Genomics, Vol: 3, ISSN: 2057-5858
Antibiotic resistance forms a serious threat to the health of hospitalised patients, rendering otherwise treatable bacterial infections potentially life-threatening. A thorough understanding of the mechanisms by which resistance spreads between patients in different hospitals is required in order to design effective control strategies. We measured the differences between bacterial populations of 52 hospitals in the United Kingdom and Ireland, using whole-genome sequences from 1085 MRSA clonal complex 22 isolates collected between 1998 and 2012. The genetic differences between bacterial populations were compared with the number of patients transferred between hospitals and their regional structure. The MRSA populations within single hospitals, regions and countries were genetically distinct from the rest of the bacterial population at each of these levels. Hospitals from the same patient referral regions showed more similar MRSA populations, as did hospitals sharing many patients. Furthermore, the bacterial populations from different time-periods within the same hospital were generally more similar to each other than contemporaneous bacterial populations from different hospitals. We conclude that, while a large part of the dispersal and expansion of MRSA takes place among patients seeking care in single hospitals, inter-hospital spread of resistant bacteria is by no means a rare occurrence. Hospitals are exposed to constant introductions of MRSA on a number of levels: (1) most MRSA is received from hospitals that directly transfer large numbers of patients, while (2) fewer introductions happen between regions or (3) across national borders, reflecting lower numbers of transferred patients. A joint coordinated control effort between hospitals, is therefore paramount for the national control of MRSA, antibiotic-resistant bacteria and other hospital-associated pathogens.
Mostowy RJ, Croucher NJ, De Maio N, et al., 2017, Pneumococcal capsule synthesis locus cps as evolutionary hotspot with potential to generate novel serotypes by recombination, Molecular Biology and Evolution, Vol: 34, Pages: 2537-2554, ISSN: 1537-1719
Diversity of the polysaccharide capsule in Streptococcus pneumoniae -- main surface antigen and the target of the currently used pneumococcal vaccines -- constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared to the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centred approach, we analysed the evolutionary history of twelve major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to non-random associations between co-colonising serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasise the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination.
Bayliss SC, Verner-Jeffreys DW, Bartie KL, et al., 2017, The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens, FRONTIERS IN MICROBIOLOGY, Vol: 8, ISSN: 1664-302X
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- Citations: 54
Grundmann H, Glasner C, Albiger B, et al., 2017, Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study., Lancet Infect Dis, Vol: 17, Pages: 153-163
BACKGROUND: Gaps in the diagnostic capacity and heterogeneity of national surveillance and reporting standards in Europe make it difficult to contain carbapenemase-producing Enterobacteriaceae. We report the development of a consistent sampling framework and the results of the first structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals. METHODS: National expert laboratories recruited hospitals with diagnostic capacities, who collected the first ten carbapenem non-susceptible clinical isolates of K pneumoniae or E coli and ten susceptible same-species comparator isolates and pertinent patient and hospital information. Isolates and data were relayed back to national expert laboratories, which made laboratory-substantiated information available for central analysis. FINDINGS: Between Nov 1, 2013, and April 30, 2014, 455 sentinel hospitals in 36 countries submitted 2703 clinical isolates (2301 [85%] K pneumoniae and 402 (15%) E coli). 850 (37%) of 2301 K pneumoniae samples and 77 (19%) of 402 E coli samples were carbapenemase (KPC, NDM, OXA-48-like, or VIM) producers. The ratio of K pneumoniae to E coli was 11:1. 1·3 patients per 10 000 hospital admissions had positive clinical specimens. Prevalence differed greatly, with the highest rates in Mediterranean and Balkan countries. Carbapenemase-producing K pneumoniae isolates showed high resistance to last-line antibiotics. INTERPRETATION: This initiative shows an encouraging commitment by all participants, and suggests that challenges in the establishment of a continent-wide enhanced sentinel surveillance for carbapenemase-producing Enterobacteriaeceae can be overcome. Strengthening infection control efforts in hospitals is crucial for controlling spread through local and national health care networks. FUNDING: European Centre for Disease Prevention and Control.
Grundmann H, Glasner C, Albiger B, et al., 2017, Occurrence of carbapenemase-producing <i>Klebsiella pneumoniae</i> and <i>Escherichia coli</i> in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study, LANCET INFECTIOUS DISEASES, Vol: 17, Pages: 153-163, ISSN: 1473-3099
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- Citations: 418
Argimón S, Abudahab K, Goater RJE, et al., 2016, Microreact: visualizing and sharing data for genomic epidemiology and phylogeography, Microbial Genomics, Vol: 2, ISSN: 2057-5858
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
Argimon S, Aanensen DM, 2016, Species Mash-up, NATURE REVIEWS MICROBIOLOGY, Vol: 14, Pages: 730-730, ISSN: 1740-1526
Didelot X, Dordel J, Whittles LK, et al., 2016, Genomic analysis and comparison of two gonorrhoea outbreaks, mBio, Vol: 7, ISSN: 2150-7511
Gonorrhea is a sexually transmitted disease causing growing concern, with a substantial increase in reported incidence over the past few years in the United Kingdom and rising levels of resistance to a wide range of antibiotics. Understanding its epidemiology is therefore of major biomedical importance, not only on a population scale but also at the level of direct transmission. However, the molecular typing techniques traditionally used for gonorrhea infections do not provide sufficient resolution to investigate such fine-scale patterns. Here we sequenced the genomes of 237 isolates from two local collections of isolates from Sheffield and London, each of which was resolved into a single type using traditional methods. The two data sets were selected to have different epidemiological properties: the Sheffield data were collected over 6 years from a predominantly heterosexual population, whereas the London data were gathered within half a year and strongly associated with men who have sex with men. Based on contact tracing information between individuals in Sheffield, we found that transmission is associated with a median time to most recent common ancestor of 3.4 months, with an upper bound of 8 months, which we used as a criterion to identify likely transmission links in both data sets. In London, we found that transmission happened predominantly between individuals of similar age, sexual orientation, and location and also with the same HIV serostatus, which may reflect serosorting and associated risk behaviors. Comparison of the two data sets suggests that the London epidemic involved about ten times more cases than the Sheffield outbreak.
Aanensen DM, Feil EJ, Holden MT, et al., 2016, Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive staphylococcus aureus in Europe., mBio, Vol: 7, ISSN: 2161-2129
UNLABELLED: The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools. IMPORTANCE: The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context
Crellen T, Allan F, David S, et al., 2016, Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection., Scientific Reports, Vol: 6, ISSN: 2045-2322
Schistosoma mansoni is a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics to S. mansoni based on high-coverage resequencing data from 10 global isolates and an isolate of the closely-related Schistosoma rodhaini, which infects rodents. Using population genetic tests, we document genes under directional and balancing selection in S. mansoni that may facilitate adaptation to the human host. Coalescence modeling reveals the speciation of S. mansoni and S. rodhaini as 107.5-147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate that S. mansoni originated in East Africa and experienced a decline in effective population size 20-90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence that S. mansoni migrated to the New World with the 16-19(th) Century Atlantic Slave Trade.
Reuter S, Toeroek ME, Holden MTG, et al., 2016, Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland, Genome Research, Vol: 26, Pages: 263-270, ISSN: 1549-5469
The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, and the Republic of Ireland over a decade. We sequenced 1013 MRSA submitted to the British Society for Antimicrobial Chemotherapy by 46 laboratories between 2001 and 2010. Each isolate was assigned to a regional healthcare referral network in England and was otherwise grouped based on country of origin. Phylogenetic reconstructions were used to contextualize MRSA outbreak investigations and to detect the spread of resistance. The majority of isolates (n = 783, 77%) belonged to CC22, which contains the dominant United Kingdom epidemic clone (EMRSA-15). There was marked geographic structuring of EMRSA-15, consistent with widespread dissemination prior to the sampling decade followed by local diversification. The addition of MRSA genomes from two outbreaks and one pseudo-outbreak demonstrated the certainty with which outbreaks could be confirmed or refuted. We identified local and regional differences in antibiotic resistance profiles, with examples of local expansion, as well as widespread circulation of mobile genetic elements across the bacterial population. We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance.
Grundmann H, Schouls LM, Aanensen DM, et al., 2014, The dynamic changes of dominant clones of <i>Staphylococcus aureus</i> causing bloodstream infections in the European region: Results of a second structured survey, EUROSURVEILLANCE, Vol: 19, Pages: 35-44, ISSN: 1560-7917
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- Citations: 7
Aanensen DM, Huntley DM, Menegazzo M, et al., 2014, EpiCollect+: linking smartphones to web applications for complex data collection projects., F1000Res, Vol: 3, Pages: 199-199
Previously, we have described the development of the generic mobile phone data gathering tool, EpiCollect, and an associated web application, providing two-way communication between multiple data gatherers and a project database. This software only allows data collection on the phone using a single questionnaire form that is tailored to the needs of the user (including a single GPS point and photo per entry), whereas many applications require a more complex structure, allowing users to link a series of forms in a linear or branching hierarchy, along with the addition of any number of media types accessible from smartphones and/or tablet devices (e.g., GPS, photos, videos, sound clips and barcode scanning). A much enhanced version of EpiCollect has been developed (EpiCollect+). The individual data collection forms in EpiCollect+ provide more design complexity than the single form used in EpiCollect, and the software allows the generation of complex data collection projects through the ability to link many forms together in a linear (or branching) hierarchy. Furthermore, EpiCollect+ allows the collection of multiple media types as well as standard text fields, increased data validation and form logic. The entire process of setting up a complex mobile phone data collection project to the specification of a user (project and form definitions) can be undertaken at the EpiCollect+ website using a simple 'drag and drop' procedure, with visualisation of the data gathered using Google Maps and charts at the project website. EpiCollect+ is suitable for situations where multiple users transmit complex data by mobile phone (or other Android devices) to a single project web database and is already being used for a range of field projects, particularly public health projects in sub-Saharan Africa. However, many uses can be envisaged from education, ecology and epidemiology to citizen science.
Jombart T, Aanensen DM, Baguelin M, et al., 2014, OutbreakTools: A new platform for disease outbreak analysis using the R software, Epidemics, Vol: 7, Pages: 28-34, ISSN: 1755-4365
The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools, and a unified platform for the analysis of disease outbreaks is still lacking. In this paper, we present the new R package OutbreakTools, which aims to provide a basis for outbreak data management and analysis in R. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data. It includes real and simulated outbreak datasets. Together with a number of tools for infectious disease epidemiology recently made available in R, OutbreakTools contributes to the emergence of a new, free and open-source platform for the analysis of disease outbreaks.
Chewapreecha C, Harris SR, Croucher NJ, et al., 2014, Dense genomic sampling identifies highways of pneumococcal recombination, NATURE GENETICS, Vol: 46, Pages: 305-+, ISSN: 1061-4036
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- Citations: 260
Limmathurotsakul D, Wongsuvan G, Aanensen D, et al., 2014, Melioidosis Caused by <i>Burkholderia pseudomallei</i> in Drinking Water, Thailand, 2012, EMERGING INFECTIOUS DISEASES, Vol: 20, Pages: 265-268, ISSN: 1080-6040
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- Citations: 47
Zhang L, Thomas JC, Miragaia M, et al., 2013, Multilocus Sequence Typing and Further Genetic Characterization of the Enigmatic Pathogen, <i>Staphylococcus hominis</i>, PLOS ONE, Vol: 8, ISSN: 1932-6203
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- Citations: 25
Cheng L, Connor TR, Siren J, et al., 2013, Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 30, Pages: 1224-1228, ISSN: 0737-4038
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- Citations: 392
Holden MTG, Hsu L-Y, Kurt K, et al., 2013, A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic, Genome Research, Vol: 23, Pages: 653-664, ISSN: 1549-5469
The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens.
Theethakaew C, Feil EJ, Castillo-Ramirez S, et al., 2013, Genetic Relationships of <i>Vibrio parahaemolyticus</i> Isolates from Clinical, Human Carrier, and Environmental Sources in Thailand, Determined by Multilocus Sequence Analysis, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 79, Pages: 2358-2370, ISSN: 0099-2240
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- Citations: 49
Olson DH, Aanensen DM, Ronnenberg KL, et al., 2013, Mapping the Global Emergence of <i>Batrachochytrium</i> <i>dendrobatidis</i>, the Amphibian Chytrid Fungus, PLOS ONE, Vol: 8, ISSN: 1932-6203
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- Citations: 292
Boonsilp S, Thaipadungpanit J, Amornchai P, et al., 2013, A Single Multilocus Sequence Typing (MLST) scheme for seven athogenic Leptospira species, PLOS Neglected Tropical Diseases, Vol: 7, ISSN: 1935-2735
Background:The availableLeptospiramultilocus sequence typing (MLST) scheme supported by a MLST website is limited toL. interrogansandL. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenicspecies.Methodology and Findings:We modified the existing scheme by replacing one of the seven MLST loci (fadDwas changedtocaiB), as the former gene did not appear to be present in some pathogenic species. Comparison of the original andmodified schemes using data forL. interrogansandL. kirschneridemonstrated that the discriminatory power of the twoschemes was not significantly different. The modified scheme was used to further characterize 325 isolates (L. alexanderi [n = 5], L. borgpetersenii[n = 34], L. interrogans [n = 222], L. kirschneri [n = 29], L. noguchii [n = 9], L. santarosai [n = 10], and L.weilii [n = 16]). Phylogenetic analysis using concatenated sequences of the 7 loci demonstrated that each speciescorresponded to a discrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs) represented by at least two isolates, 18 STs included isolates assigned to two or three different serovars. Conversely, 14 serovars were identified that contained between 2 to 10 different STs. New observations were made on the global phylogeography ofLeptospira spp., and the utility of MLST in making associations between human disease and specific maintenance hosts was demonstrated.Conclusion:The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic species associated with leptospirosis.
Cornelius DC, Robinson DA, Muzny CA, et al., 2012, Genetic Characterization of <i>Trichomonas vaginalis</i> Isolates by Use of Multilocus Sequence Typing, JOURNAL OF CLINICAL MICROBIOLOGY, Vol: 50, Pages: 3293-3300, ISSN: 0095-1137
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- Citations: 32
McAdam PR, Templeton KE, Edwards GF, et al., 2012, Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant <i>Staphylococcus aureus</i>, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 9107-9112, ISSN: 0027-8424
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- Citations: 136
Ahmed A, Thaipadungpanit J, Boonsilp S, et al., 2011, Comparison of Two Multilocus Sequence Based Genotyping Schemes for Leptospira Species, PLOS Neglected Tropical Diseases, Vol: 5, ISSN: 1935-2735
Background: Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of thisstudy was to genotype a collection of clinical and reference isolates using the two most commonly used schemes andcompare and contrast the results.Methods and Findings: A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7locus 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 threenucleotides 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/dSratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees werereconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groupscorresponding 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 twodiscrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by7L than by 6L.Conclusions: This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantagesand disadvantages.
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