The Experts below are selected from a list of 295266 Experts worldwide ranked by ideXlab platform
Estee M Torok - One of the best experts on this subject based on the ideXlab platform.
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rapid single colony whole Genome Sequencing of bacterial pathogens
Journal of Antimicrobial Chemotherapy, 2014Co-Authors: Claudio U Koser, Jennifer Becq, Estee M Torok, Matthew T. G. Holden, Matthew J. Ellington, Louise Fraser, Avgousta Ioannou, Sandra ReuterAbstract:Objectives As a result of the introduction of rapid benchtop sequencers, the time required to subculture a bacterial pathogen to extract sufficient DNA for library preparation can now exceed the time to sequence said DNA. We have eliminated this rate-limiting step by developing a protocol to generate DNA libraries for whole-Genome Sequencing directly from single bacterial colonies grown on primary culture plates.
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whole Genome Sequencing for rapid susceptibility testing of m tuberculosis
The New England Journal of Medicine, 2013Co-Authors: Claudio U Koser, Josephine M Bryant, Geoffrey Paul Smith, Jennifer Becq, Estee M Torok, Marc A Martirenom, Matthew J. Ellington, Julian Parkhill, A J Carmichael, Sharon J. PeacockAbstract:As reported here, whole-Genome Sequencing has the potential to rapidly facilitate the determination of antimicrobial susceptibility, especially for slower-growing pathogens, such as Mycobacterium tuberculosis.
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whole Genome Sequencing for analysis of an outbreak of meticillin resistant staphylococcus aureus a descriptive study
Lancet Infectious Diseases, 2013Co-Authors: Simon R Harris, Edward J. P. Cartwright, Amanda Ogilvystuart, Estee M Torok, Michael A Quail, Matthew T. G. Holden, Matthew J. Ellington, Nick Brown, Stephen D BentleyAbstract:Summary Background The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages of MRSA means that it is necessary to understand transmission dynamics in terms of hospitals and the community as one entity. We assessed the use of whole-Genome Sequencing to enhance detection of MRSA transmission between these settings. Methods We studied a putative MRSA outbreak on a special care baby unit (SCBU) at a National Health Service Foundation Trust in Cambridge, UK. We used whole-Genome Sequencing to validate and expand findings from an infection-control team who assessed the outbreak through conventional analysis of epidemiological data and antibiogram profiles. We sequenced isolates from all colonised patients in the SCBU, and sequenced MRSA isolates from patients in the hospital or community with the same antibiotic susceptibility profile as the outbreak strain. Findings The hospital infection-control team identified 12 infants colonised with MRSA in a 6 month period in 2011, who were suspected of being linked, but a persistent outbreak could not be confirmed with conventional methods. With whole-Genome Sequencing, we identified 26 related cases of MRSA carriage, and showed transmission occurred within the SCBU, between mothers on a postnatal ward, and in the community. The outbreak MRSA type was a new sequence type (ST) 2371, which is closely related to ST22, but contains genes encoding Panton-Valentine leucocidin. Whole-Genome Sequencing data were used to propose and confirm that MRSA carriage by a staff member had allowed the outbreak to persist during periods without known infection on the SCBU and after a deep clean. Interpretation Whole-Genome Sequencing holds great promise for rapid, accurate, and comprehensive identification of bacterial transmission pathways in hospital and community settings, with concomitant reductions in infections, morbidity, and costs. Funding UK Clinical Research Collaboration Translational Infection Research Initiative, Wellcome Trust, Health Protection Agency, and the National Institute for Health Research Cambridge Biomedical Research Centre.
Josephine M Bryant - One of the best experts on this subject based on the ideXlab platform.
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whole Genome Sequencing to establish relapse or re infection with mycobacterium tuberculosis a retrospective observational study
The Lancet Respiratory Medicine, 2013Co-Authors: Josephine M Bryant, Rodney Dawson, Aziah A Mahayiddin, Charoen Chuchottaworn, Ian Sanne, Simon R Harris, Paul D. Van Helden, Julian Parkhill, Andreas H. Diacon, Cheryl LouwAbstract:Summary Background Recurrence of tuberculosis after treatment makes management difficult and is a key factor for determining treatment efficacy. Two processes can cause recurrence: relapse of the primary infection or re-infection with an exogenous strain. Although re-infection can and does occur, its importance to tuberculosis epidemiology and its biological basis is still debated. We used whole-Genome Sequencing—which is more accurate than conventional typing used to date—to assess the frequency of recurrence and to gain insight into the biological basis of re-infection. Methods We assessed patients from the REMoxTB trial—a randomised controlled trial of tuberculosis treatment that enrolled previously untreated participants with Mycobacterium tuberculosis infection from Malaysia, South Africa, and Thailand. We did whole-Genome Sequencing and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing of pairs of isolates taken by sputum sampling: one from before treatment and another from either the end of failed treatment at 17 weeks or later or from a recurrent infection. We compared the number and location of SNPs between isolates collected at baseline and recurrence. Findings We assessed 47 pairs of isolates. Whole-Genome Sequencing identified 33 cases with little genetic distance (0–6 SNPs) between strains, deemed relapses, and three cases for which the genetic distance ranged from 1306 to 1419 SNPs, deemed re-infections. Six cases of relapse and six cases of mixed infection were classified differently by whole-Genome Sequencing and MIRU-VNTR. We detected five single positive isolates (positive culture followed by at least two negative cultures) without clinical evidence of disease. Interpretation Whole-Genome Sequencing enables the differentiation of relapse and re-infection cases with greater resolution than do genotyping methods used at present, such as MIRU-VNTR, and provides insights into the biology of recurrence. The additional clarity provided by whole-Genome Sequencing might have a role in defining endpoints for clinical trials. Funding Wellcome Trust, European Union, Medical Research Council, Global Alliance for TB Drug Development, European and Developing Country Clinical Trials Partnership.
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whole Genome Sequencing for rapid susceptibility testing of m tuberculosis
The New England Journal of Medicine, 2013Co-Authors: Claudio U Koser, Josephine M Bryant, Geoffrey Paul Smith, Jennifer Becq, Estee M Torok, Marc A Martirenom, Matthew J. Ellington, Julian Parkhill, A J Carmichael, Sharon J. PeacockAbstract:As reported here, whole-Genome Sequencing has the potential to rapidly facilitate the determination of antimicrobial susceptibility, especially for slower-growing pathogens, such as Mycobacterium tuberculosis.
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inferring patient to patient transmission of mycobacterium tuberculosis from whole Genome Sequencing data
BMC Infectious Diseases, 2013Co-Authors: Josephine M Bryant, Henk Van Deutekom, Jessica L De Beer, Kristin Kremer, Simon R Harris, Victor De Jager, Anita C. Schürch, Sacha A. F. T. Van HijumAbstract:Background: Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole Genome Sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the Genome over relevant timescales is required. Methods: We attempted to estimate a molecular clock by Sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years. Results: Multiple analyses support an average mutation rate of ~0.3 SNPs per Genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links. Conclusions: This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole Genome Sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole Genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole Genome Sequencing.
Daniel J Wilson - One of the best experts on this subject based on the ideXlab platform.
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whole Genome Sequencing shows that patient to patient transmission rarely accounts for acquisition of staphylococcus aureus in an intensive care unit
Clinical Infectious Diseases, 2014Co-Authors: James Price, Kevin Cole, Derrick W. Crook, Rory Bowden, Daniel J Wilson, Tanya Golubchik, Guy E Thwaites, Sarah A Walker, T E A PetoAbstract:BACKGROUND: Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-Genome Sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS: Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-Genome Sequencing to investigate their relatedness at high resolution. RESULTS: Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-Genome Sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS: Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-Genome Sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-Genome Sequencing should replace conventional methods for detection of nosocomial S. aureus transmission.
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Transforming clinical microbiology with bacterial Genome Sequencing
Nature Reviews Genetics, 2012Co-Authors: Xavier Didelot, Tim E A Peto, Rory Bowden, Daniel J Wilson, Derrick W. CrookAbstract:Whole-Genome Sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation Sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation Sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.
Derrick W. Crook - One of the best experts on this subject based on the ideXlab platform.
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whole Genome Sequencing shows that patient to patient transmission rarely accounts for acquisition of staphylococcus aureus in an intensive care unit
Clinical Infectious Diseases, 2014Co-Authors: James Price, Kevin Cole, Derrick W. Crook, Rory Bowden, Daniel J Wilson, Tanya Golubchik, Guy E Thwaites, Sarah A Walker, T E A PetoAbstract:BACKGROUND: Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-Genome Sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS: Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-Genome Sequencing to investigate their relatedness at high resolution. RESULTS: Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-Genome Sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS: Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-Genome Sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-Genome Sequencing should replace conventional methods for detection of nosocomial S. aureus transmission.
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Transforming clinical microbiology with bacterial Genome Sequencing
Nature Reviews Genetics, 2012Co-Authors: Xavier Didelot, Tim E A Peto, Rory Bowden, Daniel J Wilson, Derrick W. CrookAbstract:Whole-Genome Sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation Sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation Sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.
Rui Chen - One of the best experts on this subject based on the ideXlab platform.
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performance comparison of whole Genome Sequencing platforms
Nature Biotechnology, 2012Co-Authors: Michael J. Clark, Maeve Ohuallachain, Lukas Habegger, Frederick E. Dewey, Euan A. Ashley, Georges Natsoulis, Rong Chen, Rui Chen, Mark Gerstein, Atul J. ButteAbstract:Over 90% of human whole-Genome Sequencing has been performed using instruments from two companies, Illumina and Complete Genomics. Lam et al. sequence the same DNA samples with both instruments and compare their performance for calling insertions, deletions and single-nucleotide variants.
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performance comparison of whole Genome Sequencing platforms
Nature Biotechnology, 2012Co-Authors: Hugo Y K Lam, Maeve Ohuallachain, Lukas Habegger, Michael J. Clark, Frederick E. Dewey, Euan A. Ashley, Georges Natsoulis, Rong Chen, Rui Chen, Mark GersteinAbstract:Whole-Genome Sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the Genome of an individual with both technologies to a high average coverage of ∼76×, and compared their performance with respect to sequence coverage and calling of single-nucleotide variants (SNVs), insertions and deletions (indels). Although 88.1% of the ∼3.7 million unique SNVs were concordant between platforms, there were tens of thousands of platform-specific calls located in genes and other genomic regions. In contrast, 26.5% of indels were concordant between platforms. Target enrichment validated 92.7% of the concordant SNVs, whereas validation by genotyping array revealed a sensitivity of 99.3%. The validation experiments also suggested that >60% of the platform-specific variants were indeed present in the Genome. Our results have important implications for understanding the accuracy and completeness of the Genome Sequencing platforms.
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high precision whole Genome Sequencing of laboratory strains facilitates genetic studies
PLOS Genetics, 2008Co-Authors: Anjana Srivatsan, Jianlan Peng, Ashley K Tehranchi, Jue D Wang, Richard A. Gibbs, Rui ChenAbstract:Whole-Genome Sequencing is a powerful technique for obtaining the reference sequence information of multiple organisms. Its use can be dramatically expanded to rapidly identify genomic variations, which can be linked with phenotypes to obtain biological insights. We explored these potential applications using the emerging next-generation Sequencing platform Solexa Genome Analyzer, and the well-characterized model bacterium Bacillus subtilis. Combining Sequencing with experimental verification, we first improved the accuracy of the published sequence of the B. subtilis reference strain 168, then obtained sequences of multiple related laboratory strains and different isolates of each strain. This provides a framework for comparing the divergence between different laboratory strains and between their individual isolates. We also demonstrated the power of Solexa Sequencing by using its results to predict a defect in the citrate signal transduction pathway of a common laboratory strain, which we verified experimentally. Finally, we examined the molecular nature of spontaneously generated mutations that suppress the growth defect caused by deletion of the stringent response mediator relA. Using whole-Genome Sequencing, we rapidly mapped these suppressor mutations to two small homologs of relA. Interestingly, stable suppressor strains had mutations in both genes, with each mutation alone partially relieving the relA growth defect. This supports an intriguing three-locus interaction module that is not easily identifiable through traditional suppressor mapping. We conclude that whole-Genome Sequencing can drastically accelerate the identification of suppressor mutations and complex genetic interactions, and it can be applied as a standard tool to investigate the genetic traits of model organisms.