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18 results on '"del Ojo Elias, Carlos"'

1. Insidious Risk of Severe Mycobacterium chimaera Infection in Cardiac Surgery Patients

Author

Chand, Meera, Lamagni, Theresa, Kranzer, Katharina, Hedge, Jessica, Moore, Ginny, Parks, Simon, Collins, Samuel, del Ojo Elias, Carlos, Ahmed, Nada, Brown, Tim, Smith, E. Grace, Hoffman, Peter, Kirwan, Peter, Mason, Brendan, Smith-Palmer, Alison, Veal, Philip, Lalor, Maeve K., Bennett, Allan, Walker, James, Yeap, Alicia, Martin, Antonio Isidro Carrion, Dolan, Gayle, Bhatt, Sonia, Skingsley, Andrew, Charlett, André, Pearce, David, Russell, Katherine, Kendall, Simon, Klein, Andrew A., Robins, Stephen, Schelenz, Silke, Newsholme, William, Thomas, Stephanie, Collyns, Tim, Davies, Eleri, McMenamin, Jim, Doherty, Lorraine, Peto, Tim E. A., Crook, Derrick, Zambon, Maria, and Phin, Nick

Published
2017

2. A Natural Encoding of Genetic Variation in a Burrows-Wheeler Transform to Enable Mapping and Genome Inference

Author

Maciuca, Sorina, del Ojo Elias, Carlos, McVean, Gil, Iqbal, Zamin, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Frith, Martin, editor, and Storm Pedersen, Christian Nørgaard, editor

Published
2016
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3. Effects of control interventions on Clostridium difficile infection in England: an observational study

Author

Del Ojo Elias, Carlos, Crichton, Charles, Kostiou, Vasiliki, Giess, Adam, Davies, Jim, Dingle, Kate E, Didelot, Xavier, Quan, T Phuong, Eyre, David W, Stoesser, Nicole, Golubchik, Tanya, Harding, Rosalind M, Wilson, Daniel J, Griffiths, David, Vaughan, Alison, Finney, John M, Wyllie, David H, Oakley, Sarah J, Fawley, Warren N, Freeman, Jane, Morris, Kirsti, Martin, Jessica, Howard, Philip, Gorbach, Sherwood, Goldstein, Ellie J C, Citron, Diane M, Hopkins, Susan, Hope, Russell, Johnson, Alan P, Wilcox, Mark H, Peto, Timothy E A, Walker, A Sarah, and Crook, Derrick W

Published
2017
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4. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study

Author

Pankhurst, Louise J, del Ojo Elias, Carlos, Votintseva, Antonina A, Walker, Timothy M, Cole, Kevin, Davies, Jim, Fermont, Jilles M, Gascoyne-Binzi, Deborah M, Kohl, Thomas A, Kong, Clare, Lemaitre, Nadine, Niemann, Stefan, Paul, John, Rogers, Thomas R, Roycroft, Emma, Smith, E Grace, Supply, Philip, Tang, Patrick, Wilcox, Mark H, Wordsworth, Sarah, Wyllie, David, Xu, Li, and Crook, Derrick W

Published
2016
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7. Effects of control interventions on Clostridium difficile infection in England: an observational study

Author

Dingle, Kate E, Didelot, Xavier, Quan, T Phuong, Eyre, David W, Stoesser, Nicole, Golubchik, Tanya, Harding, Rosalind M, Wilson, Daniel J, Griffiths, David, Vaughan, Alison, Finney, John M, Wyllie, David H, Oakley, Sarah J, Fawley, Warren N, Freeman, Jane, Morris, Kirsti, Martin, Jessica, Howard, Philip, Gorbach, Sherwood, Goldstein, Ellie J C, Citron, Diane M, Hopkins, Susan, Hope, Russell, Johnson, Alan P, Wilcox, Mark H, Peto, Timothy E A, Walker, A Sarah, Crook, Derrick W, Del Ojo Elias, Carlos, Crichton, Charles, Kostiou, Vasiliki, Giess, Adam, and Davies, Jim

Subjects
Infectious Diseases
Published
2017
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8. Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples

Author

Votintseva, Antonina A., primary, Bradley, Phelim, additional, Pankhurst, Louise, additional, del Ojo Elias, Carlos, additional, Loose, Matthew, additional, Nilgiriwala, Kayzad, additional, Chatterjee, Anirvan, additional, Smith, E. Grace, additional, Sanderson, Nicolas, additional, Walker, Timothy M., additional, Morgan, Marcus R., additional, Wyllie, David H., additional, Walker, A. Sarah, additional, Peto, Tim E. A., additional, Crook, Derrick W., additional, and Iqbal, Zamin, additional

Published
2017
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9. Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples

Author

Votintseva, Antonina A., primary, Bradley, Phelim, additional, Pankhurst, Louise, additional, del Ojo Elias, Carlos, additional, Loose, Matthew, additional, Nilgiriwala, Kayzad, additional, Chatterjee, Anirvan, additional, Smith, E. Grace, additional, Sanderson, Nicholas, additional, Walker, Timothy M., additional, Morgan, Marcus R., additional, Wyllie, David H., additional, Walker, A. Sarah, additional, Peto, Tim E. A., additional, Crook, Derrick W., additional, and Iqbal, Zamin, additional

Published
2016
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10. Insidious Risk of SevereMycobacterium chimaeraInfection in Cardiac Surgery Patients

Author

Chand, Meera, primary, Lamagni, Theresa, additional, Kranzer, Katharina, additional, Hedge, Jessica, additional, Moore, Ginny, additional, Parks, Simon, additional, Collins, Samuel, additional, del Ojo Elias, Carlos, additional, Ahmed, Nada, additional, Brown, Tim, additional, Smith, E. Grace, additional, Hoffman, Peter, additional, Kirwan, Peter, additional, Mason, Brendan, additional, Smith-Palmer, Alison, additional, Veal, Philip, additional, Lalor, Maeve K., additional, Bennett, Allan, additional, Walker, James, additional, Yeap, Alicia, additional, Isidro Carrion Martin, Antonio, additional, Dolan, Gayle, additional, Bhatt, Sonia, additional, Skingsley, Andrew, additional, Charlett, André, additional, Pearce, David, additional, Russell, Katherine, additional, Kendall, Simon, additional, Klein, Andrew A., additional, Robins, Stephen, additional, Schelenz, Silke, additional, Newsholme, William, additional, Thomas, Stephanie, additional, Collyns, Tim, additional, Davies, Eleri, additional, McMenamin, Jim, additional, Doherty, Lorraine, additional, Peto, Tim E. A., additional, Crook, Derrick, additional, Zambon, Maria, additional, and Phin, Nick, additional

Published
2016
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12. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

Author

Walker, Timothy M, primary, Kohl, Thomas A, additional, Omar, Shaheed V, additional, Hedge, Jessica, additional, Del Ojo Elias, Carlos, additional, Bradley, Phelim, additional, Iqbal, Zamin, additional, Feuerriegel, Silke, additional, Niehaus, Katherine E, additional, Wilson, Daniel J, additional, Clifton, David A, additional, Kapatai, Georgia, additional, Ip, Camilla L C, additional, Bowden, Rory, additional, Drobniewski, Francis A, additional, Allix-Béguec, Caroline, additional, Gaudin, Cyril, additional, Parkhill, Julian, additional, Diel, Roland, additional, Supply, Philip, additional, Crook, Derrick W, additional, Smith, E Grace, additional, Walker, A Sarah, additional, Ismail, Nazir, additional, Niemann, Stefan, additional, and Peto, Tim E A, additional

Published
2015
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13. Mycobacterial DNA Extraction for Whole-Genome Sequencing from Early Positive Liquid (MGIT) Cultures

Author

Votintseva, Antonina A., primary, Pankhurst, Louise J., additional, Anson, Luke W., additional, Morgan, Marcus R., additional, Gascoyne-Binzi, Deborah, additional, Walker, Timothy M., additional, Quan, T. Phuong, additional, Wyllie, David H., additional, Del Ojo Elias, Carlos, additional, Wilcox, Mark, additional, Walker, A. Sarah, additional, Peto, Tim E. A., additional, and Crook, Derrick W., additional

Published
2015
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14. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

Author

Walker, Timothy M, primary, Lalor, Maeve K, additional, Broda, Agnieszka, additional, Ortega, Luisa Saldana, additional, Morgan, Marcus, additional, Parker, Lynne, additional, Churchill, Sheila, additional, Bennett, Karen, additional, Golubchik, Tanya, additional, Giess, Adam P, additional, Del Ojo Elias, Carlos, additional, Jeffery, Katie J, additional, Bowler, Ian C J W, additional, Laurenson, Ian F, additional, Barrett, Anne, additional, Drobniewski, Francis, additional, McCarthy, Noel D, additional, Anderson, Laura F, additional, Abubakar, Ibrahim, additional, Thomas, H Lucy, additional, Monk, Philip, additional, Smith, E Grace, additional, Walker, A Sarah, additional, Crook, Derrick W, additional, Peto, Tim E A, additional, and Conlon, Christopher P, additional

Published
2014
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16. Assessment of Mycobacterium tuberculosistransmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

Author

Walker, Timothy M, Lalor, Maeve K, Broda, Agnieszka, Ortega, Luisa Saldana, Morgan, Marcus, Parker, Lynne, Churchill, Sheila, Bennett, Karen, Golubchik, Tanya, Giess, Adam P, Del Ojo Elias, Carlos, Jeffery, Katie J, Bowler, Ian C J W, Laurenson, Ian F, Barrett, Anne, Drobniewski, Francis, McCarthy, Noel D, Anderson, Laura F, Abubakar, Ibrahim, Thomas, H Lucy, Monk, Philip, Smith, E Grace, Walker, A Sarah, Crook, Derrick W, Peto, Tim E A, and Conlon, Christopher P

Abstract

Patients born outside the UK have contributed to a 20% rise in the UK's tuberculosis incidence since 2000, but their effect on domestic transmission is not known. Here we use whole-genome sequencing to investigate the epidemiology of tuberculosis transmission in an unselected population over 6 years.

Published
2014
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17. Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping

Author

Quan, T. Phuong, Bawa, Zharain, Foster, Dona, Walker, Tim, del Ojo Elias, Carlos, Rathod, Priti, Iqbal, Zamin, Bradley, Phelim, Mowbray, Janet, Walker, A. Sarah, Crook, Derrick W., Wyllie, David H., Peto, Timothy E. A., and Smith, E. Grace

Abstract

ABSTRACTUse of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-line Mycobacterium tuberculosisresistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728 M. tuberculosiscomplex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777 M. tuberculosiscomplex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively (P= 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made.

Published
2017
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18. Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping.

Author

Quan TP, Bawa Z, Foster D, Walker T, Del Ojo Elias C, Rathod P, Iqbal Z, Bradley P, Mowbray J, Walker AS, Crook DW, Wyllie DH, Peto TEA, and Smith EG

Subjects
Antitubercular Agents pharmacology, Drug Resistance, Bacterial drug effects, Humans, Isoniazid pharmacology, Mycobacterium tuberculosis drug effects, Mycobacterium tuberculosis genetics, Prospective Studies, Rifampin pharmacology, Sensitivity and Specificity, Time Factors, Tuberculosis diagnosis, Drug Resistance, Bacterial genetics, Genome, Bacterial genetics, Molecular Typing methods, Mycobacterium tuberculosis isolation & purification, Tuberculosis microbiology
Abstract

Use of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-line Mycobacterium tuberculosis resistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728 M. tuberculosis complex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777 M. tuberculosis complex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively ( P = 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made., (Copyright © 2018 Quan et al.)

Published
2018
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