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Integration of genomic and clinical data augments surveillance of healthcare-acquired infections
- Doyle V. Ward, Andrew G. Hoss, Raivo Kolde, Helen C. van Aggelen, Joshua Loving, Stephen A. Smith, Deborah A. Mack, Raja Kathirvel, Jeffery A. Halperin, Douglas J. Buell, Brian E. Wong, Judy L. Ashworth, Mary M. Fortunato-Habib, Liyi Xu, Bruce A. Barton, Peter Lazar, Juan J. Carmona, Jomol Mathew, Ivan S. Salgo, Brian D. Gross, Richard T. Ellison III
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 40 / Issue 6 / June 2019
- Published online by Cambridge University Press:
- 23 April 2019, pp. 649-655
- Print publication:
- June 2019
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- Article
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Background:
Determining infectious cross-transmission events in healthcare settings involves manual surveillance of case clusters by infection control personnel, followed by strain typing of clinical/environmental isolates suspected in said clusters. Recent advances in genomic sequencing and cloud computing now allow for the rapid molecular typing of infecting isolates.
Objective:To facilitate rapid recognition of transmission clusters, we aimed to assess infection control surveillance using whole-genome sequencing (WGS) of microbial pathogens to identify cross-transmission events for epidemiologic review.
Methods:Clinical isolates of Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Klebsiella pneumoniae were obtained prospectively at an academic medical center, from September 1, 2016, to September 30, 2017. Isolate genomes were sequenced, followed by single-nucleotide variant analysis; a cloud-computing platform was used for whole-genome sequence analysis and cluster identification.
Results:Most strains of the 4 studied pathogens were unrelated, and 34 potential transmission clusters were present. The characteristics of the potential clusters were complex and likely not identifiable by traditional surveillance alone. Notably, only 1 cluster had been suspected by routine manual surveillance.
Conclusions:Our work supports the assertion that integration of genomic and clinical epidemiologic data can augment infection control surveillance for both the identification of cross-transmission events and the inclusion of missed and exclusion of misidentified outbreaks (ie, false alarms). The integration of clinical data is essential to prioritize suspect clusters for investigation, and for existing infections, a timely review of both the clinical and WGS results can hold promise to reduce HAIs. A richer understanding of cross-transmission events within healthcare settings will require the expansion of current surveillance approaches.
List of Contributors
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- By Harold P. Adams, Colum F. Amory, Anne Angelillo-Scherrer, Irena Anselm, Marcel Arnold, Robert W. Baloh, Ralf W. Baumgartner, José Biller, Valérie Biousse, Matthias Bischof, Julien Bogousslavsky, Natan M. Bornstein, Marie Germaine Bousser, Robin L. Brey, John C. M. Brust, Alan Bryer, Olivier Calvetti, Louis R. Caplan, José Castillo, Hugues Chabriat, Chin-Sang Chung, Charlotte Cordonnier, Steven C. Cramer, Luís Cunha, Rima M. Dafer, John F. Dashe, Cyrus K. Dastur, Antonio Dávalos, Larry E. Davis, Patricia Davis, Stephen M. Davis, Jan L. De Bleecker, Michael A. De Georgia, Amir R. Dehdashti, Oscar H. Del Brutto, Jacques L. De Reuck, Hans-Christoph Diener, Kathleen B. Digre, Vivian U. Fritz, Nancy Futrell, Bhuwan P. Garg, Philip B. Gorelick, Glenn D. Graham, Alexander Y. Gur, John J. Halperin, Michael Hennerici, Isabel Lestro Henriques, Roberto C. Heros, Daniel B. Hier, Lorenz Hirt, Joanna C. Jen, Taro Kaibara, Sumit Kapoor, Sarosh M. Katrak, Siddharth Kharkar, Walter J. Koroshetz, Monisha Kumar, Sandeep Kumar, Emre Kumral, Tobias Kurth, Rogelio Leira, Steven R. Levine, Didier Leys, Doris Lin, Jonathan Lipton, Alfredo M. Lopez-Yunez, Betsy B. Love, Ayrton Roberto Massaro, Heinrich P. Mattle, Manu Mehdiratta, John H. Menkes, Philippe Metellus, Reto Meuli, Patrik Michel, Panayiotis Mitsias, Jorge Moncayo-Gaete, Julien Morier, Krassen Nedeltchev, Bernhard Neundörfer, Olukemi A. Olugemo, Nikolaos I. H. Papamitsakis, Stephen D. Reck, Luca Regli, Marc D. Reichhart, Daniele Rigamonti, Michael J. Rivkin, E. Steve Roach, Jose F. Roldan, David Z. Rose, Daniel M. Rosenbaum, N. Paul Rosman, Elayna O. Rubens, Sean I. Savitz, Marc Schapira, Robert J. Schwartzman, Magdy Selim, Yukito Shinohara, Aneesh B. Singhal, Michael A. Sloan, Barney J. Stern, Mathias Sturzenegger, Oriana Thompson, A. Wesley Thevathasan, Jonathan D. Trobe, Michael Varner, Dana Védy, Jorge Vidaurre, Engin Y. Yilmaz, Khaled Zamel, Mathieu Zuber
- Edited by Louis R. Caplan, Julien Bogousslavsky
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- Book:
- Uncommon Causes of Stroke
- Published online:
- 06 January 2010
- Print publication:
- 09 October 2008, pp ix-xiv
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- Chapter
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Salinity stress inhibits calcium loading into the xylem of excised barley (Hordeum vulgare) roots
- STEPHEN J. HALPERIN, LEON V. KOCHIAN, JONATHAN P. LYNCH
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- Journal:
- The New Phytologist / Volume 135 / Issue 3 / March 1997
- Published online by Cambridge University Press:
- 01 March 1997, pp. 419-427
- Print publication:
- March 1997
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Salinity stress inhibits Ca translocation to the shoot, leading to Ca deficiency. The objective of this study was to determine whether salt stress inhibits Ca translocation through effects on younger root regions, where radial Ca transport is largely apoplastic, or through effects on mature regions of the roots, where radial Ca transport is largely symplastic. Roots were excised from 4-d-old dark-grown barley seedlings. Calcium translocation was studied by application of 45Ca 3 or 6 cm from the root tip and measurement of its appearance in the root exudate. Calcium uptake along the axis of excised roots was studied with a vibrating Ca+2 microelectrode. Salt stress (60 mM NaCl) inhibited Ca translocation from the 6 cm region more than from the 3 cm region. Sodium sulphate treatments (30 and 36 mM) were more deleterious to Ca translocation than was NaCl in the 3 cm region, and 110 mM mannitol and 60 mM KCl affected Ca translocation similarly to Na2SO4. The salt and mannitol treatments were more deleterious to Ca translocation in the 6 cm region than in the 3 cm region, and mannitol and KCl inhibited Ca translocation more than the sodium treatments. Supplemental Ca could overcome the inhibition of Ca translocation by NaCl stress. Calcium uptake into the root at the 3 and 6 cm regions was not reduced by NaCl, but was retarded 0·05 cm from the apex. We conclude that symplastic Ca transport is more inhibited than apoplastic transport in salinized roots, and that the osmotic component of salt stress causes most of the inhibition. Since symplastic transport is inhibited, the possibility exists that research into the effects of salinity on the transport functions of endodermal cells will yield information that can be used to improve Ca translocation in salt-affected plants.