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Literature DB >> 25673795

Integration of whole-genome sequencing into infection control practices: the potential and the hurdles.

Abstract

Microbial whole-genome sequencing (WGS) is poised to transform many of the currently used approaches in medical microbiology. Recent reports on the application of WGS to understand genetic evolution and reconstruct transmission pathways have provided valuable information that will influence infection control practices. While this technology holds great promise, obstacles to full implementation remain. Two articles in this issue of the Journal of Clinical Microbiology (S. Octavia, Q. Wang, M. M. Tanaka, S. Kaur, V. Sintchenko, and R. Lan, J Clin Microbiol 53:1063-1071, 2015, doi:10.1128/JCM.03235-14, and S. J. Salipante, D. J. SenGupta, L. A. Cummings, T. A. Land, D. R. Hoogestraat, and B. T. Cookson, J Clin Microbiol 53:1072-1079, 2015, doi:10.1128/JCM.03385-14) describe the breadth of application of WGS to the field of clinical epidemiology.

Mesh：

Year: 2015 PMID： 25673795 PMCID： PMC4365213 DOI： 10.1128/JCM.00349-15

Source DB: PubMed Journal: J Clin Microbiol ISSN： 0095-1137 Impact factor: 5.948

13 in total

1. Performance comparison of benchtop high-throughput sequencing platforms.

Authors: Nicholas J Loman; Raju V Misra; Timothy J Dallman; Chrystala Constantinidou; Saheer E Gharbia; John Wain; Mark J Pallen
Journal: Nat Biotechnol Date: 2012-05 Impact factor: 54.908

Review 2. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions.

Authors: W Florian Fricke; David A Rasko
Journal: Nat Rev Genet Date: 2013-11-26 Impact factor: 53.242

3. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

Authors: Stephen J Salipante; Dhruba J SenGupta; Lisa A Cummings; Tyler A Land; Daniel R Hoogestraat; Brad T Cookson
Journal: J Clin Microbiol Date: 2015-01-28 Impact factor: 5.948

4. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.

Authors: Evan S Snitkin; Adrian M Zelazny; Pamela J Thomas; Frida Stock; David K Henderson; Tara N Palmore; Julia A Segre
Journal: Sci Transl Med Date: 2012-08-22 Impact factor: 17.956

5. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Authors: Claudio U Köser; Matthew T G Holden; Matthew J Ellington; Edward J P Cartwright; Nicholas M Brown; Amanda L Ogilvy-Stuart; Li Yang Hsu; Claire Chewapreecha; Nicholas J Croucher; Simon R Harris; Mandy Sanders; Mark C Enright; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Louise J Fraser; Jason R Betley; Ole B Schulz-Trieglaff; Geoffrey P Smith; Sharon J Peacock
Journal: N Engl J Med Date: 2012-06-14 Impact factor: 91.245

Review 6. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.

Authors: Claudio U Köser; Matthew J Ellington; Edward J P Cartwright; Stephen H Gillespie; Nicholas M Brown; Mark Farrington; Matthew T G Holden; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Sharon J Peacock
Journal: PLoS Pathog Date: 2012-08-02 Impact factor: 6.823

7. Diverse sources of C. difficile infection identified on whole-genome sequencing.

Authors: Derrick W Crook; Mark H Wilcox; Tim E A Peto; A Sarah Walker; David W Eyre; Madeleine L Cule; Daniel J Wilson; David Griffiths; Alison Vaughan; Lily O'Connor; Camilla L C Ip; Tanya Golubchik; Elizabeth M Batty; John M Finney; David H Wyllie; Xavier Didelot; Paolo Piazza; Rory Bowden; Kate E Dingle; Rosalind M Harding
Journal: N Engl J Med Date: 2013-09-26 Impact factor: 91.245

8. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.

Authors: Claudio U Köser; Josephine M Bryant; Jennifer Becq; M Estée Török; Matthew J Ellington; Marc A Marti-Renom; Andrew J Carmichael; Julian Parkhill; Geoffrey P Smith; Sharon J Peacock
Journal: N Engl J Med Date: 2013-07-18 Impact factor: 91.245

9. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Authors: Andreas Roetzer; Roland Diel; Thomas A Kohl; Christian Rückert; Ulrich Nübel; Jochen Blom; Thierry Wirth; Sebastian Jaenicke; Sieglinde Schuback; Sabine Rüsch-Gerdes; Philip Supply; Jörn Kalinowski; Stefan Niemann
Journal: PLoS Med Date: 2013-02-12 Impact factor: 11.069

10. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.

Authors: Timothy M Walker; Camilla L C Ip; Ruth H Harrell; Jason T Evans; Georgia Kapatai; Martin J Dedicoat; David W Eyre; Daniel J Wilson; Peter M Hawkey; Derrick W Crook; Julian Parkhill; David Harris; A Sarah Walker; Rory Bowden; Philip Monk; E Grace Smith; Tim E A Peto
Journal: Lancet Infect Dis Date: 2012-11-15 Impact factor: 25.071

6 in total

1. Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility.

Authors: Arnoud H M van Vliet; Johannes G Kusters
Journal: J Clin Microbiol Date: 2015-07-01 Impact factor: 5.948

2. Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.

Authors: Varvara K Kozyreva; Chau-Linda Truong; Alexander L Greninger; John Crandall; Rituparna Mukhopadhyay; Vishnu Chaturvedi
Journal: J Clin Microbiol Date: 2017-06-07 Impact factor: 5.948

3. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations.

Authors: Margaret M C Lam; Ryan R Wick; Kelly L Wyres; Claire L Gorrie; Louise M Judd; Adam W J Jenney; Sylvain Brisse; Kathryn E Holt
Journal: Microb Genom Date: 2018-07-09