Characterizing an outbreak of vancomycin-resistant enterococci using hidden Markov models

Journal of the Royal Society Interface

Volumn 4, Issue 15, 2007, Pages 745-754

  McBryde, E S ^a   Pettitt, A N ^a   Cooper, B S ^b   McElwain, D L S ^a  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

^b PUBLIC HEALTH ENGLAND   (United Kingdom)

Author keywords

Genotyping; HMM; Nosocomial pathogens; Statistical modelling; VRE

Indexed keywords

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL TRANSMISSION; BACTERIUM CONTAMINATION; CLUSTER ANALYSIS; CONTROLLED STUDY; ENTEROCOCCAL INFECTION; GENOTYPE; HIDDEN MARKOV MODEL; HUMAN; INFECTION CONTROL; PHENOTYPE; PULSED FIELD GEL ELECTROPHORESIS; VANCOMYCIN RESISTANT ENTEROCOCCUS;

EID: 34547637084     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2007.0224     Document Type: Article

References (28)

1. Bailey, N. 1975 The biomathematics of malaria. London, UK: Charles Griffin.
2. Bartley, P. B., Schooneveldt, J. M., Looke, D. F., Morton, A., Johnson, D. W. & Nimmo, G. R. 2001 The relationship of a clonal outbreak of Enterococcus faecium VanA to methicillin-resistant Staphylococcus aureus incidence in an Australian hospital. J. Hosp. Infect. 48, 43-54. (doi:10. 1053/jhin.2000.0915)
3. Baum, L., Petrie, T., Soules, G. & Weiss, N. 1970 A maximisation technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat. 41, 164-171.
4. Boyce, J. M. 2001 MRSA patients: proven methods to treat colonization and infection. J. Hosp. Infect. 48(Suppl. A), S9-S14. (doi:10.1016/S0195-6701(01)90005-2)
5. Bradley, S. J., Kaufmann, M. E., Happy, C., Ghori, S., Wilson, A. L. & Scott, G. M. 2002 The epidemiology of glycopeptide-resistant enterococci on a haematology unit: analysis by pulsed-field gel electrophoresis. Epidemiol. Infect. 129, 57-64. (doi:10.1017/S0950268802007033)
6. Cooper, B. & Lipsitch, M. 2004 The analysis of hospital infection data using Hidden Markov models. Biostatistics 5, 223-237. (doi:10.1093/biostatistics/5.2.223)
7. Cox, D. R. & Miller, H. D. 1965 The theory of stochastic processes. London, UK: Methuen.
8. D'Agata, E. M., Gautam, S., Green, W. K. & Tang, Y. W. 2002 High rate of false-negative results of the rectal swab culture method in detection of gastrointestinal colonization with vancomycin-resistant enterococci. Clin. Infect. Dis. 34, 167-172. (doi:10.1086/338234)
9. Donskey, C. J., Hoyen, C. K., Das, S. M., Helfand, M. S. & Hecker, M. T. 2002 Recurrence of vancomycin-resistant enterococcus stool colonization during antibiotic therapy. Infect. Control Hosp. Epidemiol. 23, 436-440. (doi:10.1086/ 502081)
10. Forrester, M. & Pettitt, A. N. 2005 Use of stochastic epidemic modeling to quantify transmission rates of colonization with methicillin-resistant Staphylococcus aureus in an intensive care unit. Infect. Control Hosp. Epidemiol. 26, 598-606. (doi:10.1086/502588)
11. Gelman, A., Carlin, J., Stern, H. & Rubin, D. B. 2004 Bayesian data analysis 2nd edn., p. Fla. Boca Raton, FL: Chapman and Hall/CRC.
12. Giesecke, J. 1994 Modern infectious disease epidemiology. London, UK: Edward Arnold.
13. Gilks, W., Richardson, S. & Spiegelhalter, D. 1996 Markov Chain Monte Carlo in practice. London, UK: Chapman and Hall.
14. Green, P. 1995 Reversible jump Markov Chain Monte Carlo computation and Bayesian Model determination. Biometrika 82, 711-732. (doi:10.1093/biomet/82.4.711)
15. Le Strat, Y. & Carrat, F. 1999 Monitoring epidemiologic surveillance data using hidden Markov models. Stat. Med. 18, 3463-3478. (doi:10.1002/(SICI)1097-0258(19991230) 18:24〈3463::AID-SIM409〉3.0. CO;2-I)
16. Lemmen, S. W., Hafner, H., Zolldann, D., Amedick, G. & Lutticken, R. 2001 Comparison of two sampling methods for the detection of Gram-positive and Gram-negative bacteria in the environment: moistened swabs versus rodac plates. Int. J. Hyg. Environ. Health 203, 245-248. (doi:10. 1078/S1438-4639(04)70035-8)
17. Lodise, T. P., McKinnon, P. S., Tarn, V. H. & Rybak, M. J. 2002 Clinical outcomes for patients with bacteremia caused by vancomycin-resistant enterococcus in a level 1 trauma center. Clin. Infect. Dis. 34, 922-929. (doi:10.1086/339211)
18. MacDonald, I. & Zucchini, W. 1997 Hidden Markov models for discrete valued time series. London, UK: Chapman and Hall.
19. Murray, B. 2006 Overview of enterococci. In UpToDate (ed. B. D. Rose). Massachusetts, MA: UpToDate. (CD-rom.)
20. Pelupessy, I., Bonten, M. J. & Diekmann, O. 2002 How to assess the relative importance of different colonization routes of pathogens within hospital settings. Proc. Natl Acad. Sci. USA 99, 5601-5605. (doi:10.1073/pnas.082412899)
21. Petrushin, V. 2000 Hidden Markov models: fundamentals and applications. Part2 Discrete and continuous hidden Markov models. In Online Symp. for Electronics Engineers. http:// www.techonline.com/osee/.
22. Reisner, B. S., Shaw, S., Huber, M. E., Woodmansee, C. E., Costa, S., Falk, P. S. & Mayhall, C. G. 2000 Comparison of three methods to recover vancomycin-resistant enterococci (VRE) from perianal and environmental samples collected during a hospital outbreak of VRE. Infect. Control Hosp. Epidemiol. 21, 775-779. (doi:10.1086/501734)
23. Stephens, M. 2000 Bayesian analysis of mixture models with an unknown number of components-an alternative to reversible jump methods. Ann. Stat. 28, 40-74. (doi:10. 1214/aos/1016120364)
24. Suppola, J. P., Kolho, E., Salmenlinna, S., Tarkka, E., Vuopio-Varkila, J. & Vaara, M. 1999 van A and vanB incorporate into an endemic arnpicillin-resistant vancomycin-sensitive Enterococcus faecium strain: effect on interpretation of clonality. J. Clin. Microbiol. 37, 3934-3939.
25. Tenover, F., Arbeit, R., Goering, R., Mickelsen, P., Murray, B., Persing, D. & Swaminathan, B. 1995 Interpreting chromosomal DNA restriction patterns produced by pulsed field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33, 2233-2239.
26. Trick, W. E., Kuehnert, M. J., Quirk, S. B., Arduino, M. J., Aguero, S. M., Carson, L. A., Hill, B. C., Banerjee, S. N. & Jarvis, W. R. 1999 Regional dissemination of vancomycin-resistant enterococci resulting from interfacility transfer of colonized patients. J. Infect. Dis. 180, 391-396. (doi:10. 1086/314898)
27. Trick, W. E., Paule, S. M., Cunningham, S., Cordell, R. L., Lankford, M., Stosor, V., Solomon, S. L. & Peterson, L. R. 2004 Detection of vancomycin-resistant enterococci before and after antimicrobial therapy: use of conventional culture and polymerase chain reaction. Clin. Infect. Dis. 38, 780-786. (doi:10.1086/381552)
28. Weinstein, J. 2005 Hospital-acquired (nosocomial) infections with vancomycin-resistant enterococci. In UpToDate (ed. B. D. Rose), p. 2006. Massachusetts, MA: UpToDate. (CD-rom.)