The Annals of Applied Statistics

Statistical methods for automated drug susceptibility testing: Bayesian minimum inhibitory concentration prediction from growth curves

Xi Kathy Zhou, Merlise A. Clyde, James Garrett, Viridiana Lourdes, Michael O’Connell, Giovanni Parmigiani, David J. Turner, and Tim Wiles

Source: Ann. Appl. Stat. Volume 3, Number 2 (2009), 710-730.

Abstract

Determination of the minimum inhibitory concentration (MIC) of a drug that prevents microbial growth is an important step for managing patients with infections. In this paper we present a novel probabilistic approach that accurately estimates MICs based on a panel of multiple curves reflecting features of bacterial growth. We develop a probabilistic model for determining whether a given dilution of an antimicrobial agent is the MIC given features of the growth curves over time. Because of the potentially large collection of features, we utilize Bayesian model selection to narrow the collection of predictors to the most important variables. In addition to point estimates of MICs, we are able to provide posterior probabilities that each dilution is the MIC based on the observed growth curves. The methods are easily automated and have been incorporated into the Becton–Dickinson PHOENIX automated susceptibility system that rapidly and accurately classifies the resistance of a large number of microorganisms in clinical samples. Over seventy-five studies to date have shown this new method provides improved estimation of MICs over existing approaches.

Keywords: Bayes; BIC; decision theory; logistic regression; model selection; model uncertainty

Full-text: Access denied (no subscription detected)

In 2007, access to the Annals of Applied Statistics was open. Beginning in 2008, you must hold a subscription or be a member of the IMS to view the full journal. For more information on subscribing, please visit: http://imstat.org/orders.
If you are already an IMS member, you may need to update your Euclid profile following the instructions here: http://imstat.org/publications/eaccess.htm.
Links and Identifiers

Permanent link to this document: http://projecteuclid.org/euclid.aoas/1245676192
Digital Object Identifier: doi:10.1214/08-AOAS217
Zentralblatt MATH identifier: 1166.62087

References

Akaike, H. (1973). Information theory and an extension of the maximum likelihood principle. In, Second International Symposium on Information Theory (B. Petrox and F. Caski, eds.) 267–281. Akadémiai Kiado, Budapest.
Mathematical Reviews (MathSciNet): MR483125
Zentralblatt MATH: 0283.62006
Akaike, H. (1983a). Information measures and model selection (STMA V25 937)., Bulletin of the International Statistical Institute 50 277–290.
Mathematical Reviews (MathSciNet): MR820726
Akaike, H. (1983b). On minimum information prior distributions., Ann. Inst. Statist. Math. 35 139–149.
Mathematical Reviews (MathSciNet): MR716025
Zentralblatt MATH: 0525.62005
Digital Object Identifier: doi:10.1007/BF02480970
Barenfanger, J., Drake, C. and Kacich, G. (1999). Clinical and financial benefits of rapid bacterial identification and antimicrobial susceptibility testing., Journal of Clinical Microbiology 37 1415–1418.
CLSI (2006)., Methods for Dilution Antimicrobial Susceptibility Testing for Bacteria that Grow Aerobically; Approved Standard M7–A7, 7th ed. Clinical and Laboratory Standards Institute, Wayne, PA.
CLSI (2008)., Performance Standards for Antimicrobial Susceptibility Testing; Eightenenth Informational Supplement M100–S18, 18th ed. Clinical and Laboratory Standards Institute, Wayne, PA.
Clyde, M. and George, E. I. (2004). Model uncertainty., Statist. Sci. 19 81–94.
Mathematical Reviews (MathSciNet): MR2082148
Digital Object Identifier: doi:10.1214/088342304000000035
Project Euclid: euclid.ss/1089808274
Deal, M., Votta, M., Turng, S. H. B., Wiles, T. and Reuben, J. (2002). Detection of glycopeptide intermediate or resistant, staphylococcus aureus strains using BD Phoenixtm automated microbiology system. In 101st General Meeting of the American Society for Microbiology. Salt Lake City, Utah. Poster C-119.
Donay, J.-L., Mathieu, D., Fernandes, P., Prégermain, C., Bruel, P., Wargnier, A., Casin, I., Weill, F. X., Lagrange, P. H. and Herrmann, J. L. (2004). Evaluation of the automated Phoenix system for potential routine use in the clinical microbiology laboratory., Journal of Clinical Microbiology 42 1542–1546.
Fahr, A.-M., Eigner, U., Armbrust, M., Caganic, A., Dettori, G., Chezzi, C., Bertoncini, L., Benecchi, M. and Menozzi, M. G. (2003). Two-center collaborative evaluation of the performance of the BD Phoenix automated microbiology system for identification and antimicrobial susceptibility testing of, Enterococcus spp. and Staphylococcus spp. Journal of Clinical Microbiology 41 1135–1142.
FDA (2007)., Class II Special Controls Guidance Document: Antimicrobial Susceptibility Test (AST) System; Guidance for Industry and FDA. Center for Devices and Radiological Health, Food and Drug Administration, U.S. Department of Health and Human Services, Washington, DC.
Ferraro, M. J. and Jorgensen, J. H. (2003). Susceptibility testing instrumentation and computerized expert systems for data analysis and interpretation. In, Manual of Clinical Microbiology (P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller and R. H. Yolken, eds.) 208–217. Am. Soc. Microbiol., Washington, DC.
Hoeting, J. A., Madigan, D., Raftery, A. E. and Volinsky, C. T. (1999). Bayesian model averaging: A tutorial (with discussion)., Statist. Sci. 14 382–417. Corrected version at http://www.stat.washington.edu/www/research/online/hoeting1999.pdf.
Mathematical Reviews (MathSciNet): MR1765176
Digital Object Identifier: doi:10.1214/ss/1009212519
Project Euclid: euclid.ss/1009212519
Horstkotte, M. A., Knobloch, J. K.-M., Rohde, H., Dobinsky, S. and Mack, D. (2004). Evaluation of the BD Phoenix automated microbiology system for detection of methicillin resistance in coagulase-negative staphylococci., Journal of Clinical Microbiology 42 5041–5046.
Jorgensen, J. H. and Turnidge, J. D. (2003). Susceptibility test methods: Dilution and disk diffusion methods. In, Manual of Clinical Microbiology (P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller and R. H. Yolken, eds.) 1108–1127. Am. Soc. Microbiol., Washington, DC.
Kass, R. E. and Raftery, A. E. (1995). Bayes factors., J. Amer. Statist. Assoc. 90 773–795.
Schwarz, G. (1978). Estimating the dimension of a model., Ann. Statist. 6 461–464.
Mathematical Reviews (MathSciNet): MR468014
Zentralblatt MATH: 0379.62005
Digital Object Identifier: doi:10.1214/aos/1176344136
Project Euclid: euclid.aos/1176344136
Tenover, F. C., Kalsi, R. K., Williams, P. P., Carey, R. B., Stocker, S., Lonsway, D., Rasheed, J. K., Biddle, J. W., J. E. McGowan, Jr. and Hanna, B. (2006). Carbapenem resistance in, klebsiella pneumoniae not detected by automated susceptibility testing. Emerging Infectious Diseases 12 1209–1213.
Turnidge, J. D., Ferraro, M. J. and Jorgensen, J. H. (2003). Susceptibility test methods: General considerations. In, Manual of Clinical Microbiology (P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller and R. H. Yolken, eds.) 1102–1107. Am. Soc. Microbiol., Washington, DC.
Wheat, P. F. (2001). History and development of antimicrobial susceptibility testing methodology., Journal of Antimicrobial Chemotherapy 48 1–4.

2009 © Institute of Mathematical Statistics