Bibliography
Published Bacterial Identification Matrices
The following table lists probabilistic identification matrices that has been complied by various means including bibliographic searching and cross referencing of known papers. The list covers papers published since 1980. This list is not be exhaustive, but it was compiled with the intention of identifying as many probabilistic identification matrices as possible. If you know of any omissions please let me know T.N.Bryant@southampton.ac.uk
| Species/Groups covered | Taxa | Tests | Data pub. | Matrix eval | Clus Anal | Method | % id | ID coef | Media | References |
| Gram-negative, aerobic, non-fermenters | 66 | 83 | y | y | n | 2 | 91.5 | .999 | Conventional | Holmes et al., 1986b |
| Gram-negative, aerobic rod-shaped fermenters | 110 | 66 | y | y | n | 2 | 89.2 | .999 | Conventional | Holmes et al., 1986a |
| Enterobacteriaceae | 41 | 16 | y | y | n | 2 | 91.8 | .95 | Conventional Multipoint inoculation | Clayton et al., 1986 |
| Enterobacteriaceae | 90 | 50 | y | y | . | . | . | . | Conventional | Holmes & Costas, 1992 |
| Pseudomonas species | 26 | 70 | y | y | . | . | . | . | Conventional | Costas et al., 1992 |
| Vibrios | 31 | 50 | y | y | n | 2 | 79.4 | .99 | ConventionalAPI 20E | Dawson & Sneath, 1985 |
| Vibrio and related species | 38 | 81 | y | y | y | 1 | 74.0 | .999 | Conventional | Bryant et al., 1986 |
| Aeromonas species | 14 | 30 | y | y | y | 1 | 71.5 | .90 | microtitre | Kämpfer & Altwegg, 1992 |
| Aeromonas hybridization groups | 15 | 32 | y | y | . | . | . | . | Conventional | Oakley et al., 1996 |
| Aeromonas species | 14 | 31 | y | Carson et al., 2000 | ||||||
| Campylobacteria | 23 | 42 | n | y | y | 1 | . | 1 | Conventional | Holmes et al., 1992 |
| Lactic acid bacteria | 37 | 49 | n | n | n | 3 | 79.0 | .90 | API 50CH | Cox & Thomsen, 1990 |
| Lactic acid bacteria | 59 | 27 | y | n | n | 3 | 98.0 | .70 | Conventional | Döring et al., 1988 |
| Lactic acid bacteria | 11 | 53 | y | n | n | 2 | . | .999 | API 50CH | Maissin et al., 1987 |
| Streptomyces species | 23 | 41 | y | y | y | 1 | 81.3 | .85 | Conventional | Williams et al., 1983 |
| Streptomyces species (minor clusters) | 26 28 |
50 39 |
y | y | y | 1 | 77.0 | .85 | Conventional | Langham et al., 1989 |
| Streptomyces species | 52 | 50 | y | y | y | 1 | 78.1 | .90 | Miniaturised | Kämpfer & Kroppenstedt, 1991 |
| Streptoverticillum species | 24 | 41 | y | y | y | 1 | . | .95 | Conventional | Williams et al., 1985 |
| Actinomyces species | 25 | 53 | y | y | y | 1 | 71.9. | . | Conventional | Seong et al., 1995 |
| Actinomyces species | 20 | 18 | y | n | n | 2 | . | . | Conventional | Sarkonen et al., 2001 |
| Actionplanes species | 15 | 53 | y | y | y | 1 | . | . | Conventional | Long, 1994 |
| Phytopathogenic corynebacteria (subclusters) | 35 | 19 27 |
y | y | y | 1 | . | . | Conventional | Firrao & Locci, 1989 |
| Coryneform bacteria | 31 | 58 | y | y | y | 1 | 82.5 | .90 | Miniaturised | Kampfer et al., 1993 |
| Nocardioform bacteria | 25 | 35 | y | y | y | 1 | 80 | .90 | Miniaturised | Kampfer et al., 1990 |
| Slowly growing mycobacteria | 24 | 33 | y | n | y | 1 | . | . | Conventional | Wayne et al., 1991 |
| Non-tuberculous mycobacteria | 27 | 23 | y | n | n | 3 | 94.5 | . | Conventional | Tortoli et al., 1992 |
| Bacillus species | 44 | 30 | y | y | y | 1 | 70.0 | .95 | Conventional | Priest & Alexander, 1988 |
| Bacillus sphaericus | 14 | 29 | y | y | y | 1 | 100 | .999 | Conventional | Alexander & Priest, 1990 |
| Bacillus species | 36 | 44 | y | y | y | 1 | 73.4 | .99 | Miniaturised | Kampfer 1991 |
| Aerobic Gram-positive cocci catalase positive | 39 | 60 | y | y | y | 1 | 93.0 | .999 | API 50CH API 20E |
Feltham & Sneath, 1982 |
| Aerobic Gram-positive cocci catalase negative | 33 | 60 | y | y | y | 1 | 85.0 | .999 | API 50CH API 20E |
Feltham & Sneath, 1982 |
| Micrococcus | 29 | 35 | n | y | y | 1 | . | . | . | Alderson et al., 1991 |
| Staphylococcus species | 12 | 15 | y | y | n | 2 | 94.6 | . | API Staph | Geary et al., 1989 |
| Alaskan marine bacteria | 86 | 61 | n | n | y | 1 | 93.0 | .999 | Conventional | Davis et al., 1983 |
| Medical bacteria to genus level | 60 | 20 | y | y | n | 3 | . | .99 | various | Feltham et al., 1984 |
| Acinetobacter | 10 | 22 | y | y | y | 1 | 98 | .90 | conventional | Kampfer et al., 1993 |
Key to Abbreviations
Data Pub = Identification data given in publication
Matrix eval = Identification matrix evaluated for overlap or uniqueness of taxa
Clus Anal = Data analysed using Cluster analysis prior to creation of starting matrix
Method = The method used to collect the data for the identification matrix
- Cluster Analysis of strain data
- Use of data from identified isolates
- Data collected from the literature
%id = Percentage of strains identified when matrix evaluated
ID coef = Threshold (Willcox score) used for identification
References
Alderson, G., Amadi, E.N., Pulverer, G. and Zai, S. (1991) Recent advances in the classification and identification of the genus Micrococcus. In: Jeljaszewicz/Ciborowski, (Ed.) The Staphylococci, Zentralblatt für Bakteriologie Supplement 21, pp. 103-109. Stuggart: Gustav Fisher Verlag.
Alexander, B. and Priest, F.G. (1990) Numerical classification and identification of Bacillus sphaericus including some strains pathogenic for mosquito larvae. Journal of General Microbiology 136, 367-376.
Bryant, T.N., Lee, J.V., West, P.A. and Colwell, R.R. (1986) A probability matrix for the identification of species of Vibrio and related genera. Journal of Applied Bacteriology 61, 469-480.
Carson, J., Wagner,T., Wilson,T. and Donachie, L. (2001) Miniaturized tests for computer-assisted identification of motile Aeromonas species with an improved probability matrix. Journal of Applied Microbiology 90, 190-200.
Clayton, P., Feltham, R.K.A., Mitchell, C.J. and Sneath, P.H.A. (1986) Constructing a database for low cost identification Gram negative rods in clinical laboratories. Journal of Clinical Pathology 39, 798-802.
Costas, M., Holmes, B., On, S.L.W. and Stead, D.E. (1992) Identification of medically important Pseudomonas species using computerized methods. In: Board, R.G., Jones, D. and Skinner, F.A. (Eds.) Identification methods in applied and environmental microbiology, pp. 1-27. Oxford: Blackwell Scientific Publications]
Cox, R.P. and Thomsen, J.K. (1990) Computer-aided identification of lactic acid bacteria using the API 50 CHL system.Letters in Applied Microbiology 10, 257-259.
Davis, A.W., Atlas, R.M. and Krichevsky, M.I. (1983) Development of probability matrices for identification of marine bacteria. International Journal of Systematic Bacteriology 33, 803-810.
Dawson, C.A. and Sneath, P.H.A. (1985) A probability matrix for the identification of vibrios. Journal of Applied Bacteriology 58, 407-423.
Döring, B., Ehrhardt, S., Lücke, F. and Schillinger, U. (1988) Computer-assisted identification of lactic acid bacteria from meats. Systematic and Applied Microbiology 11, 67-74.
Feltham, R.K.A. and Sneath, P.H.A. (1982) Construction of matrices for computer-assisted identification of aerobic Gram-positive cocci. Journal of General Microbiology 128, 713-120.
Feltham, R.K.A., Wood, P.A. and Sneath, P.H.A. (1984) A general-purpose system for characterizing medically important bacteria to genus level. Journal of Applied Bacteriology 57, 279-290.
Firrao, G. and Locci, R. (1989) Identification by probabilistic methods of plant pathogenic corynebacteria. Annuals of Microbiology 39, 81-92.
Geary, C., Stevens, M., Sneath, P.H.A. and Mitchell, C.J. (1989) Construction of a database to identify Staphylococcus species. Journal of Clinical Pathology 42, 289-294.
Holmes, B. and Costas, M. (1992) Identification of Enterobacteriaceae by computerized methods. In: Board, R.G., Jones, D. and Skinner, F.A. (Eds.) Identification methods in applied and environmental microbiology, pp. 127-149. Oxford: Blackwell Scientific Publications]
Holmes, B., Dawson, C.A. and Pinning, C.A. (1986) A revised probability matrix for the identification of Gram-negative, aerobic, rod-shaped, fermentative bacteria. Journal of General Microbiology 132, 3113-3135.
Holmes, B., On, S.L.W., Ganner, M. and Costas, M. (1992) Some new applications of probabilistic identification. In: Schindler, J. (Ed.) Proceedings of the conference on taxonomy and automated identification of bacteria, pp. 6-9. Prague:
Holmes, B., Pinning, C.A. and Dawson, C.A. (1986) A probability matrix for the identification of Gram-negative, aerobic, non-fermentative bacteria that grow on nutrient agar. Journal of General Microbiology 132, 1827-1842.
Jilly, B.J. (1988) Microcomputer application of bayesean probability testing for the identification of bacteria.International Journal of Biomedical Computing 22, 107-119.
Kämpfer, P. (1991) Application of Miniaturised physiological tests in numerical classification and identification of some Bacilli . Journal of General and Applied Microbiology 37, 225-247.
Kämpfer, P. and Altwegg, M. (1992) Numerical classification and identification of Aeromonas genospecies. Journal of Applied Bacteriology 72, 341-351.
Kämpfer, P. Dott, W. and Kroppenstedt, R.M. (1990) Numerical classification and identification of some nocardioform bacteria. Journal of General and Applied Microbiology 36, 309-301.
Kämpfer, P. and Kroppenstedt, R.M. (1991) Probabilistic identification of streptomyces using miniaturized physiological tests. Journal of General Microbiology 137, 1893-1902.
Kämpfer, and Seiler, H. (1993) Probabilistic identification of coryneform bacteria. Journal of General and Applied Microbiology 39, 215-236.
Kämpfer, P. Tjernberg, I. and Ursing, J. (1993) Numerical classification and identification of Acinetobacter genomic species. Journal of Applied Bacteriology 75, 259-268.
Langham, C.D., Williams, S.T., Sneath, P.H.A. and Mortimer, A.M. (1989) New probability matrices for identification of Streptomyces. Journal of General Microbiology 135, 121-133.
Long, P.F. (1994) Identification of some industrially important Actioplanes species. Journal Industrial Microbiology 13, 300-310.
Maissin, R., Bernard, A., Duquenne, V., Baeten, S., Gerard, G. and Decallonne, J. (1987) Characteristics of a computer-aided procedure for the identification of lactobacilli. Belgian Journal of Food Chemistry and Biotechnology 42, 176-183.
Oakley, H.J., Ellis, J.E. and Gibson, L.F. (1996) A biochemical protocol for the differentiation of current genomospecies of Aeromonas. Zentralblatt fur bakteriologie-International Journal of Medical Microbiology Virology Parasitology and Infectious diseases 284, 32-46.
On, S.L.W., Holmes, B. and Sackin, M.J. (1996) A probability matrix for the identification of Campylobacters Helicobacters and allied taxa. Journal of Applied Bacteriology 81,425-432.
Priest, F.G. and Alexander, B. (1988) A frequency matrix for the probabilistic identification of some bacilli. Journal of General Microbiology 134, 3011-3018.
Seong, C.N., Park, S.K., Goodfellow, M., Kim, S.B., and Hah Y.C. (1995) Construction of probability matrix and selective medium for acidophilic actinomycetes using numerical classification data. Journal of Microbiology 33, 95-102.
Sarkonen, N., Könnönen, E., Summanen, P., Könnönen, M., and Jousimies-Somer, H., (2001) Phenotypic identification of Actinomyces and related species isolated from Human sources. Journal of Clinical Microbiology 39, 3955-3961.
Tortoli, E., Boddi, V. and Penati, V. (1992) Development and evaluation of a program and probability matrix for the computer-aided identification of non-tuberculous mycobacteria. Binary - Computing in Microbiology 4, 200-203.
Wayne, L.G., Good, R.C., Krichevsky, M.I., Blacklock, Z., David, H.L., Dawson, D., Gross, W., Hawkins, J., Vincent Levy-Frebault, V., McManus, C., Portaels, F., Rusch-Gerdes, S., Schroder, K.H., Silcox, V.A., Tsukamura, M., Van Den Breen, L. and Yarkrus, M.A. (1991) Fourth report of the cooperative, open-ended study of slowly growing mycobacteria by the international working group on mycobacterial taxonomy. International Journal of Systematic Bacteriology 41, 463-472.
Williams, S.T., Goodfellow, M., Wellington, E.M.H., Vickers, J.C., Alderson, G., Sneath, P.H.A., Sackin, M.J. and Mortimer, A.M. (1983) A probability matrix for identification of some streptomycetes. Journal of General Microbiology129, 1815-1830.
Williams, S.T., Locci, R., Vickers, J.C., Schofield, G.M., Sneath, P.H.A. and Mortimer, A.M. (1985) Probabilistic identification of Streptoverticillium species. Journal of General Microbiology 131, 1681-1689.