- Volume 24, Issue 4, 1974

The generic name Rhodopseudomonas Czurda and Maresch emend, van Niel has been conserved by the Judicial Commission of the International Committee on Systematic Bacteriology.

The epithet fortuitum in the combination Mycobacterium fortuitum da Costa Cruz has been conserved by the Judicial Commission of the International Committee on Systematic Bacteriology.

All identification processes are strictly probabilistic. Identification allocates initially unidentified operational taxonomic units (U-OTUs) to taxa contained in previously established classifications. Identification is therefore subject to a number of a priori conditions, such as the probabilistic nature of classifications, the manner in which classifications are made, the adequacy of classifications, and the adequacy of the set of characters describing U-OTUs. The advantages and disadvantages of continuous reclassification, incorporating U-OTUs, are discussed. Numerical identification is concerned with extracting from a classification a minimum, or near minimum, amount of information necessary to effect separation of all the taxa defined by the classification. Several strategies are available for achieving this-test reduction, OTU reduction, a combination of both of these, and key generation.

Computer-assisted probabilistic identification of 1,079 reference and 516 field strains of gram-negative, rod-shaped bacteria are described. Success rates have been achieved which compare favorably with those obtained by conventional identification. The choice of tests and taxa for inclusion in a probability matrix and estimation of the probabilities are discussed. Problems arise when information is unavailable or tests are meaningless or inapplicable. Mathematical methods are needed for these problems and for tests that are linked causally or logically. The allotment of probabilities is made more difficult by the existence of known biotypes within particular taxa and by the geographical distribution of such biotypes. Automatic modification in the computer of the allotted probabilities for the taxa by the results found for fresh strains is not recommended. A method for selecting those tests with the greatest discriminating power between suggested taxa from tests not already used is described.

Test errors are much greater than usually thought and their investigation requires good statistical design. Analysis of variance of blind randomized trials is especially valuable. For representative selections of tests currently used in bacterial taxonomy and identification, the discrepancies within one laboratory are usually less than 4%; with care they can be reduced to 2% or less. Between-laboratory variation is much greater; discrepancies of about 8% are usual under routine conditions, and even 15% is common. The effect of errors on identification is due to (a) error in the reference descriptions of taxa, (b) error in the description of the unknown strain to be identified. Simultaneous polythetic methods (e.g., using matching coefficients or analogues of these) are robust to both types of error, and misidentifications are usually minor in degree, i.e., the unknown is allocated to a taxon close to the correct one. The rate of failure is expected to be greatest when the reference descriptions are based on the tightest clusters. Sequential identification methods are especially sensitive to errors because the unknown may then be allocated to a taxon far from the correct one. Monothetic sequential keys are sensitive to errors of type (b), whereas type (a) error is usually screened out during construction of the key.

Determinative bacteriology inherently involves acquisition and manipulation of many small pieces of information. Much of this information is codable directly in binary (i.e., "yes" or "no") form. Digital computers are uniquely suited to perform the desired data processing. Although at least one extensive coding system with some associated computer programs has been developed, much remains to be done before a universally applicable microbial data system is available. Some of these remaining computer technology tasks are the development of complete systems for data handling, data compression methods, and common specifications for data communication. Common specifications also are required for the methods for elucidating the bacterial characteristics which are to be encoded. Some classes of data cannot be coded reasonably in binary form. In such cases, different coding methods will have to be developed along with computer techniques to manipulate and analyze these classes. Some examples of these classes, each with their unique problems, are sources of isolation, nucleic acid hybridization, serological typing, and genetic mapping.