Identification of Bacteria by Computer: Identification of Reference Strains

Bascomb, Shoshana; Lapage, S. P.; Curtis, Michael; Willcox, W. R.

doi:10.1099/00221287-77-2-291

Cited by 90 publications

(33 citation statements)

References 29 publications

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“…For Bascomb et al (1973), the factors which determined the success of a probabilistic identification scheme were uncertain. They found no correlation between the successful identification of strains of a taxon and the number of biopatterns which strains of that taxon gave.…”

Section: G E N E R a L Discussionmentioning

confidence: 99%

“…Type strains, strains from culture collections and those from experts in the relevant groups were taken as correctly designated. The remaining strains used to evaluate the matrix were identified only by the computer method using the original matrix of Bascomb et al (1973), although subject to final assessment by us. All strains were then assigned to taxa in the matrix.…”

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confidence: 99%

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A Revised Probability Matrix for the Identification of Gram-negative, Aerobic, Rod-shaped, Fermentative Bacteria

Holmes¹,

Dawson²,

Pinning³

1986

Microbiology

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The results of the identification of 933 strains of Gram-negative, aerobic, rod-shaped, fermentative bacteria ( Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) by a probabilistic method, in a computer, are given. The identification rate on the matrix was 89.2%. Many of the strains were atypical and had caused difficulty in identification in medical diagnostic laboratories. The results are given for each taxon by genus and species. I N T R O D U C T I O NA computer-assisted conditional probability method for the identification of enterobacteria was first described by Dybowski & Franklin (1968) and Lapage et al. (1970) used a similar scheme to successfully identify up to 80% of 279 freshly isolated strains. Later, Bascomb et al. (1973) published a matrix for the identification of Gram-negative rods of clinical importance and discussed its use in the identification of 1079 reference strains; the general aspects of probabilistic identification and the mathematical model used were described by Lapage et al. (1973) and Willcox et al. (1973), respectively. This latter matrix was then used as the basis for an identification service in our laboratory, the methods for which were reviewed by Willcox et al. (1980). In the operation of the identification service, the test results obtained for strains submitted for identification were accumulated by computer. These results were then sorted by taxon and printed in the form of summaries, as described by Holmes & Hill (1985). From these summarized results a revised matrix was derived for the fermentative organisms and, following evaluation, this matrix is now in current use for the routine identification service.In this paper we present the results obtained in the identification of 933 strains of bacteria belonging to 110 taxa in the revised probability matrix. METHODS Overallprocedure.A matrix was constructed which gave the probability of a strain of any given taxon yielding a positive result in each of the chosen tests (Table 1). Individual strains were then identified on the basis of these results.Taxa. Of the taxa chosen for the matrix (Table I), the majority gave a fermentative result in the oxidation/fermentation (O/F test) of Hugh & Leifson (1953). A few non-fermentative taxa were also included; these were taxa that produce acid from glucose in peptone/water/sugar media and that may possess other characteristics by which they may be confused with fermentative organisms.Although the range of taxa was selected primarily to include those of known medical importance and those likely to occur in medical specimens, efforts were made to include as many recently described species as possible, so as to facilitate recognition of the latter should they occur in human clinical or veterinary material. Particular attention was paid to ensure inclusion of all Enterobacteriaceae taxa described in Bergeys Manual of Systematic Bacteriology (Brenner, 1984). The majority of the taxa are recognized species, genera or subgenera. Some are t Present address: Gibco-Sensititre, Imberhorne La...

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Section: G E N E R a L Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

A Revised Probability Matrix for the Identification of Gram-negative, Aerobic, Rod-shaped, Fermentative Bacteria

Holmes¹,

Dawson²,

Pinning³

1986

Microbiology

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“…Phenon Colwell & Mandel(1965), to Serratia biotype I of Bascomb et al (1971Bascomb et al ( , 1973 and to phenon A of Grimont & Dulong de Rosnay (1972), as shown by the inclusion in phenon A of strains 287, 504, 290 and 5. We have recently identified S. indica (Eisenberg, I 886) Bergey et al 1923 (monotype ~1~5 3 -9 8 , ATCC4002) and Erythrobaciffus pyosepticus Fortineau I904 (monotype cIP53-91, ATCC275) as both belonging to subphenon AI.…”

Section: Clusteringmentioning

confidence: 99%

Taxonomy of the Genus Serratia

Grimont

Dulong

et al. 1977

Journal of General Microbiology

121

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S U M M A R YThe following conclusions were drawn. ( I ) There are three species of enterobacteria producing prodigiosin : S. marcescens, S. plymuthica and S. marinorubra.(2) There are four species of Serratia, one colourless (S. liquefaciens). (3) Subphenons (biovars) are described within the four species of Serratia. (4) Non-pigmented wild-type strains of S. marcescens can generally be differentiated from pigmented strains by characters other than pigmentation, because subphenons are homogeneous with respect to pigmentation.This survey raised some problems of nomenclature because old descriptions could be found that could loosely fit the present phenons. Comparison with an authentic culture was considered to be the most objective way of identifying these phenons with earlier named species.

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“…In recent years there have been many reports concerning the identification of bacteria by the use of the probability of occurrence of various phenotypic properties (2,10,12,20,25,27). However, in the majority of these studies the organisms used in the data base were themselves INT.…”

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confidence: 99%

Taxonomy of the Bacteroides: II. Correlation of Phenotypic Characteristics with Deoxyribonucleic Acid Homology Groupings for Bacteroides fragilis and Other Saccharolytic Bacteroides Species

Johnson

Ault

1978

International Journal of Systematic Bacteriology

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Two hundred ninety strains of Bacteroides, each belonging to B. fragilis, B. thetaiotaomicron, B. ovatus, B. uniformis, B. vulgatus, B. distasonis, or B. eggerthii, or to one of three unnamed taxa designated "B. fragilis subsp. a," "3452-A," and "T4-1," were used to compare the patterns of 34 phenotypic traits with deoxyribonucleic acid (DNA) homology groupings. The responses for all but 13 of the traits were very similar for all of the DNA homology groups. The responses for the 13 traits (the production of indole, catalase, and hydrogen, and acid production from arabinose, cellobiose, melibiose, melezitose, raffinose, rhamnose, ribose, salicin, sucrose, and trehalose) varied between the various homology groups. Similarity coefficients, for which all of the strains were compared with the DNA reference strains, were calculated. Similarity coefficient averages of strains within a given DNA homology group with the DNA reference strains of that group ranged form 83 to 94%. Organisms having about 60 to 65% DNA homology to each other were in most cases also phenotypically very similar. In a couple of instances, however, homology groups with strains having 72 to 95% intrastrain homology were quite variable with respect to certain phenotypic traits. There was no general pattern between levels of intergroup homologies and phenotypic properties. For example, B. eggerthii and the "subsp. a" homology groups, having about 50% intergroup homology, had average intergroup phenotypic similarity values of 65 and 69%, whereas B. ovatus and B. thetaiotaomicron homology groups, having only about 35% intergroup DNA homology, had intergroup similarity values that ranged from 86 to 93%. Similarity coefficients between homology groups having low levels of DNA homology ranged from 38 to 78%. Response probability values for the phenotypic traits were estimated for strains belonging to each of the DNA homology groups. The probability values obtained with 20 to 40 strains were not altered significantly by including more strains. A test identification matrix was constructed using the probability values of the 13 phenotypic traits listed above. On the basis of these traits, 93% of the strains could be assigned to the correct homology group if groups having 60% or greater intragroup homology were considered to be phenotypically the same.

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Identification of Bacteria by Computer: Identification of Reference Strains

Cited by 90 publications

References 29 publications

A Revised Probability Matrix for the Identification of Gram-negative, Aerobic, Rod-shaped, Fermentative Bacteria

A Revised Probability Matrix for the Identification of Gram-negative, Aerobic, Rod-shaped, Fermentative Bacteria

Taxonomy of the Genus Serratia

Taxonomy of the Bacteroides: II. Correlation of Phenotypic Characteristics with Deoxyribonucleic Acid Homology Groupings for Bacteroides fragilis and Other Saccharolytic Bacteroides Species

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