APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 1979, p. 559-563 0099-2240/79/09-0559/05$02.00/0
Vol. 38, No. 3
MICRID: a Computer-Assisted Microbial Identification System S. T. KELLOGGt
Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822
Received for publication 24 April 1979
An extensive computer-assisted identification system for bacteria and yeasts (117 genera and 1,430 species) was developed, and applications proved very useful in teaching situations.
The success of computer-assisted identification of microorganisms (CAIM) has been reported for some bacterial groups (7, 11, 18, 19). Most previous computer identification systems, however, have dealt with limited groups of organisms. Therefore, a decision was made to create a system that would encompass a wide range of diverse microorganisms for use in research and education. After the development of this expanded system, its most intensive use was found to be in the microbiological teaching laboratory. This communication is limited to the report of these findings on one such CAIM system, known as MICRID. The procedures for developing a comprehensive CAIM system followed previous models and were based upon a Bayesian probability model (33). Bayesian probability identification systems rely on the calculation of a set of likelihoods based on previously determined individual probabilities. Unknown identifications were computed by obtaining "identification scores" via: determining each species probability, summing all probabilities, and normalizing each score by the sum. These scores were sorted in descending order, with a threshold set at 0.01. MICRID was written in BASIC and developed on a Hewlett-Packard 2000 Access timeshared computer. Originally MICRID consisted of several programs, i.e., CLINID (enterics), GRAMPS (streptococci, bacilli, lactobacilli), CLINIE (nonenteric gram-negative bacteria), ANROBE (anaerobic bacteria), PSEUDO (pseudomonads), ACTINO (actinomycetes and related organisms), and YEASTS (yeasts). These programs and data bases were subsequently merged into one system, i.e., MICRID. MICRID has also been translated into FORTRAN for an IBM System 370/158 operating under the Time Sharing Option. The data bases for MICRID were obtained t Present address: Department of Microbiology and Immunology, University of Illinois at the Medical Center, Chicago, IL 60680.
from several sources: Enterobacteriaceae (9), gram-positive bacteria (3, 5, 12, 14, 25), miscellaneous gram-negative bacteria (2, 8, 10, 20, 22, 24, 29-32), anaerobic bacteria (16, 18), pseudomonads (17), actinomycetes and related organisms (4, 13, 15, 21, 23, 26, 27), and yeasts (1, 28). The number of species or biovars or both contained in MICRID was 1,426 and they were distributed over 67 bacterial genera and 41 yeast genera (Table 1). Geotrichium was included among the yeasts due to its yeastlike behavior (28). The genera Pseudomonas, Lactobacillus, and Streptococcus occur in two different data bases due to different tests and sources and do not necessarily contain the same species. The probability values were generated as previously reported (18) for all groups except the enteric and miscellaneous gram-negative bacteria, where exact reference values were used. One of the most perplexing problems facing microbiology undergraduates, when confronting microbial identification, is the problem of "aberrant" microorganisms. The occurrence of aberrant or atypical cultures is many times simply due to student error in test performance or test result interpretation. However, truly atypical strains are fairly common, and the use of dichotomous identification keys with atypical strains easily leads to erroneous results. The use of identification tables helps somewhat if one allows for atypical results. However, most students do not have sufficient experience to recognize which test results are more reliable than others. Students were introduced to the computer and computer terminals via a brief audio-visual orientation, an accompanying instruction sheet, and a set of diverse "paper unknowns." These unknowns were turned in for examination, and the students were informed that they need never use CAIM again. When confronting real unknowns, students were given the option of using CAIM on their cultures, and most chose to do so. All students were required to submit their 559
560
NOTES
APPL. ENVIRON. MICROBIOL.
TABLE 1. Genera contained in the computer identification program MICRID No. of
Genus
species/ biovars
Enterobacteriaceae (42)" Salmonella....
7
6
Shigella Escherichia Proteus Erwinia Kiebsiella..... Edwardsiella Hafnia Citrobacter.......... Yersinia Serratia Enterobacter...... Miscellaneous gram-negative bacteria (75) Aeromonas Vibrio Pasteurella.......... Brucella Bordetella Chromobacterium Eikenella
Alcaligenes ......... Achromobacter....... Flavobacterium Cardiobacterium. Moraxella Neisseria ........... Acinetobacter Pseudomonas......... Pseudomonadaceae (14) Pseudomonas......... Gram-positive bacteria (77)
Streptococcus........ Bacillus Lactobacillus..... Leuconostoc Anaerobic bacteria (256) Eubacterium
5
6 4
3 3 3 2
2 3
14 6 3 2
4 2
15
10 6 2
14 14 21 22 28
6 28
Propionibacterium Actinomyces Bifidobacterium Lactobacillus.......
Streptomyces......... Mycobacterium Corynebacterium Animnal............. Plant Rothia Listeria
6 17 24
Arachnia Bacterionema
Yeasts (461) Clinical (27)
Cryptococcus........
8
Rhodotorula
2
Saccharomyces Torulopsis.......... Trichospora........
2 5
Geotrichium
1
General (434) Ambrosiozyma Brettanomyces Bullera
Citeromyces Cryptococcus........ Debaromyces........ Dekkera
............
Endomycopsis Hansensiaspora
Hansenula.......... Kloeckera.......
Kluyveromyces...~.......... Leucosporidium Lipomyces.... Lodderomyces...... Nadsonia......... Nematospora...... Oosporidium Pachysolen...... Pichia
8
Rhodotorula
Veillonella..........
Megasphaera Gemmiger......... Fusobacterium
Butyrivibrio Bacteroides
2
Selenomonas......... Succinovibrio
Leptotrichia Anaerovibrio......... "Vi brio". Desulfomonas Treponema
Saccharomyces...... Saccharomycodes Saccharopsis........ Schizoblastosporin Schizosaccharomyces Schwanniomyces Selonotila...
15 2
11 2
2
9
104 1 19 10 2 10
Filobasidium
Ruminococcus Sarcina
Acidaminococcus
1
3
Candida............
Rhodosporidium
7
1 1 8
4
3 5
14 4
Erysipelothrix
Peptostreptococcus
"Gaffkya" Peptococcus Coprococcus Streptococcus..
467 18
12 1
Metschnikowia 10
species!
]biovars Actinomycetes and Related Organisms (519)
Candida
Lachnospira ........... Arachnia
No. of
Genus
Sporidiobolus Sporobolomyces.. Sterigmatomyces Sympodomyces Torulopsis Trichosporon........ Trigonopsis..... Wickerhamia
Wingea
69
Borrelia Clostridium "Number in parentheses is total number of species or biovars identified.
3 28 4 19 7 3
1 5 2 1 1 1
45 2
10 44 1 1
1 4 4 2
11 4 1 51 12 1 1 1
VOL. 38, 1979
NOTES
561
run MICRID M I C R I D COMPUTER IDENTIFICATION OF MICROORGANISMS
"'§
"I0
'WOULD YOU LIKE GENERAL INSTRUCTIONS'?no GROUP NO.
MICROORGANISMS
(1)-->
Enterobacteriaceae
(2)-->
Vibrio,Aeromonas,Neisseriaceae,Pseudomonas(enteric tests), Alcaligenes,Achrombacter,Flavobacterium,Chromobacterium, Pasteurella,Brucella,Bordetella,Cardiobacterium,Eikenella
(3)-->
Pseudomonas(non-enteric tests)
(4)-_>
Unknown gram-negative (Groups 1-3 simultaneously)
(5)-->
Gram positive facultatives & aerobes(Bacillus,Streptoooccus, Lactobacil lu , Leuconostoc)
(6)-->
Anaerobic Bacteria
(7)-->
Actinomycetales(Streptomyces,Mycobacterium,Corynebacterium,
Listeria,Rothia,Arachnia,Bacterionema,Erysipelothrix) (8)-->
Yeasts(clinical & non-clinical)
#YOUR GROUP NUMBER*--> ?1 'HORIZONTAL OR VERTICAL TEST LISTINGS0 ?v 'WHAT IS YOUR STRAIN NUMBER' ?Test 1 OALOCHUIVGMISRSMAA NDDDI2RNPEANOHUEMR PHCCTSED LNORACLYA G
'SYSTEM WILL NOW TAKE A FEW SECONDS(MIN?), PLEASE WAIT' "f COMPUTER DIAGNOSIS " K. pneumoniae
" IDENTIFICATION SCORE "
.974111
'ISOLATE TEST RESULTS AGAINST K. pneumoniae' MAN INO
.9997
+
.969
+
'COMPUTER ANALYSIS COMPLETED FOR STRAIN # Test 1
'WOULD YOU LIKE PROBABILITIES FOR ONE OF THE STRAINS' ?no 'ANOTHER ISOLATE IDENTIFICATION' ?no DONE
562
NOTES
results and diagnoses with original source citations for their conclusions (see Fig. 1 for an example of a MICRID session). It should be emphasized that MICRID, as well as all other CAIM systems, is still only an aid to microbial identification. Although CAIM is a very powerful tool, its fixed test batteries sometimes must be supplemented with additional data found in the literature. The most common problem encountered in poor identifications was due to a significant number of missing results, since this led to low identification scores and ambiguous identifications. There was also a tendency to rely on CAIM because "the computer said so, therefore it must be so." This latter point is the most difficult problem to overcome.
Mean time spent by users varied from ca. 2 to 15 min per unknown. Execution times on the Hewlett-Packard minicomputer varied from 2 s to 8 min (Table 2). It should be noted that the yeast (434 species) and Streptomyces (467 species) data files were the slowest running (ca. 3 to 7 min per identification) and probably should be restricted to use on a high-speed computer. User impatience greatly increased if 1 or more min was required. Identification times were essentially instantaneous on the IBM 370 for all microbial groups. The Hewlett-Packard minicomputer adequately satisfied all teaching needs and was continuously available and less costly. CAIM has been successfully used in the following courses: introductory microbiology (nursing), general microbiology (majors), medical microbiology, and advanced general microbiology. An example of MICRID accuracy was seen when specific mutants were distributed as unknowns. For example, Escherichia coli with one or more deletions was distributed, i.e., lac, ara, lys, and mtl. This generated great difficulty in identification since students were not told of the possibility of mutants; however, E. coli was still successfully identified by computer. Mention must be made of success and success criteria with CAIM. Success was measured by comparing CAIM identification with literature results and known replicates. Although the CAIM systems successfully identified unknowns 100% of the time, this was mostly with typical members of the Enterobacteriaceae, Bacillaceae, and Micrococcaceae. However, further extensive testing, especially with yeasts, streptomycetes, and rarer species, is needed. In summary, CAIM has proven to be a valuable heuristic instrument yielding its inherent speed and accuracy to both researcher and stu-
APPL. ENVIRON. MICROBIOL. TABLE 2. MICRID data base sizes and execution times Microbial group
Enterobacteriaceae Miscellaneous gram-negative (nonenteric) bacteria Pseudomonas species Total facultative and aerobic gram-negative bacteria Streptococcus species Bacillus species Lactic acid bacteria Anaerobic bacteria Gram-positive nonsporing rods Cocci Gram-negative rods Spirochaetes Gram-positive sporing rods
Streptomyces species Mycobacterium species Coryneform bacteria
Data base size Mean exe(organisms x cution time tests) (8) 8 42 x 18 18 75 x 22 14 x 30 117 x 22
5 30
21 x 22 22 x 29 34 x 23
7 7 7
89 x 69
73
38 63 30 56 x 23 x 17
11 47 3 43 160 3
33 64 13 69 467 18
x x x x
4 14 x 18 Animal 1 12 x 12 Plant Yeasts 12 27 x 27 Clinical 434 x 52 403 General a Based on three executions (all negatives, positives, and mixed) with a Hewlett-Packard 2000 Access computer.
dent. Currently, MICRID is the most diverse CAIM system developed (1,426 species), although a recent report by Edwards (7) on a 500species system also indicates a trend towards data base diversity. The most significant problem encountered in 3 years of experimental trials was user over-reliance on computer diagnoses. Instruction in the capabilities and limitations of CAIM, as well as literature verification, should offset this effect. MICRID greatly diminished the effect of user error, accepted missing results, and still provided excellent identifications. These CAIM attributes are highly desirable in the field of microbial identification, whether in the research or the teaching environment. Program copies and data bases are available from the author. I thank R. W. Kelley for kindly supplying the anaerobic bacteria data bases and for critical suggestions on the development of MICRID. I thank M. A. Levine for help with data base entries, and also thank the many users (mostly students) who were part of this experimental project.
LITERATURE CITED 1. Barnett, J. A., and R. J. Plankhurst. 1974. A new key to the yeasts. American Elsevier, New York. 2. Brinley-Morgan, W. J., and N. B. McCullough. 1974.
Genus Brucella Meyer and Shaw 1920, p. 278-282. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's
FIG. 1. Example computer printout for a MICRID session. Test names are printed vertically in this example.
VOL. 38, 1979 manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 3. Cowan, S. T. 1974. Streptococcus, p. 51-55. In S. T. Cowan, Manual for the identification of medical bacteria. Cambridge University Press, London. 4. Cummins, C. S., R. A. Lelliott, and M. Rogosa. 1974. Genus I. Corynebacterium Lehmann and Neumann 1896, p. 602-617. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 5. Deibel, R. H., and H. W. Seeley, Jr. 1974. Genus I. Streptococcus Rosenbach 1884, p. 490-509. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 6. Dybowski, W., and D. A. Franklin. 1968. Conditional probability and the identification of bacteria: a pilot study. J. Gen. Microbiol. 54:215-229. 7. Edwards, J. G. 1978. Computer-assisted identification of unknown bacteria, p. 280-292. In A. N. Sharpe and D. S. Clark (ed.), Mechanizing microbiology. Charles C Thomas, Publisher, Springfield, Ill. 8. Ewing, W. H., and R. Hugh. 1974. Aeromonas, p. 230237. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 9. Ewing, W. H., and W. J. Martin. 1974. Enterobacteriaceae, p. 189-221. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 10. Feeley, J. C., and A. Balows. 1974. Vibrio, p. 238-245. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 11. Friedman, R. B., D. Bruce, J. MacLowry, and V. Brenner. 1973. Computer-assisted identification of bacteria. Am. J. Clin. Pathol. 60:395-403. 12. Garvie, E. I. 1974. Genus II. Leuconostoc van Tieghem 1878, emend. mut. char. Hucker and Pederson 1930, p. 510-513. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 13. Georg, L. K. 1974. Genus V. Rothia Georg and Brown 1967, p. 679-681. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 14. Gibson, T., and R. E. Gordon. 1974. Genus I. Bacillus, Cohn 1872, p. 529-550. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 15. Gilmour, M. N. 1974. Genus IV. Bacterionema Gilmour, Howell and Bibby 1961, p. 676-679. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 16. Holdeman, L. V., E. P. Cato, and W. E. C. Moore (ed.). 1977. Anaerobe laboratory manual, 4th ed. Virginia Polytechnic Institute and State University, Blacksburg. 17. Hugh, R., and G. L. Gilardi. 1974. Pseudomonas, p. 250-269. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 18. Kelley, R. W., and S. T. Kellogg. 1978. Computer-assisted identification of anaerobic bacteria. Appl. Environ. Microbiol. 35:507-511. 19. Lapage, S. P., S. Bascomb, W. R. Willcox, and M. A.
NOTES
563
Curtis. 1970. Computer identification of bacteria, p. 122. In A. Baille and R. J. Gilbert (ed.), Automation mechanization and data handling in microbiology. Academic Press Inc., New York. 20. Lautrop, H. 1974. Genus III. Moraxella Lwoff 1939, p. 433-436. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 21. Pine, L, and L K. Georg. 1974. Genus II. Arachnia Pine and Georg 1969, p. 668-669. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 22. Pittman, M. 1974. Genus Bordetella Moreno-Lopez 1952, p. 282-283. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 23. Pridham, T. G., and H. D. Tresner. 1974. Genus I. Streptomyces Waksman and Henrici 1943, p. 748-829. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 24. Reyn, A. 1974. Genus I. Neisseria Trevisan 1885, p. 428432. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 25. Rogosa, M. 1974. Genus I. Lactobacillus Beijerinck 1901, p. 576-593. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 26. Runyon, E. H., L. G. Wayne, and G. P. Kubica. 1974. Genus I. Mycobacterium Lehmann and Neumann 1896, p. 682-701. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 27. Seeliger, H. P. R., and H. J. Wel8himer. 1974. Listeria Pirie 1940, p. 593-596. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 28. Silva-Hutner, M., and B. H. Cooper. 1974. Medically important yeasts, p. 491-507. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 29. Smith, J. E. 1974. Genus Pasteurella Trevisan 1887, p. 370-373. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 30. Sneath, P. H. A. 1974. Genus Chromobacterium Bergonzini 1881, p. 354-357. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 31. Tatum, H. W., W. H. Ewing, and R. E. Weaver. 1974. Miscellaneous gram-negative bacteria, p. 270-294. In E. H. Lennette, E. H. Spaulding, and J. P. Truant (ed.), Manual of clinical microbiology, 2nd ed. American Society for Microbiology, Washington, D.C. 32. Weeks, 0. B. 1974. Genus Flavobacterium Bergey et al. 1923, p. 357-364. In R. E. Buchanan and N. E. Gibbons (ed.), Bergey's manual of determinative bacteriology, 8th ed. The Williams & Wilkins Co., Baltimore. 33. Willcox, W. R., and S. P. Lapage. 1975. Methods used in a program for computer-assisted identification of bacteria, p. 103-119. In R. J. Pankhurst (ed.), Biological identification with computers. Academic Press Inc., New York.
Vol. 38, No. 3
MICRID: a Computer-Assisted Microbial Identification System S. T. KELLOGGt
Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822
Received for publication 24 April 1979
An extensive computer-assisted identification system for bacteria and yeasts (117 genera and 1,430 species) was developed, and applications proved very useful in teaching situations.
The success of computer-assisted identification of microorganisms (CAIM) has been reported for some bacterial groups (7, 11, 18, 19). Most previous computer identification systems, however, have dealt with limited groups of organisms. Therefore, a decision was made to create a system that would encompass a wide range of diverse microorganisms for use in research and education. After the development of this expanded system, its most intensive use was found to be in the microbiological teaching laboratory. This communication is limited to the report of these findings on one such CAIM system, known as MICRID. The procedures for developing a comprehensive CAIM system followed previous models and were based upon a Bayesian probability model (33). Bayesian probability identification systems rely on the calculation of a set of likelihoods based on previously determined individual probabilities. Unknown identifications were computed by obtaining "identification scores" via: determining each species probability, summing all probabilities, and normalizing each score by the sum. These scores were sorted in descending order, with a threshold set at 0.01. MICRID was written in BASIC and developed on a Hewlett-Packard 2000 Access timeshared computer. Originally MICRID consisted of several programs, i.e., CLINID (enterics), GRAMPS (streptococci, bacilli, lactobacilli), CLINIE (nonenteric gram-negative bacteria), ANROBE (anaerobic bacteria), PSEUDO (pseudomonads), ACTINO (actinomycetes and related organisms), and YEASTS (yeasts). These programs and data bases were subsequently merged into one system, i.e., MICRID. MICRID has also been translated into FORTRAN for an IBM System 370/158 operating under the Time Sharing Option. The data bases for MICRID were obtained t Present address: Department of Microbiology and Immunology, University of Illinois at the Medical Center, Chicago, IL 60680.
from several sources: Enterobacteriaceae (9), gram-positive bacteria (3, 5, 12, 14, 25), miscellaneous gram-negative bacteria (2, 8, 10, 20, 22, 24, 29-32), anaerobic bacteria (16, 18), pseudomonads (17), actinomycetes and related organisms (4, 13, 15, 21, 23, 26, 27), and yeasts (1, 28). The number of species or biovars or both contained in MICRID was 1,426 and they were distributed over 67 bacterial genera and 41 yeast genera (Table 1). Geotrichium was included among the yeasts due to its yeastlike behavior (28). The genera Pseudomonas, Lactobacillus, and Streptococcus occur in two different data bases due to different tests and sources and do not necessarily contain the same species. The probability values were generated as previously reported (18) for all groups except the enteric and miscellaneous gram-negative bacteria, where exact reference values were used. One of the most perplexing problems facing microbiology undergraduates, when confronting microbial identification, is the problem of "aberrant" microorganisms. The occurrence of aberrant or atypical cultures is many times simply due to student error in test performance or test result interpretation. However, truly atypical strains are fairly common, and the use of dichotomous identification keys with atypical strains easily leads to erroneous results. The use of identification tables helps somewhat if one allows for atypical results. However, most students do not have sufficient experience to recognize which test results are more reliable than others. Students were introduced to the computer and computer terminals via a brief audio-visual orientation, an accompanying instruction sheet, and a set of diverse "paper unknowns." These unknowns were turned in for examination, and the students were informed that they need never use CAIM again. When confronting real unknowns, students were given the option of using CAIM on their cultures, and most chose to do so. All students were required to submit their 559
560
NOTES
APPL. ENVIRON. MICROBIOL.
TABLE 1. Genera contained in the computer identification program MICRID No. of
Genus
species/ biovars
Enterobacteriaceae (42)" Salmonella....
7
6
Shigella Escherichia Proteus Erwinia Kiebsiella..... Edwardsiella Hafnia Citrobacter.......... Yersinia Serratia Enterobacter...... Miscellaneous gram-negative bacteria (75) Aeromonas Vibrio Pasteurella.......... Brucella Bordetella Chromobacterium Eikenella
Alcaligenes ......... Achromobacter....... Flavobacterium Cardiobacterium. Moraxella Neisseria ........... Acinetobacter Pseudomonas......... Pseudomonadaceae (14) Pseudomonas......... Gram-positive bacteria (77)
Streptococcus........ Bacillus Lactobacillus..... Leuconostoc Anaerobic bacteria (256) Eubacterium
5
6 4
3 3 3 2
2 3
14 6 3 2
4 2
15
10 6 2
14 14 21 22 28
6 28
Propionibacterium Actinomyces Bifidobacterium Lactobacillus.......
Streptomyces......... Mycobacterium Corynebacterium Animnal............. Plant Rothia Listeria
6 17 24
Arachnia Bacterionema
Yeasts (461) Clinical (27)
Cryptococcus........
8
Rhodotorula
2
Saccharomyces Torulopsis.......... Trichospora........
2 5
Geotrichium
1
General (434) Ambrosiozyma Brettanomyces Bullera
Citeromyces Cryptococcus........ Debaromyces........ Dekkera
............
Endomycopsis Hansensiaspora
Hansenula.......... Kloeckera.......
Kluyveromyces...~.......... Leucosporidium Lipomyces.... Lodderomyces...... Nadsonia......... Nematospora...... Oosporidium Pachysolen...... Pichia
8
Rhodotorula
Veillonella..........
Megasphaera Gemmiger......... Fusobacterium
Butyrivibrio Bacteroides
2
Selenomonas......... Succinovibrio
Leptotrichia Anaerovibrio......... "Vi brio". Desulfomonas Treponema
Saccharomyces...... Saccharomycodes Saccharopsis........ Schizoblastosporin Schizosaccharomyces Schwanniomyces Selonotila...
15 2
11 2
2
9
104 1 19 10 2 10
Filobasidium
Ruminococcus Sarcina
Acidaminococcus
1
3
Candida............
Rhodosporidium
7
1 1 8
4
3 5
14 4
Erysipelothrix
Peptostreptococcus
"Gaffkya" Peptococcus Coprococcus Streptococcus..
467 18
12 1
Metschnikowia 10
species!
]biovars Actinomycetes and Related Organisms (519)
Candida
Lachnospira ........... Arachnia
No. of
Genus
Sporidiobolus Sporobolomyces.. Sterigmatomyces Sympodomyces Torulopsis Trichosporon........ Trigonopsis..... Wickerhamia
Wingea
69
Borrelia Clostridium "Number in parentheses is total number of species or biovars identified.
3 28 4 19 7 3
1 5 2 1 1 1
45 2
10 44 1 1
1 4 4 2
11 4 1 51 12 1 1 1
VOL. 38, 1979
NOTES
561
run MICRID M I C R I D COMPUTER IDENTIFICATION OF MICROORGANISMS
"'§
"I0
'WOULD YOU LIKE GENERAL INSTRUCTIONS'?no GROUP NO.
MICROORGANISMS
(1)-->
Enterobacteriaceae
(2)-->
Vibrio,Aeromonas,Neisseriaceae,Pseudomonas(enteric tests), Alcaligenes,Achrombacter,Flavobacterium,Chromobacterium, Pasteurella,Brucella,Bordetella,Cardiobacterium,Eikenella
(3)-->
Pseudomonas(non-enteric tests)
(4)-_>
Unknown gram-negative (Groups 1-3 simultaneously)
(5)-->
Gram positive facultatives & aerobes(Bacillus,Streptoooccus, Lactobacil lu , Leuconostoc)
(6)-->
Anaerobic Bacteria
(7)-->
Actinomycetales(Streptomyces,Mycobacterium,Corynebacterium,
Listeria,Rothia,Arachnia,Bacterionema,Erysipelothrix) (8)-->
Yeasts(clinical & non-clinical)
#YOUR GROUP NUMBER*--> ?1 'HORIZONTAL OR VERTICAL TEST LISTINGS0 ?v 'WHAT IS YOUR STRAIN NUMBER' ?Test 1 OALOCHUIVGMISRSMAA NDDDI2RNPEANOHUEMR PHCCTSED LNORACLYA G
'SYSTEM WILL NOW TAKE A FEW SECONDS(MIN?), PLEASE WAIT' "f COMPUTER DIAGNOSIS " K. pneumoniae
" IDENTIFICATION SCORE "
.974111
'ISOLATE TEST RESULTS AGAINST K. pneumoniae' MAN INO
.9997
+
.969
+
'COMPUTER ANALYSIS COMPLETED FOR STRAIN # Test 1
'WOULD YOU LIKE PROBABILITIES FOR ONE OF THE STRAINS' ?no 'ANOTHER ISOLATE IDENTIFICATION' ?no DONE
562
NOTES
results and diagnoses with original source citations for their conclusions (see Fig. 1 for an example of a MICRID session). It should be emphasized that MICRID, as well as all other CAIM systems, is still only an aid to microbial identification. Although CAIM is a very powerful tool, its fixed test batteries sometimes must be supplemented with additional data found in the literature. The most common problem encountered in poor identifications was due to a significant number of missing results, since this led to low identification scores and ambiguous identifications. There was also a tendency to rely on CAIM because "the computer said so, therefore it must be so." This latter point is the most difficult problem to overcome.
Mean time spent by users varied from ca. 2 to 15 min per unknown. Execution times on the Hewlett-Packard minicomputer varied from 2 s to 8 min (Table 2). It should be noted that the yeast (434 species) and Streptomyces (467 species) data files were the slowest running (ca. 3 to 7 min per identification) and probably should be restricted to use on a high-speed computer. User impatience greatly increased if 1 or more min was required. Identification times were essentially instantaneous on the IBM 370 for all microbial groups. The Hewlett-Packard minicomputer adequately satisfied all teaching needs and was continuously available and less costly. CAIM has been successfully used in the following courses: introductory microbiology (nursing), general microbiology (majors), medical microbiology, and advanced general microbiology. An example of MICRID accuracy was seen when specific mutants were distributed as unknowns. For example, Escherichia coli with one or more deletions was distributed, i.e., lac, ara, lys, and mtl. This generated great difficulty in identification since students were not told of the possibility of mutants; however, E. coli was still successfully identified by computer. Mention must be made of success and success criteria with CAIM. Success was measured by comparing CAIM identification with literature results and known replicates. Although the CAIM systems successfully identified unknowns 100% of the time, this was mostly with typical members of the Enterobacteriaceae, Bacillaceae, and Micrococcaceae. However, further extensive testing, especially with yeasts, streptomycetes, and rarer species, is needed. In summary, CAIM has proven to be a valuable heuristic instrument yielding its inherent speed and accuracy to both researcher and stu-
APPL. ENVIRON. MICROBIOL. TABLE 2. MICRID data base sizes and execution times Microbial group
Enterobacteriaceae Miscellaneous gram-negative (nonenteric) bacteria Pseudomonas species Total facultative and aerobic gram-negative bacteria Streptococcus species Bacillus species Lactic acid bacteria Anaerobic bacteria Gram-positive nonsporing rods Cocci Gram-negative rods Spirochaetes Gram-positive sporing rods
Streptomyces species Mycobacterium species Coryneform bacteria
Data base size Mean exe(organisms x cution time tests) (8) 8 42 x 18 18 75 x 22 14 x 30 117 x 22
5 30
21 x 22 22 x 29 34 x 23
7 7 7
89 x 69
73
38 63 30 56 x 23 x 17
11 47 3 43 160 3
33 64 13 69 467 18
x x x x
4 14 x 18 Animal 1 12 x 12 Plant Yeasts 12 27 x 27 Clinical 434 x 52 403 General a Based on three executions (all negatives, positives, and mixed) with a Hewlett-Packard 2000 Access computer.
dent. Currently, MICRID is the most diverse CAIM system developed (1,426 species), although a recent report by Edwards (7) on a 500species system also indicates a trend towards data base diversity. The most significant problem encountered in 3 years of experimental trials was user over-reliance on computer diagnoses. Instruction in the capabilities and limitations of CAIM, as well as literature verification, should offset this effect. MICRID greatly diminished the effect of user error, accepted missing results, and still provided excellent identifications. These CAIM attributes are highly desirable in the field of microbial identification, whether in the research or the teaching environment. Program copies and data bases are available from the author. I thank R. W. Kelley for kindly supplying the anaerobic bacteria data bases and for critical suggestions on the development of MICRID. I thank M. A. Levine for help with data base entries, and also thank the many users (mostly students) who were part of this experimental project.
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FIG. 1. Example computer printout for a MICRID session. Test names are printed vertically in this example.
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