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An Approach to Microbiologic Diagnosis and
Matrix Problems for the Small Hospital
Laboratory Using a Small Computer
F. SPENCER, F . I . M . L . T . , A N D T. A. HYDE,
M.D.
Department of Pathology, Hotel-Dieu of St. Joseph, Windsor, Ontario, Canada
ABSTRACT
Spencer, F., and Hyde, T. A.: An approach to microbiologic diagnosis and
matrix problems for the small hospital laboratory using a small computer.
Am. J. Clin. Pathol. 60: 264^267, 1973. An approach to microbiologic diagnosis and matrix problems for small hospital laboratories using the Programma 101. A scheme is described whereby the physical and biochemical
data used to identify microorganisms, generally assembled as "character
tables," are converted into a binary number which is subsequently processed
by a described program. Two routine sets of organisms are characterized
using this approach. It is considered that this approach offers both versatility
and potential to small laboratories. Furthermore, it can be applied to diagnostic and matrix problems other than those of a microbiologic nature.
IN ROUTINE microbiologic diagnosis, first an
organism is isolated and then its biochemical activity is investigated. Most laboratories utilize a standard profile of tests such
as catalase, oxidase production, the mode
of carbohydrate degradation and others,
from which a characteristic and diagnostic
pattern can usually be obtained. Tables
such as those in Cowan and Steel3 are
typical of this approach. While the combinations of a small number of tests are easily
matched against a table of results, problems
can arise in the comparison of a large number of tests, particularly in the hands of inexperienced technicians and when doubtful
and late reactions occur. Indeed, as Cowan
and Steel 3 state: ". . . with tables we are
restricted by our memories or limited by
Received August 22, 1972; received revised manuscript September 25, 1972; accepted for publication
October 4, 1972.
our ability to recognize similarities and differences when making multiple comparisons simultaneously."
We felt that a possible solution to this
problem might lie in the use of a minicomputer. However, the Olivetti Programma 101, which is in use in many hospital laboratories, is not suited to matrix
problems due to its limited storage and
program capacity.
T h e approach utilized in the present
program is to take, in a definite sequence,
the results from a standard battery of tests,
coding the reactions so that (0) represents
a negative result or absence of a particular
characteristic; (1) represents a positive result; and (2) represents a doubtful or late
result. In the present scheme (1) is also
used if acid and gas are produced together
in a fermentation reaction, while (2) is used
for the production of acid alone. Following
264
August 1973
this code the test results can be expressed
in that way, using Escherichia coli as an
example, indicated in Table 1. Clearly this
sequence can be regarded as a binary number, that is, a number utilizing the base 2.
Thus, in the example, E. coli, the binary
number is 10001110. The basic algorithm
oE the program, given in Figure 1, converts
this binary number into the more comprehensible decimal form, that is, using the
base 10. The decimal number produced is
apparently quite arbitrary, as it depends
only on the original binary sequence. This
number also varies in length; consequently,
the next step in the program is to split off
the first three significant digits. As too
many of the numbers produced in this way
were found to begin with the same digit,
the program next reverses the sequence of
digits and finally prints the three digit
number. Reference to Tables 2 and 3 then
allows a diagnosis to be rapidly established.
Test Procedures and Data Entry
In the present paper, two groups of organisms are classified, the first being representatives of the Enterobacteriaceae family
(Table 1) and the second being a group of
miscellaneous organisms loosely designated
the "nonfermentative Gram-negative bacteria" (Table 3). The predicted results of
those tests employed were assembled acTable 1. Method of Coding Test Responses
for Escherichia coli
1
Test
Reaction*
Indole
Citrate
H2S
Urease
Motility
Lactose
Glucose
Gelatin
+
:
-f- ~* positive;
265
USE OF COMPUTER IN MICROBIOLOGY
AV
C*
a I
ci
Ei
d J
bx
b t
El
M I
CW
MT
AZ
E X
C I
BW
d -
MS
b J
/w
cv
M-
aw
/Y
A*
aV
A
CI
CW
a i
CI
EX
C*
M0*
/ t
Ct
MDT
/ I
c t
M-
c i
dX
c*
d*
T
M A
/ I
CI
c1
DX
0*
DX
d -
C*
/v
AO
BV
/ 0
d •
Reaction
Coded as
—
—
—
+
AG
AG
—
• negative; AG = acid/gas.
1
0
0
0
1
1
1
0
MV
10
1000
01
d
1
FIG. 1. Program for bacteriologic diagnosis using
the OliveUi P101. T h e program begins at the top
left corner and is read down the vertical columns;
it is entered into the calculator according to the
manufacturer's instructions.
266
SPENCER AND HYDE
Table 2. Representative Members of the
Enterobacteriaceae Family, Assembled
in Numerical-code Order*
Organism
Code
Klebsiella
Serralia
A Icaligenes faecalis
Salmonella
Proteus mirabilis
Enterobacter cloacae
Proteus vulgaris
Providence
Shigella
Escherichia coli
Citrobacter
Proteus rellgeri
Proteus morganii
Arizona
Pseudomonas aeruginosa
1.0
124.0
180.0
228.0
303.0
345.0
403.0
418.0
491.0
501.0
601.0
751.0
838.0
865.0
873.0
* Pseudomonas aeruginosa and Alcaligenes fecalis are included in the table for convenience—they are not members of
this family.
Tabic 3. Code Numbers for a Group of Miscellaneous Organisms Designated the "Nonfermentative Gram-negative Bacteria"
A cinetobacter wolffi
Pseitdomonas
fluorescens
Flavobacterium I I I
Pseudomonas aeruginosa
Alcaligenes faecalis
Chromobacterium typhiflavum
Pseitdomonas mitltivarum
Flavobacterium I
Pseitdomonas acidovarum
A Icaligenes dentificans
Alcaligenes odoram
Pseitdomonas pseudomallei
Xanthomonas
Pseitdomonas maltophilia
Pseitdomonas stutzeri
Pseitdomonas putida
Pseitdomonas pseudoalcaligenes
Pseitdomonas stutzeri
Bordelella bronchoseptica
Pseudomonas alcaligenes
Pseitdomonas diminula
Pseudomonas kingii
Moraxella non-liquefaciens
Moraxella osloensis
Moraxella phenylpyronvica
Pseudomonas stutzeri
A cinetobacter anitralum
Pseudomonas maltophilia
Flavobacterium II
0
76
118
296
321
366
376
395
421
478
478
496
501
576
586
656
656
656
656
656
656
657
691
691
691
776
811
856
894
A.J.C.P.—Vol, 59
cording to data furnished from Breed and
associates,2 Cowan and Steel,3 and Blair,
Lennette, and Truant. 1 For clarity, only
the final printout for each organism is
given in the respective tables; the basic
data are to be found in the above references or can be obtained on application to
the authors.
Table 2, Enterobacteriaceae
After initiating the program (Fig. 1) by
pressing key V, the results of the following
tests, using the code described above, are
entered in the precise order given:
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Indole production
Citrate utilization
H 2 S production
Urease activity
Motility
Fermentation of lactose
Fermentation of glucose
Gelatin liquefaction
Between the entry of each parameter, the
S key is pressed. It should be noted that
of the 15 organisms listed in Table 2, two
of them are not legitimate members of the
Enterobacteriaceae family, namely, Pseudomonas aeruginosa and Alcaligenes faecalis;
these were included for convenience. As
can be seen the binary number derived
from the test results represents an organism; pressing key Z results in the printout
of a decimal number, for example 501,
which is looked up in Table 2 and thus
identified.
Table 3, Nonfermentative
Bacteria
Gram-negative
Employing the procedure outlined above,
the group of organisms designated the
"nonfermentative gram-negative bacteria"
was characterized using the following parameters:
August 1973
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
(i)
(j)
(k)
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USE OF COMPUTER IN MICROBIOLOGY
Oxidase activity
Gluconate
Fluorescence
Lysine decarboxylase
Indole production
Fermentation of 10% lactose
Pigment production
Nitrogen
Motility
Penicillin sensitivity
Fructose
As Table 3 indicates, there are several
organisms showing the same code number,
but differentiation can be achieved by performing a further short series of tests, for
example, nitrate reduction, gelatin liquefaction, and fermentation of rhamnose.
Note
The basic algorithm converts any number
of base n to its decimal equivalent. Thus,
if (2) is used for coding, as described, then
a sequence such as 11021 is in fact a ternary
not a binary number. However, the procedure for data entry remains exactly the
same.
References
1. Blair JB, Lenette EH, Truant JP: Manual for
the Identification of Medical Bacteria. Bethesda, Maryland, American Society for Microbiology, 1970, pp 191-198
2. Breed RS, Murray EGD, Smith NR, et al: Bergey's Manual of Determinative Bacteriology.
Baltimore, Williams and Wilkins, 1957, pp 299332
3. Cowan ST, Steel KJ: Manual for the Identification of Medical Bacteria. Cambridge, England,
University Press, 1965, pp 17, 78