Developing a data retrieval and statistics program Essay

We created our own data base management program for microbiology,
using Applesoft Basic language. Although it is slower than commercial
software, it is an inexpensive way to maintain current statistics on
departmental activity, including organisms cultured and susceptibility patterns.

Our microbiology department serves a 500-bed medical center.
Statistics, compiled manually, had been dropping lower and lower on the
list of prioritiers after prospective payment led to layoffs and
attrition. When up-to-date, monthly susceptibility summaries could no
longer be provided to clinicians and the infection control committee, we
turned to our Apple II Plus. Till then, The microcomputer had been used
exclusively for automatic recording of data from our blood culturing

The data base management program was actually constructed by author
Kay McConnell with input on microbiology’s needs from her
co-authors. McConnell had learned Applesoft Basic at home on her own
Apple II Plus.

Data entered on each specimen include patient name, lab or specimen
accession number, room, age, billing number, admission date, requisition date, specimen type, organisms cultured, and susceptibility patterns.

From all the individual test records, we generate complete monthly
list of microbiology testing, sorted by patient name, room number (for
infection control purposes), specimen type, and type of organism. In
addition, we generate overall statistics on identifications and
susceptibilities by specimen type and by organism.

The information is stored on a floppy disk, with printouts for
backup. The Apple II Plus has dual disk drives and 48K RAM, and we use
an Epson FX-100 printer.

Here are different aspects of the program:

* Code files. These three files are directories covering the
numerical codes for organisms (101, E. Coli) and the alphabetical codes
for specimens (BRON, bronchial) and antibiotics (GM, gentamicin). While
any number of specimen and organism codes can be specified, the
antibiotic file is limited to a maximum of 25 for space reasons, since
all the drug codes have to be shown in each report on susceptibilities.

If we want to modify the antibiotic file, we must wait until the
beginning of a new year. Computer generation of monthly and yearly
susceptibility statistics depends on the codes and their order.

* Data entry. The data entry format on the computer screen (Figure
1) corresponds to the sequence in which informatin appears on our
requisition form. The specimen code is entered alongside SPEC.
Antibiotic codes are read vertically. The first code is just the letter
P for penicillin; the second is AK for amikacin; the third, AM for
ampicillin; and so on. Beneath each of these, on the organism code
line, is an S for susceptible, R for resistant, or a period if the drug
has not been tested. When several consecutive drugs are not tested,
periods are easier to count than blank spaces.

Up to four organisms per specimen can be entered at one time. If
any more organisms are cultured from the same specimen, a second record
must be created. This was one of the points we paused over when
developing the program. How many organisms would each culture yield?
Rarely more than four, but frequently more than three, a review of past
reports revealed.

At the top left of the data entry screen is an exit option,
allowing a return to the main menu. At the bottom of the screen, the
user has a chance to enter the displayed data into the main patient
file, revise the data, or delete it all. Also at the bottom is the
latest total of patient records for the month.

Data entry is performed whenever any employee has a spare 10 or 15
minutes. It is the only employee time devoted to organism and
susceptibility statistics now. The Apple and the Epson do the rest.

* Search and edit. The main file can be searched by either patient
name or specimen accession number. Data for an individual test record
are displayed on the screen, and the following options are given:
continue search, edit data, delete data, or return (to the main menue).
Continued search by name calls up all the specimens cultured that month
on the same patient. Continued search by specimen number allows us to
see any added organisms cultured on a specimen, beyond the maximum of
four in th first record displayed on the screen.

Searches are usually conducted with some editing purpose in mind.
For example, when we find out the identity of a patient originally
admitted as John Doe, we go into the files and change the name.
Occasionally, a physician will ask for all the culture data on a
patient. Retrieval takes less than a minute.

We also have an Apple program called FID that enables us to copy
computer files and programs for backup.

* Calculations and printouts. Among the availabe screen displays
and hard copies are: a CRT listing and printout of the names and
computer-record numbers of all patients in a monthly file, for use as an
index; a CRT listing of statistics on a single organism, needed when a
physician asks for drug susceptibilities; and printouts of all data in
the main file, sorted by patient name, by floor, by organism, or by
specimen. These last printouts serve as hardcopy backup to the disk.

In additin, we have monthly and annual printouts of statistics by
organism and by specimen. The former shows the number of times each
organism was cultured and the percentage of organisms tested that were
susceptible to each drug (Figure II). The data are used by
microbiologists, clinicians, and the infection control committee to
compare susceptibilities among new and old drugs and to monitor
increasing antibiotic resistance by organisms.

The printout of specimen statistics lists each specimen type, how
many were cultured during the month or year, and the percentage of those
cultured that grew any of the coded organisms. Infection control is
particularly interested in this information.

There are drawbacks to our data base management software. For one
thing, a wide carriage printer is needed for some of the printouts. For
another, the program is slow compared with commercial software, as we
have mentioned. With 338 entries in the main patient file, 119 entries
in the organism file, 22 entries in the antibiotic file, and 21 entries
in the specimen file, it would take: 29 seconds to search by name
through the entire patient file; 2 minutes, 40 seconds to load from the
disk to the computer and sort by patient, and 14 minutes to print out; 2
minutes, 17 seconds to load and sort by floor, and 13 minutes to print
out; 60 minutes to sort and print out by organism; 10 minutes to sort
and print out by specimen; 66 minutes to calculate and print out monthly
statistics by organism; and 38 minutes to calculate and print out
monthly statistics by specimen.

Now for the advantages. Since we already had the Apple II Plus and
since the program was written by a laboratory employee on her own time,
the only supply costs we have run up are for 14 floppy disks per year
and printer paper.

Even though the software is relatively slow, it is still much
faster than our previous system of manual sorting and calculations. We
have cut 50 per cent off the time technologists and volunteer hospital
workers used to spend in compiling our statistics. Since all data are
now kept on floppy disks and a small collection of printouts, we have
also reduced the space needed to store our data.

We can continually monitor microbiology data and get
up-to-the-minute interim reports on our overall activity.

With programming knowledge and ability to handle random access
files in Applesoft Basic, the program can constantly be updated and
improved. Modifications can be accomplished within days–sometimes
within minutes–therefore providing us with a program tailored to our


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