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Making organism identification cost-effective.

Making organism identification cost-effective

Budget constraints have deepened microbiologists' interest in cost-effective approaches to organism identification. Too often, however, the test that has the lowest supply, labor, and equipment costs wins out automatically.

Two other factors must also be considered in evaluating the cost-effectiveness of alternative methods: accuracy and impact on patient care. An error rate below 10 per cent and results in less than five hours are desirable features of an organism identification system, along with low cost.

At a minimum, the system should accurately identify more than 90 per cent of organisms likely to be encountered in clinical laboratories. Many systems today have accuracy in the range of 95 per cent, which is as good as can be achieved even with reference methods performed repeatedly.

As for turnaround time, rapid organism ID can shorten hospital stays, head off unnecessary or inappropriate antibiotic therapy, and prevent unnecessary repeat cultures. Some observers have questioned the ability of rapid methods to reduce length of stay. Rapid testing, however, can shorten hospital stays if results are conveyed without delay--by rapid reporting--and if clinicians make timely use of the data to institute appropriate therapy.

Five hours is an arbitrary but useful standard for rapid organism ID through newer techniques, as opposed to the 24 to 48 hours required by conventional methods. Individual organisms might sometimes even be identified in minutes, but no system enables microbiologists to identify a broad range of organisms such as Enterobacteriaceae in so short a time.

Rapid identification methods directly applicable to clinical specimens include fluorescent antibody tests (for Bacteroides, pertussis, Legionella); enzyme immunoassays (N. gonorrhoeae, rotavirus); and particle agglutination tests (group A strep, H. influenzae, N. meningitidis, S. pneumoniae, etc.). Reagents of this type are available for only a limited number of organisms.

Rapid identification methods requiring isolated colonies include spot biochemical tests, particle agglutination tests, and more elaborate commercial systems. It is most cost-effective to use colony morphology and the spot tests first. The latter apply only to a limited number of organisms, but they are a substantial portion of the organisms encountered in clinical labs. For every E. coli that can be identified by a spot test, the lab can avoid spending $2 to $3 on identification by a commercial system. Spot tests are 98 to 99 per cent accurate for P. aeruginosa, E. coli, and P. mirabilis.

As we noted, rapid organism identification without rapid reporting is not likely to improve patient care. While computerized reporting is the best approach, the results must be available at times when clinicians will see them. Traditionally, clinicians make rounds early in the morning and late in the afternoon. They do not see results issued at 9 a.m. until 5 or 6 p.m. Labs must get reports to the charts first thing in the morning whenever possible. Labs may also have to train clinicians to check the charts for later reports.

Laboratory staffing patterns may also limit the usefulness of rapid tests. Laboratories with eight-hour coverage, for example, usually set up identifications at 2 or 3 in the afternoon; technologists go home and read results the next morning. Thus the advantage of having results available in five hours or less is lost. If eight-hour staffing cannot be extended, it may be better to use a traditional overnight method--or use one of the few rapid instruments that reports results automatically into a computer system.

Hospital size also bears on selection of an organism identification system. In an institution with less than 500 beds, it will probably be most cost-effective to perform spot tests for the most commonly occurring organisms and identify the rest with manual commercial systems. In fact, spot tests tend to reduce costs in a hospital setting of virtually any size. When there are 500 or more beds, the workload may be great enough to also justify replica plating methods or an automated system.

Adequate laboratory staffing also influences the selection of identification systems. If the workload is less than or equal to 35 cultures per technologist per day, an inexpensive manual system may be the most cost-effective. With heavier workloads per technologist, labor becomes a limiting factor, and labor-saving automated systems may become more cost-effective.

In Figure I, the factors of cost, accuracy, and speed are used to evaluate different methods for identification of Enterobacteriaceae, on which more than 90 per cent of commercial systems are used. All of the systems listed, except one, have greater than 90 per cent identification accuracy and therefore are acceptable. Spot tests are recommended because they cost less than $1 and are highly accurate and rapid. Classic biochemical test media--the reference method--require overnight incubation and are labor-intensive. The cost of materials, although reasonable at $1 to $2, is higher than in spot tests.

The next method shown in Figure I, replica plating, can become very cost-effective in high-volume laboratories because it allows testing of a number of organisms in a single operation.

Most of the following cost-effective approaches to identification of specific organism groups have been used at our 1,300-bed hospital. Our basic philosophy is not to do more than is necessary.

Staphylococci. For identification of staphylococci, colony morphology and catalase and coagulase reactions are sufficient on the vast majority of isolates, which can be reported as S. aureus or as coagulase-negative staphylococci. Although speciation of coagulase-negative staphylococci may be indicated in selected cases, routine identification of these organisms is not of proved value. The expense of routinely identifying coagulasenegative staphylococci cannot be justified except possibly for Staphylococci saprophyticus from urine specimens, and this organism can be identified simply by the novobiocin disk test.

Streptococci. Colony morphology, hemolysis, and catalase reaction are useful for preliminary grouping of most isolates of streptococci. Those isolates that are potentially significant can then be identified by particle agglutination tests.

Direct identification of group A streptococci from throat swabs using latex agglutination tests may also be cost-effective for laboratories serving large outpatient populations where rapid testing may reduce unnecessary antibiotic use.

The direct bile solubility test is a simple way to identify pneumococci. Speciation of viridans streptococci is difficult to justify in terms of expense except for special circumstances such as endocarditis.

Anaerobes. It may be better for some labs to use commercial anaerobe identification systems, but most products have unacceptably low accuracy rates. Only one system provides better than 90 per cent accuracy for genus level ID.1, 2 None exceeds 80 per cent accuracy for species level ID.

Presumptive identification is adequate in many cases, using kanamycin-vancomycin laked blood agar, cycloserine-cefoxitin fructose egg yolk agar, or fluorescent antibody tests. Keep in mind that complete speciation of anaerobic isolates, taking a minimum of two to four days, is often not required. By the time the result is known, clinical decisions have been made and antibiotic therapy is well under way.

Because of the time and expense involved in anaerobic organism identification, it is cost-effective to offer various levels of identification. The laboratory can offer clinicians a choice as to the extent of identification or make the choice internally, based on such criteria as the number of organisms isolated and the quality and source of the specimen.

We have found three extents of identification to be useful: 1) rule out anaerobes, 2) species level identification, and 3) complete ID. Tests to determine the presence or absence of anaerobes are often sufficient to provide the information needed by the clinician.

In addition, when the rule-out anaerobes option is chosen, the lab can identify Bacteroides fragilis using fluorescent antibody reagents and Clostridium perfingens, which can be identified from colony morphology and hemolysis on the primary growth medium. In practice, the rule-out anaerobes option is the most often selected, followed by genus level identification. Species level identification is rarely requested.

Nonfermenters. P. aeruginosa, accounting for at least 80 per cent of nonfermenter isolates in most laboratories, can be identified with 98 per cent accuracy through colony morphology and the spot oxidase test. For more extensive testing on the other 10 to 20 per cent of nonfermenter isolates, classic biochemical tests are recommended because of their accuracy and low cost. More expensive commercial systems have less than 90 per cent accuracy.

Complete identification of nonfermenters is often unnecessary because they occur with multiple organisms in wound and sputum specimens and are therefore of questionable significance.

Gram-positive bacilli. Since the vast majority of gram-positive bacilli isolates are contaminants and not associated with disease, these organisms require only a minimal workup. Evaluation should be adequate enough to detect significant organisms, such as Listeria, Corynebacterium JK, C. diphtheriae, B. anthracis, etc. They should be ruled out when isolated from normally sterile body fluids and when clinically suspected from other sites.

If, for example, a diphtheroid is isolated from a spinal fluid specimen, it would be important to rule out Listeria with a hanging drop motility test. If there is motility, additional testing should be done to identify a potential Listeria. For most gram-positive bacilli, such tests as Gram stain, catalase, hanging drop motility, colony morphology, and susceptibility pattern will suffice.

The extent of organism identification also depends on the type of specimen yielding the organism. Figure II shows the extent of workup for isolates from blood and body fluids, sputum, throat, urine, and wound specimens.

Organisms present in specimens such as blood or normally sterile body fluids merit extensive identification because they are likely to be associated with infections. All blood and body fluid isolates, therefore, should be identified.

With sputum, the degree of testing depends upon the quantity of organisms and the cytological quality of the specimen. Gramnegative bacilli, staphylococci, beta streptococci, and possible pneumococci should be worked up if the quantity is 2 (10 or more colonies in the primary inoculation area). When more than two potential pathogens are present in a sputum culture, it is reasonable to identify the predominant organism and report morphological types for the others.

With throat specimens, labs should consider the methods now available for directly extracting the antigen of group A streptococci from throat swabs without culturing.3 These tests compare reasonably well in accuracy and cost with traditional throat cultures, and they are much faster.

These approaches to organism identification may be compromises, but they are reasonable and acceptable in terms of patient care, given the economic climate.

1. Burlage, R.S., and Ellner, P.D. Comparison of the Pras II, Anldent, and RaplD Ana systems for identification of anaerobic, bacteria. J. Clin. Microbiol. 22: 32-35, 1985.

2. Murray, P.R.; Weber, C.J.; and Niles, A.C. Comparative evaluation of three identification systems for anaerobes. J. Clin. Microbiol. 22: 52-55, 1985.

3. Slifkin, M., and Gil, G.M. Evaluation of the Culturette brand 10-minute group A strep ID technique. J. Clin. Microbiol. 20: 12-14, 1984.

Table: Figure I Evaluation of methods for Enterobacteriaceae identification

Photo: Figure II Workups on isolates from various body sites
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Author:Kelly, Michael T.
Publication:Medical Laboratory Observer
Date:Mar 1, 1986
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