Cases in Medical Microbiology and Infectious Diseases. Melissa B. Miller
clinical point of view, are those in which the laboratory reports an organism as susceptible to a particular antibiotic to which, in fact, it is resistant. In some cases, additional tests are employed to minimize the risk of this occurring. For example, in addition to standard testing using either an automated or a manual method, recommended susceptibility testing of Enterococcus includes the use of Mueller-Hinton agar in which the antibiotic vancomycin is present at a known concentration. Even if the results of the standard susceptibility testing indicate susceptibility to vancomycin, if there is growth of the Enterococcus isolate on the vancomycin-containing Mueller-Hinton plate, the organism is reported as resistant to vancomycin.
Unfortunately, very few such checks exist to correct erroneous bacterial susceptibility assays. In general, there is a delay in the ability of automated susceptibility methods to reliably identify newly described mechanisms of antibiotic resistance. As a result, manual methods are often required. The performance of automated susceptibility testing methods varies, and certain combinations of organism and antibiotic have an unacceptably high error rate. In such cases, backup methods, such as disk diffusion or MIC testing, should be employed. Laboratories with a significant number of susceptibility tests to perform commonly use automated susceptibility methods because of the labor-intensive nature of manual testing and the speed with which automated systems are able to report results—often in a few hours as compared with overnight incubation, as is the case with manual methods.
Diagnostic tests vary in their sensitivity and specificity. As an example, consider a hypothetical STI (sexually transmitted infection) clinic in which the rapid plasma reagin (RPR) test, a screening test for syphilis, is being evaluated in 1,000 patients with genital ulcer disease who are suspected of having primary syphilis:
| PRIMARY SYPHILIS | ||||
| PRESENT | ABSENT | |||
| RPR TEST RESULT | POSITIVE | 420 | 60 | Positive predictive value = 420/(420 + 60) = 0.88Positive predictive value = 88% |
| NEGATIVE | 220 | 300 | Negative predictive value = 300/(300 + 220) = 0.58Negative predictive value = 58% | |
| Sensitivity = 420/(420 + 240) = 0.66Sensitivity = 66% | Specificity = 300/(300 + 60) = 0.83Specificity = 83% | |||
On the basis of these data, the sensitivity of this test (the true-positive rate, calculated as true-positive results divided by the number of patients with disease) in primary syphilis is 66%. The specificity (1 minus the false-positive rate) is 83%. Note that in this high-prevalence population (the prevalence here is the total number of cases in which primary syphilis is present—640 divided by the total number of individuals, 1,000—and is thus 0.64 or 64%), the predictive value of a positive test is fairly good, at 88%. The positive predictive value of an assay varies with the prevalence of the disease in the population. This is a key point. An example of this in our syphilis serology example in a low-prevalence population will serve to illustrate the point.
The same RPR serologic assay is being used in a hypothetical population of octogenarian nuns, none of whom are or have been sexually active in at least 6 decades.
| SYPHILIS | ||||
| PRESENT | ABSENT | |||
| RPR TEST RESULT | POSITIVE | 1 | 169 | Positive predictive value = 1/170 = 0.006Positive predictive value = 0.6% |
| NEGATIVE | 0 | 830 | Negative predictive value = 830/830 = 1.00Negative predictive value = 100% | |
| Specificity = 830/999 = 0.83Specificity = 83% | ||||
In this patient population, there is only one true case of syphilis, presumably acquired many years previously. The specificity of the test in this patient population is the same as it is in the individuals attending the STI clinic (in reality, it is likely to be different in different populations and also in different stages of syphilis). Because there is one case of syphilis, and 169 of the positive RPR results are false-positive test results, the positive predictive value in this patient population is only 0.6%. Clearly, this is a patient population in which the decision to test for syphilis using the RPR assay is not cost-effective.
In making a decision to order a specific test, the physician should know what he or she will do with the test results—essentially, how the results will alter the care of the patient. In a patient who the physician is certain does not have a specific disease, if the test for that disease has an appreciable rate of false-positive results, a positive test result is likely to be false positive and should not alter clinical care. Conversely, if the physician is certain that a patient has a disease, there is no good reason to order a test with a low sensitivity, as a negative result will likely be false negative. Tests are best used when there is uncertainty and when the results will alter the posttest probability and, therefore, the management of the patient.
SPECIMEN SELECTION, COLLECTION, AND TRANSPORT
Each laboratory test has three stages.
1 1. The preanalytical stage: The caregiver selects the test to be done, determines the type of specimen to be collected for analysis, ensures that it is properly labeled with the patient’s name, and facilitates rapid and proper transport of this specimen to the laboratory.
2 2. The analytical stage: The specimen is analyzed by the laboratory for the presence of specific microbial pathogens. The remaining sections of this chapter describe various analytic approaches to the detection of pathogens.
3 3. The postanalytical stage: The caregiver uses the laboratory results to determine what therapies, if any, to use in the care of the patient.
The preanalytical stage is the most important stage in laboratory testing! If the wrong test is ordered, if the wrong specimen is collected, if the specimen is labeled with the wrong patient’s name, or if the correct specimen