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16 Laboratory Patrick R D Clinical Microbiology The Clinician and the Microbiology 16 Laboratory Patrick R. Murray* The clinician and the microbiologist must actively work together to The responsibilities of the clinician, particularly of the infectious maximize the clinical value of diagnostic microbiology testing. Unfor- diseases physician, include acquiring a substantive understanding of tunately, the current trend to consolidate laboratory services and to the laboratory’s test menu, specimen collection and transport guide- move them off-site has made timely communication between labora- lines, and testing policies. The clinician should know the appropriate tory personnel and patient care providers more difficult.1 In addition, specimens and diagnostic tests for detection of specific pathogens and these changes potentially increase the time between specimen collec- be prepared to alert the laboratory personnel when a specific fastidious tion and laboratory processing, compromising the specimen integrity (e.g., Corynebacterium diphtheriae, Bartonella spp.) or highly patho- and delaying the availability of critical test results. These changes, along genic (e.g., Francisella tularensis, drug-resistant Mycobacterium tuber­ with other cost-cutting measures, make it even more important that culosis, Coccidioides immitis) organism is considered. The clinician the infectious diseases physician and the microbiologist work together. should also be prepared to prioritize test requests when only a limited The following expectations regarding the microbiologist’s and the clini- quantity of specimen can be collected. In this situation, discussions cian’s responsibilities should be recognized and addressed (Table 16-1). with the laboratory director can facilitate modification of the routine The menu of tests offered by the laboratory should be sufficient to laboratory practices to optimize the testing process (e.g., need for satisfy the patient care needs. Selection of these tests and the avail- routine stains, selection of media, and testing conditions to optimize ability of infrequently offered tests should be determined after discus- recovery of both bacteria and fungi on a limited number of media). sions with key members of the medical staff and should be revised as Communication with the laboratory director is also important when patient care needs change. If the performance of infrequent, expensive, the clinical testing needs are not satisfied by the available test menu or or sophisticated testing is shifted to an external laboratory, the micro- test turnaround time, when a laboratory policy causes patient care biologist should ensure that timely transport and appropriate test pro- problems, or when test results are inconsistent with a patient’s clinical cedures for these send-out tests are maintained so that test accuracy is presentation. not compromised. The microbiologist should provide the medical staff One inevitable difficulty that confronts both the microbiologist with a menu of the offered tests, including cutoff times for receipt of and clinician is the continuous revision of the taxonomic nomencla- specimens and turnaround times for test results. Guidelines for collec- ture, particularly for bacteria and fungi. Much of the taxonomic reor- tion of appropriate specimens, transport of the specimens to the testing ganization now under way is driven by our increased ability to classify site, and laboratory policies (e.g., limits on the number of specimens organisms by using gene sequencing and, more recently, mass spec- that can be submitted for a specific test, list of pathogens routinely trometry. The advantages of using these tools to classify and identify sought in stool cultures) should be available. The test menu and guide- organisms are greater precision than by using traditional phenotypic lines should be readily available on the hospital computerized informa- tests and a better understanding of the relationship between newly tion system and ideally integrated with electronic ordering of tests. The described organisms and disease. The disadvantages are the practical computer system should document receipt of specimens in the labora- challenges of remembering a rapidly expanding list of new names and tory, provide a record of testing in progress, and report preliminary the difficulties this presents for performing searches of the medical and final results. The microbiologist should coordinate with key literature. Fortunately, an up-to-date list of all validly published names members of the medical staff a policy of immediate telephone notifica- of bacteria, as well as the historical names of the organisms, is acces- tion of critical laboratory results, such as positive blood or other nor- sible on the Internet (www.bacterio.cict.fr/). The International Com- mally sterile fluid and tissue cultures, isolation of highly infectious mittee of Taxonomy of Viruses publishes a similar database for viruses pathogens, and significant positive stain results from clinical speci- (www.ictvonline.org). The scientific names of fungi and parasites mens. In addition, the microbiologist and medical staff should develop are defined by the International Code of Botanical Nomenclature guidelines for reporting antibiotic susceptibility results for bacteria, (www.bgbm.org/iapt/nomenclature/code/default.htm) and the Inter- mycobacteria, and fungi. Periodic publication of antimicrobial suscep- national Code of Zoological Nomenclature (www.iczn.org), respec- tibility patterns for the most common bacteria can be used to guide tively; however, up-to-date lists of validly named fungi and parasites empirical therapy.2 The laboratory must ensure that its operation meets do not currently exist. all current regulatory requirements (Clinical Laboratory Improvement Hospital epidemiology is an area of shared interest for the micro- Amendments), including initial verification and ongoing validation biology service and the hospital infection-control officers. Although a of procedures that are used by the laboratory.3,4 Participation in exter- hospital surveillance program can monitor infection rates and non- nal proficiency surveys, an effective program of quality control, and compliance with established infection prevention policies, the most the use of established quality assurance benchmarks can ensure the effective component to any infection control program is vigilance—on accuracy of the laboratory test results. Minimizing testing costs is the part of the microbiologist and clinician. The microbiologist has the essential for an efficient laboratory operation but must be done without unique perspective of seeing all the organisms isolated from patients significant compromise of the quality of results. Finally, a system of throughout the hospital and may be the first to recognize a small short-term storage of all specimens and long-term storage of important cluster of unique organisms. The clinician also has a unique isolates should be established to facilitate additional testing if required. perspective—the ability to assess the likelihood that an infection in his or her patient is nosocomial. Working in concert, the microbiologist *All material in this chapter is in the public domain, with the exception of any borrowed and clinician play an important role in guiding a potential outbreak figures or tables. investigation. 191 Downloaded for dr.Rahmat Dani Satria, M.Sc, Sp.PK ([email protected]) at Universitas Gadjah Mada from ClinicalKey.com by Elsevier on July 28, 2018. For personal use only. No other uses without permission. Copyright ©2018. Elsevier Inc. All rights reserved. 191.e1 KEYWORDS antigen detection; bacteriology; clinical microbiology laboratory; culture; laboratory diagnosis; molecular diagnosis; mycobacteriology; Chapter 16 mycology; parasitology; serology; virology The The Clinician and the Microbiology Laboratory Downloaded for dr.Rahmat Dani Satria, M.Sc, Sp.PK ([email protected]) at Universitas Gadjah Mada from ClinicalKey.com by Elsevier on July 28, 2018. For personal use only. No other uses without permission. Copyright ©2018. Elsevier Inc. All rights reserved. 192 TABLE 16-1 Microbiologist and Clinician rapid but typically insensitive and nonspecific method for detection of Partnership pathogens. Thus, if the quantity of specimen is limited, the value of microscopy must be balanced with the need for other diagnostic tests. Microbiologist’s Responsibilities If microscopy is the primary diagnostic test (e.g., examination of Provide an appropriate, comprehensive test menu that is responsive to physician peripheral blood smears for plasmodia, Babesia, Borrelia), then mul- needs tiple specimens may need to be examined by using specialized stains Diseases Establish a relationship with an external laboratory for performance of infrequent, or microscopy techniques. Selection of the appropriate specimen for expensive, or sophisticated testing that cannot be performed on site detection of microbial antigens is determined by the suspected patho- Provide cut-off times for processing test requests and turnaround times for reporting results gen. For example, cerebrospinal fluid (CSF) would be appropriate for diagnosis of cryptococcal meningitis, but both CSF and urine should Infectious Provide guidelines for specimen collection and transport be collected for diagnosis of pneumococcal meningitis. Likewise, the of Maintain an effective computerized system for acknowledging receipt of specimens, testing in-progress, and reporting of results; immediate
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