The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including Tickborne Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.
b Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories.Editor's Note: In this issue of the Journal of Clinical Microbiology, Paul Bourbeau and Nate Ledeboer provide an informed review of an exciting new concept in clinical microbiology, the use of instrumentation to automate the front-end processing and workup of specimens submitted to a laboratory for analysis. The potential value of such instrumentation includes the possibility of substantial cost savings, standardization of initial specimen processing, more rapid and consistent provision of both identification and antimicrobial susceptibility test results, and a diminished risk for laboratory-acquired infections. However, as with any new diagnostic modality in clinical microbiology, there now exists a pressing need for investigations aimed at elucidating the performance characteristics of this new technology. Going forward, it will be imperative that laboratorians assess this new technology in objective, comparative, and preferably prospective clinical studies. Such studies will be necessary to define the true, rather than perceived or hoped-for, value of front-end and total laboratory automation in clinical microbiology. The Journal of Clinical Microbiology enthusiastically awaits submission of manuscripts that report the results of such investigations. Gary V. Doern, Editor in Chief, Journal of Clinical MicrobiologyI n recent years, while automation has steadily spread throughout the clinical chemistry and clinical hematology areas of diagnostic laboratories, clinical microbiology laboratories have largely been excluded from this trend. Although continuous-monitoring blood culture systems, automated microbial identification, and automated antimicrobial susceptibility testing systems are widely utilized in microbiology laboratories, microbiology specimen processing and culture workup, in particular, remain largely manual tasks, and indeed, few changes to the methods used to perform these tasks have occurred for many years. While we acknowledge that some larger microbiology laboratories utilize urine-plating instrumentation, most microbiology laboratories have littleto-no automation in their specimen-processing areas, with the exception of some laboratories in Western Europe, Australia, and the Middle Eastern nations. Still fewer laboratories have implemented some version of total laboratory automation (TLA).Driven by a variety of factors, we believe th...
Bloodstream infections are an important cause of morbidity and mortality. Physician orders for blood cultures often specify that blood specimens be collected at or around the time of a temperature elevation, presumably as a means of enhancing the likelihood of detecting significant bacteremia. In a multicenter study, which utilized retrospective patient chart reviews as a means of collecting data, we evaluated the timing of blood culture collection in relation to temperature elevations in 1,436 patients with bacteremia and fungemia. The likelihood of documenting bloodstream infections was not significantly enhanced by collecting blood specimens for culture at the time that patients experienced temperature spikes. A subset analysis based on patient age, gender, white blood cell count and specific cause of bacteremia generally also failed to reveal any associations.Bloodstream infections (BSIs) occur more than 200,000 times annually in the United States, with associated mortality rates of 35 to 60% (20,33,34). Prompt administration of appropriate antimicrobial therapy plays an important role in reducing the mortality associated with this condition (9,12,14, 15,16,18,22,26,31). In patients with bacteremia, the optimization of therapy is ultimately predicated on rapid documentation of positive blood cultures, expeditious performance of in vitro antimicrobial susceptibility tests, and timely reporting of results (2,23,33). Numerous factors influence the likelihood of detecting bacteremia. These factors include the volume of blood specimens cultured and the number of blood cultures performed (1,8,10,11,17,21,25,27,29). The conventional practice has been to obtain blood specimens at or around the time of a temperature elevation as a means of enhancing the likelihood of documenting bacteremia (5, 32). This practice is based on the principle that the presence of organisms in the intravascular space leads to the elaboration of cytokines, which in turn causes body temperatures to rise.The value of attempting to time the collection of blood for culture around temperature elevations is complicated by the fact that many patients with bacteremia, especially those that are elderly, may be hypothermic at the time that they are bacteremic or may be unable to mount a febrile response to infection (7). Furthermore, there are numerous causes of fever other than bacteremia, e.g., ischemia, drug reactions, immunological conditions, and malignancy (4). This issue is further complicated by the observation made more than 50 years ago by Bennett and Beeson: bacteremia actually precedes temperature elevations by 1 or 2 h (3). These researchers noted that blood cultures were frequently negative at the time of the temperature spike and concluded that, ideally, blood cultures should be drawn some time prior to elevations in temperature. More recently, Jaimes et al. found that fever was not a useful independent predictor of bacteremia and needed to be considered in light of other factors, such as hypotension, white blood cell (WBC) counts, an...
Manufacturers generally recommend that blood culture bottles be loaded into instruments within a short time of collection. However, in our experience, delays often occur prior to loading the bottles. We examined the effect of holding bottles under various temperatures (T)-room temperature (RT), 4°C, 37°C, and RT for 2 h following incubation at 37°C (to simulate transit [TR])-and for various holding times of 4, 12, and 24 h. We utilized the BacT/ALERT system with FA and FN bottles and the BACTEC system with Plus (PL) and Lytic 10 (LY) bottles. Standardized inocula and 5 ml of blood were added to each bottle. Fifteen organisms were evaluated based upon expected performance: aerobic (FA and PL), anaerobic (FN and LY 10), and facultative (all bottles). Based upon expected performance, the FA and FN bottles recovered 458 of 468 organisms and 282 of 288 organisms, respectively, whereas the PL and LY bottles recovered 453 of 468 organisms and 257 of 288 organisms, respectively (P ؍ <0.001, FN versus LY). There were 3, 11, 21, and 27 false-negative results for bottles held at 4°C, RT, 37°C, and TR, respectively. There were 4, 8, and 50 false-negative results for bottles held for 4, 12, and 24 h, respectively. Our results support holding these four bottle types at 4°C or at RT for up to 24 h and at 37°C for up to 12 h. We propose that manufacturers only need to make claims for "delayed entry" when these bottles are held for more than 24 h at 4°C or at RT or for more than 12 h at 37°C.For patients with suspected bacteremia or fungemia, the inoculation of blood culture bottles for the detection of bacteria and yeast often occurs at the patient bedside. Bottles are then transported to the laboratory and loaded into blood culture instruments or incubators. Continuous-monitoring blood culture instruments are widely used for this purpose in the United States. Ideally, the time in transit from the patient to the instrument is kept to a minimum. Although this may have been a routine occurrence at one time, the proliferation of satellite laboratories, core laboratories, and increased dependence on reference laboratories for the performance of routine microbiology testing often results in prolonged delays between the time of specimen collection and the loading of the blood culture bottles into the instruments.There have been very few studies that have examined the effects of transport time on organism recovery from blood culture bottles. The purpose of the present study was to evaluate the ability of two different continuously monitoring blood culture instruments to detect organisms from seeded blood cultures that were stored under a variety of temperatures for various lengths of time prior to loading into the instruments. MATERIALS AND METHODSThe present study was conducted in two microbiology laboratories, Geisinger Medical Center (GMC) and Pinnacle Health Laboratories (PHL), with a standard protocol in use at both institutions. The GMC laboratory utilized the BacT/ALERT blood culture system (FA and FN bottles; bioMérieux, Dur...
The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including Tickborne Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.
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