Paul P. Bourbeau

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)a

Abstract 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.

Automation in Clinical Microbiology

Editors 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. ABSTRACT 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.

Timing of Specimen Collection for Blood Cultures from Febrile Patients with Bacteremia

ABSTRACT 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.

Executive Summary: A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)a

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.

First Evaluation of the WASP, a New Automated Microbiology Plating Instrument

ABSTRACT Many laboratories are experiencing growing shortages of trained microbiology technologists and technicians. Consequently, there is considerable interest in new automation that could potentially lessen labor demands for specimen processing. In this study, we present the first published evaluation of a new microbiology instrument, the Walk Away Specimen Processor (WASP), manufactured by Copan, Inc., in which we evaluated cross-contamination, the accuracy of plating, and the quality of the results. The absence of cross-contamination was demonstrated by plating a total of 200 alternating inoculated and sterile specimen tubes. The ability of the WASP to subculture enrichment broths was evaluated with 106 Lim broth specimens, with the results being identical to those obtained by testing by routine methods. Plating of urine specimens with the WASP was compared to plating with the Dynacon Inoculab instrument. Three hundred specimens were plated in duplicate on both instruments with 1-μl loops, and 293 specimens were plated in duplicate on both instruments with 10-μl loops. The results of duplicate plating with the same instrument (replicate plating) and of the consensus agreement between the two instruments were compared. The replicate plating results were comparable for both instruments, while the WASP had more specimens with significant results than the Inoculab with the 1-μl loop only. Lastly, for the plating of 113 specimens in ESwab tubes, the manual method and WASP plating each yielded 90 potential pathogens. In summary, we report the first evaluation of a new microbiology specimen-plating instrument, the WASP, which offers opportunities for the automated plating of microbiology specimens to an extent that has not been possible to date.

Sampling Variability in the Microbiological Evaluation of Expectorated Sputa and Endotracheal Aspirates

ABSTRACT A five-center study was conducted with the aim of determining how reproducibly expectorated sputa and tracheal aspirates could be sampled when preparing Gram-stained smears and inoculating cultures. With both specimen types, excessive variation was noted among Gram stain results obtained from replicate smears. Less variation was noted among culture results, especially with tracheal aspirates.

Three Days of Incubation May Be Sufficient for Routine Blood Cultures with BacT/Alert FAN Blood Culture Bottles

ABSTRACT BacT/Alert FAN blood culture bottles have been shown to enhance the recovery of bacteria and yeast from blood compared with standard BacT/Alert bottles. It is well established that standard BacT/Alert blood culture bottles require no more than 5 days of incubation for the detection of routine bacteria and yeast. It is less clear, however, whether FAN bottles also routinely require 5 days of incubation. To address this question, we recently reviewed the results of 17,887 blood culture sets collected in FAN blood culture bottles at Geisinger Medical Center. Of these cultures, 1,780 were positive for bacteria or yeast, yielding a total of 1,242 clinically significant isolates. The numbers of isolates recovered on days 1, 2, 3, 4, and 5 were as follows: (values in parentheses are percentages of total significant isolates): 877 (71%), 269 (22%), 65 (5%), 18 (1%) and, 13 (1%), respectively. In total, 97.5% of all clinically significant isolates were detected in the first 3 days of incubation. Of the 31 significant isolates detected on day 4 or 5 of incubation, 17 were detected in concurrent blood cultures within the first 3 days of incubation. Chart reviews were conducted for the 13 patients with the remaining 14 isolates detected on day 4 or 5 to determine whether therapy was changed due to this blood culture result. Therapy was changed for only 1 patient. These results suggest that it may not be necessary to routinely incubate FAN blood culture bottles for more than 3 days.

Role of the Microbiology Laboratory in Diagnosis and Management of Pharyngitis

The microbiology laboratory plays a very important role in the diagnosis and management of patients with pharyngitis. Arguably, it is at least as important in identifying the 70 to 80% of patients with pharyngitis who do no require antimicrobial therapy as it is in identifying patients for whom antimicrobial therapy is appropriate. One of our educational responsibilities is to inform clinicians of the importance of performing diagnostic testing to establish an accurate diagnosis. Although some guidelines now suggest that clinical criteria alone may suffice for the diagnosis of GAS infection in adults (20), this topic remains controversial. Bisno et al. (4) have stated that these new recommendations should have been tested in a clinical trial before being published. Laboratorians need to be strong advocates for both appropriate testing and judicial use of antimicrobial agents for diagnosis and management of pharyngitis. Antibiotic therapy is generally only indicated for pharyngitis caused by GAS (2, 9, 39) and the rare case caused by C. diphtheriae and N. gonorrhoeae. Additional study is needed to clarify the benefit, if any, for the diagnosis and treatment of for beta-hemolytic streptococci other than GAS. As noted by Bisno (3), the benefits of antimicrobial therapy against these organisms are currently unknown.

Comparison of Recovery of Blood Culture Isolates from Two BacT/ALERT FAN Aerobic Blood Culture Bottles with Recovery from One FAN Aerobic Bottle and One FAN Anaerobic Bottle

ABSTRACT Traditionally, a routine blood culture for adult patients consisted of paired aerobic and anaerobic bottles, but the routine use of an anaerobic blood culture bottle has been challenged in recent years. In this study, we compared the recovery of two FAN aerobic bottles with one FAN aerobic and one FAN anaerobic bottle. Each pair of bottles was collected by a separate collection procedure, and each bottle held a recommended 8- to 12-ml draw. A total of 704 clinically significant isolates were recovered from 8,620 sets (17,240 pairs), with 487 (69.2%) isolates recovered from one or both bottles in each pair of bottles, 86 isolates (12.2%) recovered only from the FAN aerobic-FAN aerobic pair, and 131 isolates (18.6%) recovered only from the FAN aerobic-FAN anaerobic pair. Significantly more total organisms (P = 0.002), gram-positive cocci (P = 0.03), Staphylococcus aureus (P = 0.05), Enterobacteriaceae other than Escherichia coli (P = 0.02), and anaerobes (P = 0.01) were recovered from the FAN aerobic-FAN anaerobic pair than from the FAN aerobic-FAN aerobic pair. A separate analysis was performed on the 618 isolates that were recovered from the FAN aerobic-FAN anaerobic pair to compare recovery by bottle type. Significantly more S. aureus (P = 0.005) and anaerobes (P < 0.001) were recovered from the FAN anaerobic bottle, while significantly more coagulase-negative staphylococci (P = 0.01), Streptococcus pneumoniae (P = 0.03), and other gram-negative bacilli (P = 0.004) were recovered from the FAN aerobic bottle. These results support the routine use of a FAN anaerobic bottle for use in the culture of blood with the BacT/ALERT system in our institution. These results also suggest that the decision of whether to routinely utilize an anaerobic blood culture bottle should be influenced by the overall recovery of bacteria and yeast, the recovery of specific types of bacteria or yeast, the medium type, and the blood culture system utilized by the laboratory.

Comparative Evaluation of the AccuProbe Group B Streptococcus Culture Test, the BD GeneOhm Strep B Assay, and Culture for Detection of Group B Streptococci in Pregnant Women

ABSTRACT We compared a rigorous culture method with the Gen-Probe AccuProbe Group B Streptococcus Culture Test (APGB) and the BD GeneOhm StrepB assay (GOSB) for the detection of group B streptococci (GBS) from an 18- to 24-h LIM broth. Culture (95.3%) and GOSB (95.3%) were more sensitive than APGB (86.5%) for the detection of GBS.