Melvin P. Weinstein

Update on detection of bacteremia and fungemia.

The presence of microorganisms in a patients blood is a critical determinant of the severity of the patients illness. Equally important, the laboratory isolation and identification of a microorganism present in blood determine the etiologic agent of infection, especially when the site of infection is localized and difficult to access. This review addresses the pathophysiology and clinical characteristics of bacteremia, fungemia, and sepsis; diagnostic strategies and critical factors in the detection of positive blood cultures; characteristics of manual and instrument approaches to bacteremia detection; approaches for isolating specific microorganisms associated with positive blood cultures; and rapid methods for the identification of microorganisms in blood cultures.

Blood Culture Contamination: Persisting Problems and Partial Progress

Although it has been widely appreciated for many years among physicians and microbiologists that blood cultures are among the most important laboratory tests performed in the diagnosis of serious infections (35), it has become equally apparent in more recent years that contaminated blood cultures are common (25, 42), enormously costly (3, 29), and frequently confusing for clinicians (1, 12, 14, 26). Clinical studies of bloodstream infections over 3 decades have provided guidelines for differentiating true pathogens from contaminants or organisms of unknown significance (14, 18, 41, 42); however, a true “gold standard” for differentiating pathogens from contaminants does not exist (4, 25). Moreover, the most common blood culture contaminants, coagulase-negative staphylococci (CoNS), which were almost always such several decades ago (18, 41), now are pathogens more frequently (19, 25, 26, 42), and judging the clinical significance of this group of microorganisms in blood has proven to be especially problematic (1, 11, 22, 24, 26, 42; S. J. Peacock, I. C. Bowler, and D. W. Crook., Letter, Lancet 346:191-192, 1995). This review focuses on how pathogen-contaminant decisions are made, the phenomenon of increasing contamination of blood cultures, potential methods for addressing high contamination rates, and practical laboratory approaches to the workup of likely contaminants.

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.

Detection of Bloodstream Infections in Adults: How Many Blood Cultures Are Needed?

ABSTRACT Although several reports have shown that two to three 20-ml blood cultures are adequate for the detection of bacteremia and fungemia in adults, a recent study (F. R. Cockerill et al., Clin. Infect. Dis. 38:1724-1730, 2004) found that two blood cultures detected only 80% of bloodstream infections and that three blood cultures detected 96% of episodes. We reviewed data at two university hospitals to determine whether the recent observations by Cockerill et al. are applicable more widely. We assessed all blood cultures obtained from adult inpatients from 1 January 2004 through 31 December 2005 at Robert Wood Johnson University Hospital and Duke University Medical Center. All instances in which ≥3 blood cultures per patient were obtained during a 24-h period were included. The medical records of patients who met the inclusion criteria were reviewed retrospectively to determine the clinical significance of the positive blood culture (true infection versus contamination). Data were analyzed to determine the cumulative sensitivity of blood cultures obtained sequentially during the 24-h time period. Of 629 unimicrobial episodes with ≥3 blood cultures obtained during the 24-h period, 460 (73.1%) were detected with the first blood culture, 564 (89.7%) were detected with the first two blood cultures, 618 (98.2%) were detected with the first three blood cultures, and 628 (99.8%) were detected with the first four blood cultures. Of 351 unimicrobial episodes with ≥4 blood cultures obtained during the 24-h period, 257 (73.2%) were detected with the first blood culture, 308 (93.9%) were detected with the first two blood cultures, 340 (96.9%) were detected with the first three blood cultures, and 350 (99.7%) were detected with the first four blood cultures. Among unimicrobial episodes, Staphylococcus aureus was more likely to be detected with the first blood culture (approximately 90% detected with the first blood culture). There were 58 polymicrobial episodes in which ≥3 blood cultures were obtained. Forty-seven (81.0%) were detected with the first blood culture, 54 (93.1%) were detected with the first two blood cultures, and 58 (100%) were detected with the first three blood cultures. The results of this study indicate that two blood cultures in a 24-h period will detect approximately 90% of bloodstream infections in adults. To achieve a detection rate of >99%, as many as four blood cultures may be needed. The previously held axiom that virtually all bloodstream infections can be detected with two to three blood cultures may no longer be valid but may also depend on the definition of the “first” blood culture obtained (see Materials and Methods and Discussion in the text).

Diagnosis of Legionella Infection

Legionellae, which are important causes of pneumonia in humans, continue to be incorrectly labeled as exotic pathogens. The ability to diagnose Legionella infection is limited by the nonspecific nature of clinical features and the shortcomings of diagnostic tests. Despite recent improvements, existing diagnostic tests for Legionella infection either lack sensitivity for detecting all clinically important legionellae or are unable to provide results within a clinically useful time frame. Understanding local Legionella epidemiology is important for making decisions about whether to test for Legionella infection and which diagnostic tests to use. In most situations, the use of both the urinary antigen test plus sputum culture is the best diagnostic combination. Polymerase chain reaction (PCR) is a promising tool, but standardized assays are not commercially available. Further work needs to focus on the development of urinary antigen tests assays that detect a wider range of pathogenic legionellae and on the development of standardized PCR assays.

Detection and Identification of Microorganisms by Gene Amplification and Sequencing

Gene amplification and sequencing have led to the discovery of new pathogens as agents of disease and have enabled us to better classify microorganisms from culture. Sequence-based identification of bacteria and fungi using culture is more objective and accurate than conventional methods, especially for classifying unusual microorganisms that are emerging pathogens in immunocompromised hosts. Although a powerful tool, the interpretation of sequence-based classification can be challenging as microbial taxonomy grows more complex, without known clinical correlatives. Additionally, broad-range gene polymerase chain reaction and sequencing have emerged as alternative, culture-independent methods for detecting pathogens from clinical material. The promise of this technique has remained strong, limited mainly by contamination and inadequate sensitivity issues. This review explains sequence-based microbial classification, with emphasis on relating the complex world of microbial taxonomy to a clinical context. Additionally, this review discusses a rational approach to broad-range bacterial polymerase chain reaction and gene sequencing when applied directly to clinical samples.

Spontaneous bacterial peritonitis: A review of 28 cases with emphasis on improved survival and factors influencing prognosis

During a five year period, 28 episodes of spontaneous bacterial peritonitis were documented. The number of cases recognized annually increased during the study period. Clinical and laboratory features of spontaneous bacterial peritonitis were similar to those previously reported; however, mortality was considerably lower (57 per cent). Factors associated with adverse prognosis were increasing hepatic encephalopathy, more than 85 per cent granulocytes in peripheral blood or ascitic fluid, total bilirubin greater than 8 mg/dl and serum albumin less than 2.5 g/dl. Temperature greater than 38 degrees C was associated with increased survival. Infection by enteric organisms was associated with higher mortality than infection by nonenteric organisms. Unexpectedly, patients with bacteremia fared no worse than those whose blood remained sterile. The data suggest that in patients with leukocyte counts greater than 1,000 cells/mm3 and more than 85 per cent granulocytes in their ascitic fluid, the likelihood of spontaneous bacterial peritonitis is high. Such patients deserve empiric antibiotic therapy pending the results of appropriate cultures.

Rationale for Revised Penicillin Susceptibility Breakpoints versus Streptococcus pneumoniae: Coping with Antimicrobial Susceptibility in an Era of Resistance

In January 2008, the Clinical and Laboratory Standards Institute published revised susceptibility breakpoints for penicillin and Streptococcus pneumoniae, and shortly thereafter, the United States Food and Drug Administration similarly revised its breakpoints via changes in the package insert for penicillin. The revised susceptibility breakpoint is < or =2 microg/mL for nonmeningeal infections treated with parenteral penicillin at a dosage of 12 million units-24 million units per day. The susceptibility breakpoint of < or =0.06 microg/mL remains unchanged for pneumococcal meningitis treated with parenteral penicillin at a dosage of > or =18 million units per day. Herein, we review the scientific basis for the revisions to the breakpoints, which were supported by microbiologic, pharmacokinetic and/or pharmacodynamic, and clinical data. Clinicians, once again, should feel comfortable prescribing penicillin for pneumococcal pneumonia and other pneumococcal infections outside the central nervous system.

The Clinical and Prognostic Importance of Positive Blood Cultures in Adults

BACKGROUND Bloodstream infections are a major cause of morbidity and mortality in adults. Bloodstream infections should be reassessed periodically because of increased antibiotic resistance, more patients receiving immunomodulatory therapy, improved antiretroviral therapy, and acquisition of infection in health care settings other than hospitals. METHODS We conducted retrospective assessment by infectious disease physicians of hospitalized adults with positive blood cultures at 3 academic medical centers. RESULTS Two thousand two hundred seventy positive blood culture episodes occurred in 1706 patients. Of 2669 isolates, 51% represented true infection, 41% contamination, and 8% unknown clinical significance. Although coagulase-negative staphylococci were most common, only 10% were clinically significant. Among 1225 true bloodstream infections, the most frequent isolates were Staphylococcus aureus, Escherichia coli, Enterococcus spp., Klebsiella pneumoniae, coagulase-negative staphylococci, Pseudomonas aeruginosa, Candida albicans, Enterobacter cloacae, and Serratia marcescens. Intravenous catheters were the most common primary source of bloodstream infection (23% of episodes). Most (81%) bloodstream infections were acquired in the hospital or other health care settings. Crude and attributable in-hospital case-fatality ratios were 20% and 12%, respectively, lower than in previous studies. Increasing age, hypotension, absence of fever, hospital acquisition, extreme white blood cell count values, and the presence of the acquired immunodeficiency syndrome, malignancy, or renal disease were significantly associated with an increased risk of in-hospital attributable death in multivariable analysis. CONCLUSIONS The proportion of bloodstream infections due to intravenous catheters is continuing to increase. Most episodes were acquired in the hospital or other health care setting. In-hospital case-fatality ratios have decreased compared with previous studies. Several previously identified factors associated with an increased mortality remain statistically significant.

Laboratory Diagnosis of Invasive Pneumococcal Disease

The laboratory diagnosis of invasive pneumococcal disease (IPD) continues to rely on culture-based methods that have been used for many decades. The most significant recent developments have occurred with antigen detection assays, whereas the role of nucleic acid amplification tests has yet to be fully clarified. Despite developments in laboratory diagnostics, a microbiological diagnosis is still not made in most cases of IPD, particularly for pneumococcal pneumonia. The limitations of existing diagnostic tests impact the ability to obtain accurate IPD burden data and to assess the effectiveness of control measures, such as vaccination, in addition to the ability to diagnose IPD in individual patients. There is an urgent need for improved diagnostic tests for pneumococcal disease--especially tests that are suitable for use in underresourced countries.