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Edited by Kessler. Merritt, MD. E-mail: merritt bcm. Oxford Academic. Google Scholar.

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Citing articles via Google Scholar. It is the key to accurate laboratory diagnosis and confirmation, it directly affects patient care and patient outcomes, it influences therapeutic decisions, it impacts hospital infection control, patient length of stay, hospital and laboratory costs, it influences antibiotic stewardship, and it drives laboratory efficiency. Clinicians and other medical personnel should consult the laboratory to ensure that selection, collection, transport, and storage of patient specimens they collect are managed properly. Throughout the text, there will be caveats that are relevant to specific specimens and diagnostic protocols for infectious disease diagnosis.

However, there are some strategic tenets of specimen management and testing in microbiology that stand as community standards of care and that set microbiology apart from other laboratory departments such as chemistry or hematology.

Laboratory Diagnosis of Infectious Diseases

The microbiology laboratory policy manual should be available at all times for all medical personnel to review or consult and it would be particularly helpful to encourage the nursing staff to review the specimen collection and management portion of the manual. This can facilitate collaboration between the laboratory, with the microbiology expertise, and the specimen collection personnel, who may know very little about microbiology or what the laboratory needs to establish or confirm a diagnosis.

Changes in Clinical Diagnostics and Tracking Infectious Diseases

It is important to welcome and actively engage the microbiology laboratory as an integral part of the healthcare team and encourage the hospital or the laboratory facility to have board-certified laboratory specialists on hand or available to optimize infectious disease laboratory diagnosis. There may be a redundant mention of some organisms because of their propensity to infect multiple sites. One of the unique features of this document is its ability to assist clinicians who have specific suspicions regarding possible etiologic agents causing a specific type of disease.

Another unique feature is that in most chapters, there are targeted recommendations and precautions regarding selecting and collecting specimens for analysis for a disease process. It is very easy to access critical information about a specific body site just by consulting the table of contents.

Executive Summary

Within each chapter, there is a table describing the specimen needs regarding a variety of etiologic agents that one may suspect as causing the illness. The test methods in the tables are listed in priority order according to the recommendations of the authors and reviewers. When room temperature is specified for a certain time period, such as 2 hours, it is expected that the sample should be refrigerated after that time unless specified otherwise in that section. This is not an official guideline of the IDSA but rather an authoritative guide with recommendations for utilizing the microbiology laboratory in infectious disease diagnosis.


It is a collaborative effort between clinicians and laboratory experts focusing on optimum use of the laboratory for positive patient outcomes. Future modifications of the document are to be expected, as diagnostic microbiology is a dynamic and rapidly changing discipline. Pediatric parameters have been updated in concordance with Pediatric Clinical Practice Guidelines and Policies , 16th ed. Comments and recommendations have been integrated into the appropriate sections.

The diagnosis of bloodstream infections BSIs is one of the most critical functions of clinical microbiology laboratories.

Infectious Disease

Some microorganisms, such as mycobacteria and dimorphic fungi, require longer incubation periods; others may require special culture media or non-culture-based methods. Although filamentous fungi often require special broth media or lysis-centrifugation vials for detection, most Candida spp grow very well in standard blood culture broths unless the patient has been on antifungal therapy.

Unfortunately, blood cultures from patients with suspected candidemia do not yield positive results in almost half of patients. Table 2 provides a summary of diagnostic methods for most BSIs. For most etiologic agents of infective endocarditis, conventional blood culture methods will suffice [3—5]. However, some less common etiologic agents cannot be detected with current blood culture methods. The most common etiologic agents of culture-negative endocarditis, Bartonella spp and Coxiella burnetii , often can be detected by conventional serologic testing.

However, molecular amplification methods may be needed for detection of these organisms as well as others eg, Tropheryma whipplei , Bartonella spp. In rare instances of culture-negative endocarditis, 16S polymerase chain reaction PCR and DNA sequencing of valve tissue may help determine an etiologic agent. The volume of blood that is obtained for each blood culture request also known as a blood culture set, consisting of all bottles procured from a single venipuncture or during one catheter draw is the most important variable in recovering bacteria and fungi from adult and pediatric patients with bloodstream infections [1, 2, 5, 6].

For neonates and adolescents, an age- and weight- appropriate volume of blood should be cultured see Table 3 below for recommended volumes. A second important determinant is the number of blood culture sets performed during a given septic episode.

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Generally, in adults with a suspicion of BSI, 2—4 blood culture sets should be obtained in the evaluation of each septic episode [5, 7]. The timing of blood culture orders should be dictated by patient acuity. In urgent situations, 2 or more blood culture sets can be obtained sequentially over a short time interval minutes , after which empiric therapy can be initiated. In less urgent situations, obtaining blood culture sets may be spaced over several hours or more. Skin contaminants in blood culture bottles are common, very costly to the healthcare system, and frequently confusing to clinicians.

To minimize the risk of contamination of the blood culture with commensal skin microbiota, meticulous care should be taken in skin preparation prior to venipuncture.

Bayero Journal of Pure and Applied Sciences

In addition, new products are now available that allow diversion and discard of the first few milliliters of blood that are most likely to contain skin contaminants. Consensus guidelines [2] and expert panels [1] recommend peripheral venipuncture as the preferred technique for obtaining blood for culture based on data showing that blood obtained in this fashion is less likely to be contaminated than blood obtained from an intravascular catheter or other device.

Several studies have documented that iodine tincture, chlorine peroxide, and chlorhexidine gluconate CHG are superior to povidone-iodine preparations as skin disinfectants for blood culture [1, 2]. Iodine tincture and CHG require about 30 seconds to exert an antiseptic effect compared with 1. Two recent studies have documented equivalent contamination rates with iodine tincture and CHG [8, 9].

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Laboratories should have policies and procedures for abbreviating the workup and reporting of common blood culture contaminants eg, coagulase-negative staphylococci, viridans group streptococci, diphtheroids, Bacillus spp other than B. These procedures may include abbreviated identification of the organism, absence of susceptibility testing, and a comment that instructs the clinician to contact the laboratory if the culture result is thought to be clinically significant and requires additional workup and susceptibility results.

Physicians should expect to be called and notified by the laboratory every time a blood culture becomes positive since these specimens often represent life-threatening infections. If the physician wishes not to be notified during specific times, arrangements must be made by the physician for a delegated healthcare professional to receive the call and relay the report.

The diagnosis of catheter-associated BSIs is often one of exclusion, and a microbiologic gold standard for diagnosis does not exist. Although a number of different microbiologic methods have been described, the available data do not allow firm conclusions to be made about the relative merits of these various diagnostic techniques [10—12]. Fundamental to the diagnosis of catheter-associated BSI is documentation of bacteremia.

The clinical significance of a positive culture from an indwelling catheter segment or tip in the absence of positive blood cultures is unknown. The next essential diagnostic component is demonstrating that the infection is caused by the catheter. This usually requires exclusion of other potential primary foci for the BSI.

Some investigators have concluded that catheter tip cultures have such poor predictive value that they should not be performed [13]. Numerous diagnostic techniques for catheter cultures have been described and may provide adjunctive evidence of catheter-associated BSI; however, all have potential pitfalls that make interpretation of results problematic.

Routine culture of intravenous catheter tips at the time of catheter removal has no clinical value and should not be done [13]. Although not performed in most laboratories, the methods described include the following:. Infected mycotic aneurysms and infections of vascular grafts may result in positive blood cultures. Numerous viruses, bacteria, rickettsiae, fungi, and parasites have been implicated as etiologic agents of pericarditis and myocarditis. In many patients with pericarditis and in the overwhelming majority of patients with myocarditis, an etiologic diagnosis is never made and patients are treated empirically. In selected instances when it is important clinically to define the specific cause of infection, a microbiologic diagnosis should be pursued aggressively. Unfortunately, however, the available diagnostic resources are quite limited, and there are no firm diagnostic guidelines that can be given.

Some of the more common and clinically important pathogens are listed in Table 5 below. When a microbiologic diagnosis of less common etiologic agents is required, especially when specialized techniques or methods are necessary, consultation with the laboratory director should be undertaken. There is considerable overlap between pericarditis and myocarditis with respect to both etiologic agents and disease manifestations.

Clinical microbiology tests of value in establishing an etiologic diagnosis of infections within the central nervous system CNS are outlined below. In this section, infections are categorized as follows: meningitis, encephalitis, focal infections of brain parenchyma, CNS shunt infections, subdural empyema, epidural abscess, and suppurative intracranial thrombophlebitis. Organisms usually enter the CNS by crossing a mucosal barrier into the bloodstream followed by penetration of the blood—brain barrier.

Other routes of infection include direct extension from a contiguous structure, movement along nerves, or introduction by foreign devices. Usually 3 or 4 tubes of cerebrospinal fluid CSF are collected by lumbar puncture for diagnostic studies. The first tube has the highest potential for contamination with skin flora and should not be sent to the microbiology laboratory for direct smears, culture, or molecular studies. A minimum of 0. Larger volumes 5—10 mL increase the sensitivity of culture and are required for optimal recovery of mycobacteria and fungi.

When the specimen volume is less than required for multiple test requests, prioritization of testing must be provided to the laboratory. Whenever possible, specimens for culture should be obtained prior to initiation of antimicrobial therapy. CSF Gram stains should be prepared after cytocentrifugation and positive results called to the patient care area immediately. Identification and susceptibility testing of bacteria recovered from cultures is routinely performed unless contamination during collection or processing is suspected. Most clinical microbiology laboratories do not perform all of the testing listed in the tables.

This is especially true of serologic and many molecular diagnostic tests. Although an FDA-cleared multiplex PCR targeting 14 organisms is available for diagnosing meningitis and encephalitis, it should not be considered a replacement for culture since clinical experience with the assay is limited and specificity issues have been reported [17, 18].