Manual Infections of the Gastrointestinal Tract: Microbiology, Pathophysiology, and Clinical Features

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  1. Recommended Specimens for Microbiology and Pathology for Diagnosis of Anthrax | Anthrax | CDC
  2. Recommended Specimens for Microbiology and Pathology for Diagnosis of Anthrax
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  4. ESOPHAGITIS
  5. Gastrointestinal infections

The flocked nature of the swab allows for more efficient release of contents for evaluation. The laboratory must follow its procedure manual or face legal challenges. The procedures in the manuals should be supported by the literature, especially evidence-based literature. To request the laboratory to provide testing apart from the procedure manual places everyone at legal risk. A specimen should be collected prior to administration of antibiotics. Once antibiotics have been started, the microbiota changes and etiologic agents are impacted, leading to potentially misleading culture results.

Susceptibility testing should be done only on clinically significant isolates, not on all microorganisms recovered in culture. Microbiology laboratory results that are reported should be accurate, significant, and clinically relevant. The laboratory should set technical policy; this is not the purview of the medical staff. Good communication and mutual respect will lead to collaborative policies. Specimens must be labeled accurately and completely so that interpretation of results will be reliable. 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. 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.


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It is very easy to access critical information about a specific body site just by consulting the table of contents. 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.

Recommended Specimens for Microbiology and Pathology for Diagnosis of Anthrax | Anthrax | CDC

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. 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. There may be circumstances in which it is prudent to omit the anaerobic vial and split blood specimens between 2 aerobic vials.

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One example is when fungemia due to yeast is strongly suspected. Such requests should be made in consultation with the microbiology laboratory director. 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. 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 ].

When 10 mL of blood or less is collected, it should be inoculated into a single aerobic blood culture bottle. 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. 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 ]. 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. Do not submit catheter tips for culture without an accompanying blood culture obtained by venipuncture. Use a 2- to 3-bottle blood culture set for adults, at least 1 aerobic and 1 anaerobic; use 1—2 aerobic bottles for children and consider aerobic and anaerobic when clinically relevant. Streptococcus pneumoniae and other gram-positive organisms and facultatively anaerobic organisms may grow best in the anaerobic bottle faster time to detection.

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.

Recommended Specimens for Microbiology and Pathology for Diagnosis of Anthrax

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:. Time to positivity not performed routinely in most laboratories : Standard blood cultures BCs obtained at the same time, one from the catheter or port and one from peripheral venipuncture, processed in a continuous-monitoring BC system. Quantitative BCs not performed routinely in most laboratories : one from catheter or port and one from peripheral venipuncture obtained at the same time using lysis-centrifugation Isolator or pour plate method.

If both BCs grow the same organism and the BC drawn from the device has 5-fold more organisms than the BC drawn by venipuncture, there is a high probability of catheter-associated BSI [ 15 , 16 ]. Catheter tip or segment cultures: The semi-quantitative method of Maki et al [ 12 ] is used most commonly; interpretation requires an accompanying peripheral BC. However, meticulous technique is needed to reduce contamination and to obtain the correct length 5 cm of the distal catheter tip.

This method only detects organisms colonizing the outside of the catheter, which is rolled onto an agar plate, after which the number of colonies is counted; organisms that may be intraluminal are missed. Modifications of the Maki method have been described as have methods that utilize vortexing of the catheter tip or an endoluminal brush not performed routinely in most laboratories.

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Biofilm formation on catheter tips prevents antimicrobial therapy from clearing agents within the biofilm, thus requiring removal of the catheter to eliminate the organisms. Infected mycotic aneurysms and infections of vascular grafts may result in positive blood cultures. If anaerobes are suspected, then the culture should consist of an aerobic and anaerobic bacterial culture. 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.

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There is considerable overlap between pericarditis and myocarditis with respect to both etiologic agents and disease manifestations. If anaerobes are suspected, then the culture should consist of both a routine aerobic and anaerobic culture. 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.

Gastrointestinal infections

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.