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Molecular testing has replaced viral culture for the diagnosis of enteroviral meningitis, but is not routinely relied on for the detection of bacteria in CSF where Gram stain and bacterial culture should be ordered. Bacterial antigen testing on CSF is no longer recommended and should not be ordered nor should the laboratory provide this service. Early, incorrect assumptions held that selected antigen tests on CSF may have some value in patients who received therapy prior to specimen collection with negative Gram stain and negative culture results [22], but this is no longer recommended.

In patients suspected of having bacterial meningitis, at least 2—4 blood cultures should be performed, but therapy should not be delayed. The cryptococcal antigen test has replaced the India ink stain for rapid diagnosis of meningitis caused by Cryptococcus neoformans or Cryptococcus gattii and should be readily available in most laboratories. This test is most sensitive when performed on CSF rather than serum. Complement fixation test performed on CSF is recommended for the diagnosis of coccidioidal meningitis since direct fungal smear and culture are often negative. Detection of Coccidioides antibody in CSF by immunodiffusion has lower specificity than complement fixation.

Syndromic Testing for Infectious Diseases Part 2: Gastrointestinal Infections [Hot Topic]

Encephalitis is an infection of the brain parenchyma causing abnormal cerebral function altered mental status, behavior or speech disturbances, sensory or motor deficits. Despite advancements in molecular technology for the diagnosis of CNS infections, the etiologic agent of encephalitis often cannot be identified. Immunostatus, travel, and other exposure history insects, animals, water, sexual should guide testing. The Infectious Diseases Society of America IDSA practice guidelines provide a detailed listing of risk factors associated with specific etiologic agents [26].

Although the diagnosis of a specific viral cause is usually based on testing performed on CSF, testing of specimens collected from other sites may be helpful. Additional NAAT specific for parechoviruses is recommended for young children [29]. Because the performance characteristics of molecular testing for other causes of viral encephalitis are not well established, serology and repeat molecular testing may be required Table 7.

Focal parenchymal brain infections start as cerebritis, then progress to necrosis surrounded by a fibrous capsule. There are 2 broad categories of pathogenesis: 1 contiguous spread otitis media, sinusitis, mastoiditis, and dental infection , trauma, neurosurgical complication, or 2 hematogenous spread from a distant site of infection skin, pulmonary, pelvic, intra-abdominal, esophageal, endocarditis. A brain abscess in an immunocompetent host is usually caused by bacteria Table 8. A wider array of organisms is encountered in immunocompromised individuals.

Shunts are placed to divert CSF for the treatment of hydrocephalus. The proximal portion is placed in a cerebral ventricle, intracranial cyst, or the subarachnoid space lumbar region. The distal portion may be internalized peritoneal, vascular, or pleural space or externalized. Potential routes of shunt infection include contamination at time of placement, contamination from the distal portion retrograde , breakdown of the skin over the shunt, and hematogenous seeding.

Blood cultures should also be collected if the shunt terminates in a vascular space ventriculoatrial shunt. Most CNS shunt infections are caused by bacteria. Fungi are more likely to cause shunt infections in immunocompromised patients and those receiving total parenteral nutrition, steroids, or broad-spectrum antibiotics. Culture of shunt or drain components after removal should not be performed unless the patient has symptoms of a CNS infection [35]. Cranial subdural empyema and cranial epidural abscess are neurosurgical emergencies that are usually caused by bacteria streptococci, staphylococci, aerobic gram-negative bacilli, anaerobes, often polymicrobial Table Mycobacteria and fungi are rare causes.

Predisposing conditions include sinusitis, otitis media, mastoiditis, neurosurgery, head trauma, subdural hematoma, and meningitis infants. The pathogenesis of spinal epidural abscess includes hematogenous spread skin, urinary tract, mouth, mastoid, lung infection , direct extension vertebral osteomyelitis, discitis , trauma, or postprocedural complication surgery, biopsy, lumbar puncture, anesthesia. Spinal epidural abscess is usually caused by staphylococci, streptococci, aerobic gram-negative bacilli, and anaerobes.

Nocardia spp, mycobacteria, and fungi may also cause spinal epidural abscess. Spinal subdural empyema is similar to spinal epidural abscess in clinical presentation and causative organisms. Magnetic resonance imaging is the optimal diagnostic procedure for suppurative intracranial thrombophlebitis.

The etiologic agent may be recovered from cerebrospinal fluid and blood cultures. Causative organisms are similar to cranial epidural abscess and cranial subdural empyema. Empiric antimicrobial therapy is usually based on the predisposing clinical condition. Recommendations for the laboratory diagnosis of ocular infections are often based on studies where only small numbers of clinical specimens were examined so the evidence base for many recommendations is limited. Studies comparing multiple diagnostic approaches to determine the optimal means for detection of the infectious etiology of keratitis and endophthalmitis are further hampered by small specimen size.

Finally, frequent pretreatment with topical antibacterial agents further complicates laboratory diagnosis of both bacterial conjunctivitis and keratitis [36]. Because ocular infections may involve one or both eyes and etiologies may differ, clinicians must clearly mark specimens as to which eye has been sampled, especially in those patients who have bilateral disease. Collection of specimens from anatomical structures surrounding the eye is typically done using swabs Table The most commonly collected specimens are from the conjunctiva. Cultures for aerobic bacteria and detection of Chlamydia and viruses either by culture or NAAT are most commonly performed, although none are as yet FDA approved for detection in eye specimens.

Bayero Journal of Pure and Applied Sciences

Since direct microscopic examination may be useful in preliminary diagnosis of conjunctivitis, obtaining dual swabs, one for culture and one for smear preparation, is recommended. Smears may be made for Gram stain, calcofluor stain for fungi and Acanthamoeba , or direct fluorescent antibody DFA for Chlamydia trachomatis. Although NAAT tests are preferred for the diagnosis of viral ocular infections because of their increased sensitivity and more rapid turnaround time, if viral culture is requested, specimens should be submitted on ice using viral transport medium, especially if specimen transport is prolonged [36].

Specimens obtained from either the surface or the globe of the eye are almost always collected by ophthalmologists. The volume of specimens is always limited. This specimen limitation makes it necessary for the laboratory to prioritize procedures depending on what organisms are sought; this should always be done after discussion with the ophthalmologist who collects the specimen and the infectious disease consultant when appropriate.

This is particularly important because all major pathogen groups—viruses, parasites, bacteria, mycobacteria, and fungi—can cause ocular infection. Both epidemiology and clinical presentation are used to narrow the organism s sought and the laboratory tests requested. Because of the limited specimen size seen with scrapings and biopsies, the laboratory and ophthalmologist may agree to inoculate these specimens onto media and prepare smears at the bedside. In this case, the laboratory should supply the necessary media and slides to the ophthalmologist. Aspirates from the anterior chamber or vitreous are the optimal specimens for detection of anaerobic bacteria and viral agents; they can be submitted in syringes with needles removed.

Syringes should be placed in a leak-proof outer container for transport. Injection of the fluid into a small sterile vial provided by the laboratory is preferable. The same principles for specimen collection and transport described for conjunctival specimens apply to these specimens as well. Orbital cellulitis is almost always a complication of sinusitis and the organisms associated with it include Streptococcus pneumoniae , nontypeable Haemophilus influenzae , Streptococcus pyogenes , Moraxella spp, anaerobic bacteria, Aspergillus spp, and the Mucorales formerly Zygomycetes.

Periorbital cellulitis usually arises as a result either of localized trauma or bacteremia most often caused by Staphylococcus aureus , S. Diagnosis of these infections is either based on positive blood cultures or, in the case of orbital cellulitis, culture of drainage material aspirated from the subperiosteal region of the sinuses.

Molecular Diagnostics of Infectious Diseases

Blepharitis, canaliculitis, and dacryocystitis are all superficial infections that are generally self-limited. The organisms associated with these infections are predominantly gram-positive bacteria, although various gram-negative bacteria, anaerobes, and fungi all have been recovered [39]. A limitation of many studies of these infections is that microbiologic data on control populations are frequently lacking. The organisms commonly recovered are part of the indigenous skin microflora such as coagulase negative staphylococci and diphtheroids, so attributing a pathogenic role to these organisms in these conditions is difficult.

Cultures from these sites are rarely submitted for diagnostic workup. If cultures for canaliculitis are considered, concretions recovered during canalicular compression or canaliculotomy are recommended. Strategies for the diagnosis of these superficial infections should be similar to those for conjunctivitis. Most cases of conjunctivitis are caused by bacteria or viruses that are typically associated with upper respiratory tract infections [40, 41].

Because of the distinctive clinical presentation of both bacterial and viral conjunctivitis coupled with the self-limited nature of these infections, determining its etiology is infrequently attempted [42].

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When tests are requested, diagnosis of bacterial conjunctivitis is often compromised by the prior use of empiric antibacterial therapy [40, 41]. Sexually active patients who present with bacterial conjunctivitis should have an aggressive diagnostic workup with Gram stain and cultures because of their risk for N. This is a sight-threatening infection which can result in perforation of the globe.

In the developing world, trachoma, a form of conjunctivitis due to specific strains of C.


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Off-label use of commercial NAAT assays is used for detection of this agent in research settings [44]. This is almost always a clinical diagnosis, although for epidemiologic purposes culture or NAAT can be done [36]. Most cases of neonatal conjunctivitis are due to Neisseria gonorrhoeae , C. Pseudomonas aeruginosa is a rare but life-threatening cause of neonatal conjunctivitis in hospitalized infants. Corneal infections usually occur in 3 distinct patient populations: those with ocular trauma with foreign objects, those with postsurgical complications of corneal surgery, and in patients who practice poor hygiene associated with their extended-wear contact lenses [45, 46].

Postvaccination keratitis is a well-recognized complication of vaccinia vaccination and should be considered in the appropriate clinical setting [47].

Molecular diagnosis of infectious diseases using cytological specimens

Corneal infections can also result from reactivation of herpes viruses including HSV and varicella zoster virus [48]. It is important to note that the use of dyes and topical anesthetics may inhibit NAAT reactions used to diagnose keratitis [48]. The eye surface should be thoroughly rinsed with nonbacteriostatic saline before specimens for NAATs are obtained [48, 49] Table The most common corneal infections occur in patients who improperly use their contact lens system.

Traditional Microbial Typing

Because these patients are usually treated with antimicrobial agents prior to obtaining specimens for bacterial cultures, some ophthalmologists favor culturing contact lens solution and cases. However, culture of such solutions and cases is not recommended because of the frequency with which they are falsely positive [50, 51].

Pseudomonas aeruginosa is the most common cause of sporadic contact lens—associated keratitis, but outbreaks of keratitis due to contamination of contact lens care solutions have been recently reported with both Fusarium and Acanthamoeba [50—53]. Postsurgical keratitis infections are frequently due to either coagulase-negative staphylococci or C. This is due in part to the most widely used corneal holding medium not containing any antifungal agents [55]. Keratitis following trauma due to foreign objects is frequently caused by organisms found in the environment.

Included in this group are environmental gram-negative rods such as P.


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  • Corneal biopsies are recommended in patients in whom keratitis persists or worsens. Endophthalmitis can arise either by exogenous introduction of pathogens into the eye following trauma or surgery, or as a result of endogenous introduction of pathogens across the blood—eye barrier. Depending upon the mode of pathogenesis, the spectrum of causative agents will vary Table Specimen amounts of both aqueous and vitreous fluid are small, so discretion must be exercised in determining for which agents the specimen should be examined.

    Postoperative endophthalmitis is most often caused by gram-positive organisms with coagulase-negative staphylococci predominating; chronic postoperative endophthalmitis can be due to C. Environmental organisms such as dematiaceous fungi, Fusarium spp, Bacillus cereus , Nocardia spp, Mycobacterium chelonae , and glucose-fermenting gram-negative rods are more commonly encountered in patients with exogenous endophthalmitis [61].

    Endogenous endophthalmitis, because of its association with bacteremia and fungemia, is usually caused by those organisms most responsible for BSIs; for example, Candida albicans and related species, Aspergillus spp, S. Viruses and parasites are rarely found to cause endophthalmitis; however, as in cases of trauma or severe immunosuppression, infection due to agents such as the herpes viruses, Toxoplasma gondii , Toxocara spp, Echinococcus spp, and Onchocerca volvulus do occur [64, 65] and typically involve the uvea and retina. For further information on the diagnosis of ocular infections caused by O.

    Only infrequently is it due to infection, which is almost always caused by endogenous microbes accessing the eye via a breach in the blood—eye barrier. Because uveitis and retinitis, like endogenous endophthalmitis, are localized manifestations of systemic infections, diagnosis of the etiology of systemic infections should be coupled with a careful ocular examination, preferably performed by an ophthalmologist with specific infectious disease expertise.

    Toxocara canis and rubella are additional agents to be considered in pediatrics.