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Pertussis, classically known as whooping cough, caused by Bordetella pertussis, should be considered in an adolescent or young adult with paroxysmal cough. NAATs in combination with culture are the recommended tests of choice for B. Currently there are a few FDA-cleared platforms for B. Streptococcus pneumoniae and Haemophilus influenzae do not play an established role in acute bronchitis but they, along with Moraxella catarrhalis , do figure prominently in cases of acute exacerbation of chronic bronchitis.

These have largely replaced rapid antigen detection tests and culture in most institutions. Performance characteristics vary among the various panels and singleplex NAATs.

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Specimen sources may also vary depending upon the assay. Readers should become familiar with the platforms offered in their respective institutions and the approved specimen sources, collection devices, and transport requirements. Respiratory syncytial virus, human rhinovirus, human metapneumovirus, human coronavirus, and type 3 parainfluenza virus are significant causes of bronchiolitis in infants and young children [].

Several molecular panels for the detection of bacterial causes of pneumonia and their resistance markers are currently in clinical trials. Carefully obtained microbiological data can support the diagnosis, but often fails to provide an etiologic agent. Table 20 lists the more common causes of CAP. Other less common etiologies may need to be considered depending upon recent travel history or exposure to vectors or animals that transmit zoonotic pathogens such as Sin Nombre virus hantavirus pulmonary syndrome or Yersinia pestis pneumonic plague, endemic in the western United States.

The rationale for attempting to establish an etiology is that identification of a pathogen will focus the antibiotic management for a particular patient []. In addition, identification of certain pathogens such as Legionella spp, influenza viruses, and the agents of bioterrorism have important public health significance. Those patients who require admission should have pretreatment blood cultures, culture and Gram stain of good-quality samples of expectorated sputum and, if disease is severe, urinary antigen tests for S. The recommendations for children are in agreement with the adult recommendations with respect to when to obtain blood cultures and sputum cultures but differ slightly for other laboratory tests [].

Testing for viral pathogens is recommended in both outpatient and inpatient settings []. Although a weak recommendation, in children with appropriate signs and symptoms, Mycoplasma pneumoniae testing is indicated. There are several molecular assays available for M. Urinary antigen testing for S.

Laboratories must have a mechanism in place for screening sputum samples for acceptability to exclude those that are heavily contaminated with oropharyngeal microbiota and not representative of deeply expectorated samples prior to setting up routine bacterial culture. Poor-quality specimens provide misleading results and should be rejected because interpretation would be compromised.

A thoracentesis should be performed in the patient with a pleural effusion. Mycobacterial infections should be in the differential diagnosis of CAP that fails to respond to therapy for the typical CAP pathogens. Mycobacterium tuberculosis , although declining in the United States in recent years, is still an important pathogen among immigrant populations.

Mycobacterium avium complex is also important, not just among patients with HIV, but especially in patients with chronic lung disease or cystic fibrosis, and in middle-aged or elderly thin women []. Hospital-acquired and ventilator-associated pneumonias HAP and VAP, respectively are frequently caused by multidrug-resistant gram-negative bacteria or other bacterial pathogens.

Aside from respiratory viruses that may be nosocomially transmitted, viruses and fungi are rare causes of HAP and VAP in the immunocompetent patient. In the nonventilated patient, the specimens could include those obtained by spontaneous expectoration, sputum induction, or nasotracheal suction in an uncooperative patient and, in the ventilated patient, endonasotracheal aspirates are preferred [].

Determining the cause of the pneumonia relies upon initial Gram stain and semi-quantitative cultures of endotracheal aspirates or sputum. A smear lacking inflammatory cells and a culture absent of potential pathogens have a very high negative predictive value.

Cultures of endotracheal aspirates, while likely to contain the true pathogen, also consistently grow more mixtures of species of bacteria than specimens obtained by bronchoscopic techniques.

This may lead to additional unnecessary antibiotic therapy. Quantitative assessment of invasively obtained samples such as BAL fluid and protected specimen brush specimens is often performed []. Quantities of bacterial growth above a threshold are diagnostic of pneumonia and quantities below that threshold are more consistent with colonization. Quantitative studies require extensive laboratory work and special procedures that smaller laboratories may not accommodate and are therefore not endorsed by the guidance despite studies that show decreased antibiotic utilization with quantitative cultures [].

Bronchial washes are not appropriate for routine bacterial culture. An aging population, among other factors, has resulted in an increase in the incidence of pleural infection []. The infectious causes of pleural effusions differ between community-acquired and hospital-acquired disease. In a large multicenter study MIST1 of adult patients with pleural infection to assess streptokinase treatment, the major pathogens recovered in decreasing order of frequency were S.

Among patients with hospital-acquired infection, S. Table 22 summarizes the major pathogens. Any significant accumulation of fluid in the pleural space should be sampled by thoracentesis. Specimens should be hand carried immediately to the laboratory or placed into appropriate anaerobic transport media for transport.

In some institutions, bedside inoculation into blood culture bottles has become an established practice. If blood culture bottles are used, an additional sample should be sent to the microbiology laboratory for Gram stain and culture of nonbacterial pathogens when indicated.

Nucleic Acid-based Diagnosis and Epidemiology of Infectious Diseases

Even when optimum handling occurs, cultures may fail to yield an organism. Laboratory-developed NAATs targeting pneumococcal genes, such as those that encode pneumolysin and autolysin, in fluid from pediatric cases of pleural infection, have been very useful [].

Original Research ARTICLE

Fluid should be sent for cell count, pH, protein, glucose, lactate dehydrogenase LDH , and cholesterol. These values assist with the determination of a transudative or exudative process and in the subsequent management of the syndrome. Most infections result in an exudate or polymorphonuclear leucocytes PMNs empyema within the pleural cavity.

When tuberculosis or a fungal pathogen is thought to be the likely cause, a pleural biopsy sent for culture and histopathology increases the diagnostic sensitivity. Always notify the laboratory of a suspicion of tuberculosis so that appropriate safety precautions can be employed.

Original Research ARTICLE

It should be stressed that the quality of evidence is low and both markers should be used in conjunction with hematologic and chemical parameters and other diagnostic tests such as NAAT, culture, and histology of a pleural biopsy. Patients with cystic fibrosis CF suffer from chronic lung infections due to disruption of exocrine function that does not allow them to clear microorganisms that enter the distal airways of the lung.


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The spectrum of organisms associated with disease continues to expand and studies of the microbiome demonstrate the complex synergy between easily cultivatable and noncultivatable organisms. Table 23 lists the most frequently isolated pathogens in this patient population. Early in childhood, infections are caused by organisms frequently seen in the non-CF pediatric population such as S. Of these organisms, methicillin-resistant Staphylococcus aureus MRSA has significantly increased in prevalence [].

At some point, later in childhood or adolescence, P. The P.

Pdf Rapid Detection Of Infectious Agents Infectious Agents And Pathogenesis

Nosocomial pathogens such as Stenotrophomonas maltophilia , Achromobacter xylosoxidans , and Achromobacter ruhlandii may be acquired during a hospital or clinic visit. Burkholderia cepacia complex is a very important pathogen in these patients. Burkholderia cenocepacia is highly pathogenic and is responsible for rapid decline and death in a subset of patients who acquire the virulent clones.

Special microbiological techniques are required to recover and differentiate B. Less common gram-negative organisms that appear to be increasing in their frequency of recovery, but whose role in the pathogenesis of CF lung disease is still unclear, include Burkholderia gladioli, Ralstonia spp, Cupriavidus spp, Inquilinus spp, and Pandoraea [, ].

The reader is referred to the Parkins and Floto reference for a discussion of pathogens within the CF microbiota []. The M. There is evidence to suggest that both M. Aspergillus fumigatus is the most common fungus recovered from CF patients, in whom it causes primarily allergic bronchopulmonary disease. Scedosporium apiospermum may cause a similar syndrome. Exophiala dermatitidis has been reported by some centers to cause chronic colonization of the CF airway [].