Evaluation and Diagnosis of HIV-associated Lung Disease

Stephanie Maximous, MD; Laurence Huang, MD; Alison Morris, MD, MS


Semin Respir Crit Care Med. 2016;37(2):199-213. 

In This Article

Approach to Evaluation of the HIV-infected Patient

When a patient first presents with respiratory symptoms, the initial step in evaluation should always be an assessment of the severity of the patient's presenting illness. Crucial vital sign measurements include temperature, heart rate, blood pressure, respiratory rate, and pulse oximetry. As with any patient, the first priority is stabilization and treatment of any immediately life-threatening conditions. Subacute symptoms in a stable patient allow for more deliberate appraisal of the clinical syndrome. The evaluation begins with a history and physical examination with a focus on certain HIV-specific factors such as injection drug use (IDU), use of ART, and history of exposures related to other behavioral or environmental factors that can influence the differential. Based on this information, selection of additional laboratory and radiographic evaluation can be performed. Often, the constellation of signs, symptoms, laboratory abnormalities, and radiographic patterns can suggest a specific diagnosis or limit the differential, but providers must always be aware of atypical presentations of disease that can occur in HIV-infected individuals.

Signs and Symptoms

Patients with HIV frequently present with respiratory symptoms common to many diseases such as cough, shortness of breath, and pleuritic chest pain. Characterizing the time course of the symptoms may suggest certain diagnoses. For example, indolent, progressive dyspnea on exertion, and dry cough for several weeks suggests PCP, whereas productive cough with purulent sputum developing over 3 to 5 days are more suggestive of bacterial pneumonia.[10,11] A chronic cough can also be seen in patients with TB. The World Health Organization devised a strategy calling for evaluation of chronic cough, defined as cough of 2 to 3 weeks duration, in areas of high TB prevalence, with the goal of increasing TB detection and diagnosis.[12] Chronic respiratory symptoms are also seen in noninfectious pulmonary diseases such as COPD, asthma, congestive heart failure, and PH.

Systemic symptoms that accompany pulmonary disease can also aid in diagnosis. Constitutional symptoms including fevers, weight loss, and night sweats are indicative of systemic or disseminated disease. The presence of constitutional symptoms increases suspicion for infections such as TB or fungal disease as well as malignancies. Some pulmonary diagnoses do not present with primary respiratory symptoms. For example, patients with cryptococcosis frequently have no pulmonary complaints even after the infection spreads to the central nervous system (CNS) causing meningoencephalitic symptoms.[13] Other endemic fungal infections such as coccidioidomycosis and blastomycosis can disseminate to the skin and soft tissues, lymph nodes, bone, and CNS, which may be the earliest sites of disease.[14] Histoplasmosis may present as subacute fever and weight loss, but may also manifest as a sepsis syndrome with multiorgan system involvement and include hypotension, pancytopenia, adrenal insufficiency, lymphadenopathy, and hepatosplenomegaly.[15,16] Other diseases such as toxoplasmosis are not typically thought of as causing a pulmonary syndrome; however, pulmonary toxoplasmosis can occur in HIV-infected patients, usually presenting as subacute dyspnea, cough, and fever.[17,18] Cytomegalovirus (CMV) infection more commonly presents with retinitis and colitis in HIV-infected patients than pneumonia.[19] Symptoms of CMV pneumonia consist of cough, dyspnea, and fever over about 2 to 4 weeks.[19]

Malignancies typically present with some extrapulmonary symptoms. In particular, patients with non-Hodgkin lymphoma (NHL) commonly complain of constitutional symptoms including drenching night sweats, fever, and weight loss. For those with KS, some may have concurrent skin lesions typical of KS, but up to a quarter of HIV-infected patients with pulmonary KS do not necessarily have lesions elsewhere.[20] Their respiratory complaints usually include dry cough, dyspnea, and possibly fever, but may also be fulminant. Multicentric Castleman disease is a lymphoproliferative disorder associated with lymphadenopathy, fever, hepatosplenomegaly, and a variety of other constitutional symptoms such as night sweats, weight loss, and fatigue.[21,22] Also related to several viruses including KS-associated herpesvirus, herpesvirus 8 (HHV-8), and Epstein-Barr virus (EBV) is primary effusion lymphoma (PEL), whose presentation is characterized by the serosal surfaces affected and commonly presents with symptoms of dyspnea associated with pleural effusions.[23,24]

Systemic symptoms in the setting of recent ART initiation suggest a diagnosis of immune reconstitution inflammatory syndrome (IRIS). IRIS is related to the degree of immunosuppression and is seen most commonly in HIV-infected individuals with a CD4 cell count below 50 cells/μL.[25,26] It may have a variety of presentations depending on underlying illnesses that become more pronounced with resurgence of the host immune system. Thus, one would expect TB-associated IRIS to present with new or worsening fever, lymphadenopathy, cough, and dyspnea—similar to TB in general, but perhaps more severe.[25,27] At times, CNS manifestations may also be present in TB or Cryptococcus and frequently lead to morbidity or even death. IRIS can also be seen in the setting of HIV-associated malignancies such as KS.

Historical Assessment

A thorough history is of utmost importance in the evaluation process. Many social and demographic risk factors play a significant role in building a differential diagnosis. Areas of residence and recent travel may suggest exposure to endemic fungal or parasitic infections. Incarceration status may predispose to TB, and IDU may point to endocarditis with septic emboli or talcosis. Tobacco smoking increases the frequency of bacterial pneumonia, COPD, and malignancy, as it does in the HIV-uninfected population. MSM have been found to have an increased risk of KS.

Physical Examination

Beyond evaluating the symptoms and obtaining a complete history, objective findings on physical exam may further clarify the potential diagnoses. Examination of the respiratory system with particular attention to oxygen saturation may reveal particularly helpful characteristics. For example, pulse oximetry may be normal at rest, but oxygen saturation decreases substantially with exertion in cases of PCP or other diseases that cause impaired diffusion such as pulmonary arterial hypertension (PAH) or interstitial lung disease (ILD). Localized rales, rhonchi, or egophony would suggest a focal process such as a lobar bacterial pneumonia or localized malignancy, while diffuse findings may be more consistent with a diffuse process such as PCP, viral pneumonia, or even ILD. Obstructive lung disease is often associated with diminished breath sounds and limited air movement, expiratory wheezing, and a prolonged expiratory phase. CMV pneumonia may demonstrate faint crackles or a completely unremarkable lung exam. Diminished breath sounds and dullness to percussion are consistent with the presence of pleural effusions, common in many diseases including bacterial pneumonia and malignancies. Pulmonary TB in HIV-infected patients frequently presents as a focal consolidation occasionally accompanied by pleural effusions. Lung sounds in PCP may range from entirely normal to diffuse rales.[28]

Extrapulmonary examination findings may also lead to diagnosis of the pulmonary disease. For example, extrapulmonary manifestations of TB are common in HIV-infected patients and may prompt more thorough evaluation of the respiratory system.[29,30] Beyond the respiratory system, exam findings consistent with heart failure including pleural effusions, lower extremity edema, jugular venous distension, and ascites should raise concern for HIV-associated cardiomyopathy and PAH or prompt evaluation for TB pericarditis. Focal neurologic signs or altered mental status should trigger evaluation for OIs such as cryptococcal meningitis, toxoplasmosis, TB meningitis, and primary CNS lymphoma. Diffuse lymphadenopathy may point to disseminated TB or fungal infection or raise concern for malignancy. Visual changes are concerning for CMV retinitis, fungal endophthalmitis, or TB uveitis in addition to primary CNS disorders. Characteristic skin lesions that may suggest specific diagnoses include the umbilicated papules of Molluscum contagiosum or Cryptococcus, and the friable violaceous nodules of KS.[31] A careful exam with attention to subtle findings may allow for estimating the patient's immune status and CD4 cell count and can identify alternate sites for diagnostic studies, such as lymph node biopsy or sampling of fluid collections. The examination can also lead to specific diagnostic testing such as imaging of the CNS or point toward a particular pulmonary or systemic diagnosis.[32]

CD4 Cell Count

In addition to the past medical and social histories, the underlying immune status of the patient provides a valuable aid to constructing a differential diagnosis. The respiratory system is a site of significant immune modulation and is also highly subject to the underlying immune status of the host. For these reasons, certain pulmonary illnesses associated with HIV should be suspected or discounted based on the patient's CD4 cell count, which is a reliable surrogate marker of risk for pulmonary infections most commonly encountered in HIV. Furthermore, the clinical manifestations of certain diseases may be significantly impacted by the degree of host immunosuppression.[33] For example, reactivation TB commonly manifests as a cavitary parenchymal lung disease, but in patients with CD4 cell counts less than 200 cells/μL, the host may not be able to mount a robust enough immune response to cause the caseating necrosis that leads to cavitation.[34]

A clear inverse relationship exists between CD4 cell count and the occurrence of pulmonary complications, particularly for OIs or AIDS-associated malignancies. If available, the CD4 cell count and viral load prior to the acute illness are useful data points to stratify risk for specific OIs (Table 2).[35] If a prior CD4 cell count is not available, a current cell count may be useful, but it is important to realize that the lymphocyte count often falls in the setting of acute illness.

HIV-infected individuals with higher CD4 cell counts remain at risk for certain pulmonary complications. Sinusitis, bronchitis, influenza, bacterial pneumonia, and TB can occur at any CD4 cell count, but are seen with greater frequency at lower CD4 cell counts.[35] Noninfectious pulmonary diseases such as COPD and asthma are a more likely cause of chronic respiratory symptoms in individuals with normal CD4 cell counts, although they may be seen at low CD4 cell counts as well. Of note, lower CD4 cell counts are associated with more severe airflow obstruction, with evidence pointing to PCP colonization as a contributing factor.[36] Furthermore, nadir CD4 cell count less than 200 cells/μL has been shown to be independently associated with radiographic emphysema.[37] Several studies have also demonstrated increased risk of lung cancer in patients with lower CD4 cell counts.[38]

At a CD4 cell count below 200 cells/μL, OIs increase in frequency and should lead the differential diagnosis in patients presenting with signs and symptoms of respiratory infection. PCP is a common cause of pulmonary disease in this CD4 stratum, with the risk increasing as CD4 cell count falls.[39] Fungal infections are rare above a CD4 cell count of 200 cells/μL.[40] Other infections associated with CD4 cell counts less than 200 include disseminated mycobacterial diseases and toxoplasmosis.[5] When the CD4 cell count falls below 100 cells/μL, toxoplasmosis and pulmonary KS become more common. With profound immunosuppression (<50 cells/μL), infections such as Aspergillosis, CMV, and disseminated endemic fungal infections may be seen.

Adherence to prescribed prophylaxis and ART can raise or lower suspicion for specific OIs. Prior infections may recur if not adequately treated, if prophylaxis was not appropriately taken or administered, or may reactivate if the immune system is sufficiently suppressed. Of note, trimethoprim-sulfamethoxazole (TMP-SMX) is extremely efficacious as prophylaxis against PCP;[41] however, alternative drug regimens such as dapsone, atovaquone, and aerosolized pentamidine are less reliable and patients on these agents may have a higher risk of PCP in the correct clinical setting. Macrolides such as azithromycin and clarithromycin are indicated as prophylaxis for Mycobacterium avium complex (MAC) when the CD4 cell count drops below 50 cells/μL.[42] There is some evidence that bacterial pneumonia frequency may be decreased in patients who are already prescribed macrolide prophylaxis for MAC or TMP-SMX for PCP and Toxoplasma gondii, although resistant organisms may also emerge as a result.[43,44,45,46,47]

Laboratory Data

Basic laboratory assays may reflect the patient's underlying immune status or may be suggestive of certain acute syndromes. The complete blood count may display neutropenia, anemia, or thrombocytopenia. Pancytopenia may be caused by bone marrow suppression due to disseminated fungal, viral, or mycobacterial infections, or simply due to the degree of immunosuppression from HIV itself. A transaminitis may also point toward infiltrative or disseminated infections. Arterial blood gas analysis is useful for determining level of care, as severely hypoxemic patients should be hospitalized and may require admission to the intensive care unit. Additionally, to help limit the chance of respiratory failure and death, adjunctive corticosteroids are indicated in patients with PCP and a PaO2 ≤70 mm Hg or an alveolar-arterial oxygen gradient (A-a gradient) ≥35 mm Hg on room air.[48]

Certain laboratory values beyond the routine complete blood counts and chemistries can aid in workup for particular diseases if suspected. Serum lactate dehydrogenase (LDH) has been used as a simple serum test to aid in the diagnostic algorithm when PCP is suspected, but prior to confirmed identification of the organism.[49] However, LDH is a nonspecific marker and can be elevated in patients with other infections such as TB and bacterial pneumonia, as well as in malignancies. A study of 84 patients with HIV and otherwise undifferentiated pulmonary disease showed that the mean LDH level in those who were eventually diagnosed with PCP was significantly higher than those with other respiratory diagnoses, although there was overlap in the LDH elevation between those with PCP and those with malignancies. Normal LDH values were atypical in patients who were diagnosed with PCP.[49] By contrast, a later study demonstrated that the LDH was elevated in all the patients diagnosed with PCP, but the mean values were nearly identical in patients with PCP and disseminated TB and still significantly increased in patients with bacterial pneumonia and pulmonary TB, confirming the high sensitivity, but low specificity of LDH for PCP.[50] LDH levels correlate with prognosis and can also be used to follow response to therapy, with levels declining while on adequate treatment.[49]

Newer diagnostic tests may be useful for suspected invasive fungal pulmonary infection. The serum 1,3-β-D-glucan (BDG) assay may provide helpful supplementary data. BDG is a component of the cell wall of most fungi and the cyst wall of Pneumocystis. The sensitivity has been shown to be greater than 90% for PCP.[51,52] When comparing patients with PCP to those without, the specificity ranged from 65 to 86%, although specificity is determined in part due to the cutoff value used.[51,52] As a diagnostic aid for invasive fungal infections other than PCP, the sensitivity and specificity are slightly lower than that for PCP.[53] For example, in a meta-analysis evaluating the use of BDG for aid in diagnosis of invasive fungal infections other than PCP, the pooled sensitivity was 77% and specificity was 85%.[54] The main weakness of this test is that it cannot distinguish between PCP and other underlying fungal infections that are also common among HIV-infected patients such as candidiasis, histoplasmosis, and cryptococcosis. Its greatest utility then may be in suspected cases of PCP where both induced sputum and bronchoscopy are unavailable, although if other fungal infections remain on the differential, further diagnostic testing will be necessary. Galactomannan antigen, a cell wall component of Aspergillus, has been used as an adjunct in the diagnosis of invasive aspergillosis.[55] Unlike LDH and BDG, galactomannan is highly specific for Aspergillus. Its sensitivity limits its utility in ruling out Aspergillus. The sensitivity was as low as 71% in one meta-analysis, although HIV-infected patients were not the focus of these evaluations.[56]

Physiologic Testing

Pulmonary function tests (PFTs) can be useful in the diagnosis of certain types of HIV-associated lung diseases. Specifically, COPD is diagnosed using spirometry. Impairment in diffusion capacity of carbon monoxide (DLco) is also very commonly seen in HIV-infected individuals, and is often related to underlying emphysema; full PFTs may also therefore be useful.[57–59] For other illnesses that significantly impair gas exchange such as PAH as well as different types of ILD, DLco is also commonly impaired. Abnormality of DLco in PCP is also noted, potentially in the absence of any radiographic findings, although DLco is rarely tested in the acute setting.[60,61] For many chronic diseases, PFTs are helpful for monitoring progression of disease and response to therapy, as they provide generally objective quantitative measures of lung function and physiology.


Radiographic imaging is useful for characterizing many acute and chronic pulmonary diseases. A chest radiograph should be obtained in almost all HIV-infected individuals with respiratory complaints. Chest CT scan is also frequently needed to obtain a more detailed evaluation. Many diseases have typical radiographic appearances that can help narrow the differential (Table 3).[62] Nodules may indicate infection, particularly mycobacterial or bacterial pneumonia, or malignancy such as lymphoma. This finding usually prompts further diagnostic workup that may include biopsy.[63,64] Pleural fluid collections may also be identified and thus pursued for further diagnostic evaluation. CT scan is usually required for evaluation of lymphadenopathy, which may also be suggestive of particular diseases such as mycobacterial infection, bacterial pneumonia, and lymphoma.[65] HIV-infected patients without pulmonary symptoms who present with abnormal chest imaging have a high incidence of infectious disorders such as tuberculous or nontuberculous mycobacteria, and thus should still undergo a thorough diagnostic workup.[66]

Bacterial pneumonia most commonly presents as a lobar or multifocal airspace infiltrate(s) (Fig. 1).[67] Pleural effusions are commonly seen. In general, the presentation of bacterial pneumonia in an HIV-infected individual is similar to that in HIV-uninfected patients. Cavitation may occur, particularly in cases of Staphylococcus aureus, Rhodococcus equi, or Nocardia asteroides, but the presence of cavitation on chest imaging should also raise the suspicion of TB.[68] Similarly, nodular disease can be seen, but may also be indicative of fungal disease.

Figure 1.

Chest radiograph demonstrating left upper lobe dense consolidation in a patient with HIV and bacterial pneumonia. (Courtesy of Laurence Huang, MD. Used with permission.)

In PCP, the chest radiograph characteristically reveals bilateral, reticular, ground glass infiltrates (Fig. 2). The infiltrates are typically perihilar and spread peripherally with progression of disease. Location of the infiltrates may be atypical, particularly in patients who have received aerosolized pentamidine who are more likely to present with upper lobe disease. Pneumatoceles and pneumothoraces are classic findings and their presence should increase the suspicion for PCP (Fig. 3). The radiograph may also be completely normal or display nodular densities, cystic lesions, or lobar consolidations.[69,70] In the case of a normal chest radiograph, high-resolution CT scan can be helpful. The presence of ground glass opacities (Fig. 4) is suggestive of PCP, although not specific, and additional workup should be pursued. If there are no ground glass opacities on chest CT, PCP is essentially ruled out.[61] Pleural effusions and lymphadenopathy are uncommon and should raise the possibility of an alternative or concomitant diagnosis.

Figure 2.

Chest radiograph of a newly diagnosed HIV-infected patient with CD4 cell count less than 200 cells/μL with bilateral interstitial infiltrates related to Pneumocystis jirovecii pneumonia. Microscopy of the bronchoalveolar lavage revealed typical Pneumocystis cystic and trophic forms. (Courtesy of Meghan Fitzpatrick, MD. Used with permission.)

Figure 3.

Chest computed tomography of a patient presenting with dyspnea for 6 to 8 weeks and 2 weeks of cough, demonstrating pneumatoceles and diffuse infiltrates. Direct fluorescent antibody testing was positive for Pneumocystis pneumonia on the induced sputum. (Courtesy of Matthew Gingo, MD. Used with permission.)

Figure 4.

Chest computed tomography scan of a patient presenting with dyspnea for several weeks demonstrating diffuse ground glass infiltrates. The patient progressed to respiratory failure requiring mechanical ventilation and developed spontaneous pneumothoraces. Serum lactate dehydrogenase and 1,3-β-D-glucan were markedly elevated and bronchoalveolar lavage demonstrated cystic and trophic forms of Pneumocystis jirovecii. He was newly diagnosed with HIV, with a CD4 cell count of 11 cells/μL. (Courtesy of Stephanie Maximous, MD. Used with permission.)

Pulmonary TB in HIV-infected patients has varied radiographic findings based on the CD4 cell count. With CD4 cell counts >500 cells/μL, the pattern is usually more consistent with reactivation TB, with classic upper lobe cavitation (Fig. 5). With lower CD4 cell counts, the infiltrates may be in the middle or lower lung zones without cavitation due to the inability of the host to mount an immune response to manifest as cavitation (Fig. 6).[71] Lymphadenopathy and pleural effusions are also common with low CD4 cell counts. Even patients with normal chest radiographs can have sputum samples that are smear positive for acid-fast bacilli (AFB). It is thus crucial to maintain a high level of suspicion for TB in patients with the constellation of clinical features and exposure risk, in spite of less characteristic imaging, particularly if the CD4 cell count is low.[31,33]

Figure 5.

Chest radiograph showing right upper lobe consolidation with cavitation (noted by arrow) in a patient with HIV infection and CD4 cell count greater than 200 cells/μL. Acid-fast staining of the sputum was positive and cultures grew Mycobacterium tuberculosis. (Courtesy of Laurence Huang, MD. Used with permission.)

Figure 6.

Chest radiograph showing right lower lobe consolidation in a patient with HIV infection and CD4 cell count less than 200 cells/μL. Acid-fast staining of the sputum was negative but cultures grew rifampin-resistant Mycobacterium tuberculosis. It is important to consider tuberculosis as a possibility in the diagnostic process in profoundly immunosuppressed patients with this pattern on imaging. (Courtesy of Laurence Huang, MD. Used with permission.)

Like PCP, CMV pneumonia imaging is variable and may display findings ranging from interstitial or ground glass infiltrates to alveolar opacities and nodular infiltrates. In contrast, pleural effusions may distinguish PCP from CMV as they are rare in PCP, but occur with some frequency in CMV.[72] It is also difficult to distinguish viral pneumonias from other infectious etiologies, which may display similar radiographic findings.[73]

While pulmonary KS is typically diagnosed via bronchoscopy (visualization of the characteristic lesions in the tracheobronchial tree), chest radiograph may reveal central middle and lower lung infiltrates and nodules, as well as peribronchial cuffing, thickened interlobular septa, and pleural effusions (Fig. 7).[74] NHL presents primarily with nodules or masses, and commonly with lymphadenopathy on chest imaging.[75]

Figure 7.

Chest radiograph reveals bilateral central middle and lower lung infiltrates in a patient with HIV infection and CD4 cell count less than 100 cells/μL. Bronchoscopy ultimately revealed characteristic Kaposi sarcoma lesions, although there were no concomitant mucocutaneous lesions elsewhere. (Courtesy of Laurence Huang, MD. Used with permission.)

Culture and Other Diagnostic Studies

Obtaining culture data is a mainstay of diagnostics in immunocompromised patients. Even if suspicion is highest for noninfectious etiologies, concurrent infections must always be ruled out. All involved fluids and tissues should be sent for culture. Routine cultures should always be performed on sputum or bronchoalveolar lavage (BAL) samples, but other useful sources for culture include blood, pleural fluid, cerebrospinal fluid, bone marrow, and biopsied tissue of affected organ systems. Blood cultures in particular may be highly valuable in the diagnostic workup of bacterial pneumonia, as the yield is high in HIV-infected patients, especially in the setting of low CD4 cell counts.[76] Blood cultures may also be positive in mycobacterial infection or in fungal infections such as Histoplasma capsulatum.[15,77] Fungal isolator blood cultures should be evaluated in cases where disseminated fungal infections are suspected.[78] Viral pneumonias may be rapidly evaluated by polymerase chain reaction (PCR) of nasopharyngeal swabs, which are more sensitive than throat swabs, but less than nasopharyngeal washes.[79]

Given the increased severity of bacterial pneumonia in HIV-infected patients particularly those not already on ART, a rapid test such as the pneumococcal urine antigen enzyme-linked immunosorbent assay is a highly valuable diagnostic and prognostic tool.[80] The Histoplasma polysaccharide antigen can also be of great utility, as it can be detected in the urine in 75% of patients with early acute pulmonary histoplasmosis and in 95% of patients with disseminated disease, although it is much less sensitive in isolated pulmonary disease.[81] Similarly, the cryptococcal antigen (CrAg) via latex agglutination and enzyme immunoassay has the highest likelihood of positivity in disseminated cryptococcosis and is very specific. Of note, a more recent lateral flow immunochromatographic assay for the detection of CrAg has also been shown to be highly sensitive and accurate and is available as a rapid point-of-care diagnostic test that provides results in less than 10 minutes and at low cost.[82]

Sputum Analysis

Sputum sampling remains a cornerstone of the diagnostic investigation. A simple expectorated sample is inexpensive and readily available to obtain and process in most settings. The yield of spontaneously expectorated sputum is remarkably high in HIV-infected patients with pulmonary infiltrates, cited up to 50% in one study.[1] Furthermore, obtaining an expectorated sputum is relatively simple and efficient from a resource standpoint, and negative results correlate with sterile bronchoscopically obtained samples over 96% of the time.[83]

The techniques for obtaining sputum samples vary depending on the potential diseases being considered. For bacterial pneumonia, sputum can be used to identify the most common pathogens including Streptococcus pneumonia, Haemophilus influenza, and Pseudomonas aeroginosa.[84] Patients suspected of having TB are placed in negative pressure respiratory isolation while performing the diagnostic workup, which typically includes two to three sputum specimens for AFB smears and later, culture.[85,86] The first morning expectorated sputum specimens are noted to have the highest yield of organisms.[87] Basic Ziehl-Neelsen staining for smear microscopy sensitivity ranges widely, from 20 to 80% depending in part on the quality of the specimens and laboratory-processing techniques.[88] Although the culture is comparatively slow and may take up to 6 to 8 weeks to finalize, it is highly sensitive, cited at approximately 80 to 85%.[89–91] Expectorated sputum cannot be used to diagnose PCP, which requires an induced sputum sample.

PCR-based testing for sputum is becoming increasingly more common and has high specificity for diagnosis of TB particularly, although sensitivity is variable. The Xpert MTB/Rif test is a cartridge-based automated nucleic acid amplification test for TB detection and rifampin resistance testing that is in use in disease-endemic countries. It was developed to overcome the burden of the slow and less sensitive technique of smear microscopy and culture and to evaluate for resistance. An initial study demonstrated that among culture-positive patients, a single MTB/Rif test had a sensitivity of 98.2% in smear-positive TB and 72.5% in smear-negative TB, and also had a very high negative predictive value.[92] A Cochrane review of 27 studies found an even higher sensitivity of 89% and specificity of 99% for TB detection and that the assay had similar performance in HIV-infected and -uninfected patients.[93] This test is exceptionally suited for use in limited resource settings with endemic TB because it provides rapid and sensitive diagnosis which facilitates better access to therapy, thus lowering the morbidity associated with delays in diagnosis and further transmission of the disease.[94]

If the patient is unable to produce an adequate sample or if PCP is suspected, it is necessary to perform sputum induction using nebulized hypertonic saline. Compared with a BAL specimen, induced sputum also has high diagnostic yield and upward of 90% correspondence to BAL smear and cultures for TB.[95,96] Induced sputum for the diagnosis of PCP is useful, with reported sensitivity ranging from 55 to 95%, although sensitivity can vary with the experience of the laboratory and technique used.[97,98]

P. jirovecii diagnosis cannot be made by culture; thus, the diagnosis with induced sputum (as well as with BAL, discussed later) must be made via direct staining and microscopy of the cysts and/or trophic forms of the organism.[99,100] The sensitivity of staining and microscopy of induced sputum, however, is highly variable, ranging between 55 and 92%. Other methods of diagnosing PCP include cytology with immunofluorescent and histochemical staining, and PCR of respiratory specimens.[101,102] Improved sample preparation via centrifugation and fluorescent antibody staining increases the sensitivity of induced sputum.[98] Further, BAL sample evaluation is so sensitive that bronchoscopy should always be pursued for definitive diagnosis of PCP if adequate induced sputum cannot be obtained.[99]

PCR may also be used to diagnose PCP. The sensitivity of PCR as compared with direct fluorescent antibody (DFA) testing for BAL has been noted to be 100% and the specificity 98%, whereas the sensitivity of PCR for induced sputum was 95% compared with 82% for DFA and specificity of PCR for induced sputum was 94%.[102] High sensitivity of PCR in induced sputum specimens suggests this may be a useful and superior test to DFA and may obviate the need for bronchoscopy in some patients; however, because colonization with Pneumocystis occurs, detection of Pneumocystis DNA is not always a clinical pneumonia.


At times, despite thorough evaluation of laboratory data and imaging, the diagnosis remains elusive or unconfirmed; therefore, more invasive testing that permits pathological diagnosis is required. For pulmonary diseases, diagnostic bronchoscopy for BAL with or without transbronchial or endobronchial biopsies is typically the next step to pursue.[103] Visual inspection during bronchoscopy can identify endobronchial lesions concerning for malignancy. For example, pulmonary KS is classically diagnosed by direct visualization of typical lesions (Fig. 8).[100] BAL is particularly helpful for diagnosis of infection. Bronchoscopy is highly successful in providing diagnosis for TB and PCP if sputum is not conclusive.[99] If performing bronchoscopy, there may be some additional yield from transbronchial biopsy for the diagnosis of TB or fungal disease.[104–107] CMV may be isolated in the BAL from severely immunocompromised patients; however, the presence of CMV does not necessarily indicate infection and may only represent viral shedding.[108] Patients suspected of having CMV pneumonitis should undergo transbronchial biopsies for definitive diagnosis. The lung parenchymal specimens must be examined for the characteristic viral inclusions and cytopathic changes.[108,109]

Figure 8.

Bronchoscopy demonstrating the characteristic erythematous-violaceous lesion of Kaposi sarcoma in the trachea of an HIV-infected patient with CD4 cell count less than 100 cells/μL. (Courtesy of Laurence Huang, MD. Used with permission.)

Other Procedures

If larger sections of tissue are necessary, video-assisted thorascopic surgery or open lung biopsy should be sought out in collaboration with thoracic surgeons. When bronchoscopy is nondiagnostic, surgical lung biopsy may ultimately yield a diagnosis of parenchymal lung disease.[110,111] Other diagnostic procedures that may be required for tissue-based diagnosis include thoracentesis for pleural fluid, pleural biopsy, mediastinoscopy, CT-guided needle biopsy, or endobronchial ultrasound. CT-guided transthoracic needle biopsy is particularly useful for diagnosing peripheral nodules and localized infiltrates, with good diagnostic yield in the setting of infection and lung cancer.[112]