Molecular and Culture-Based Bronchoalveolar Lavage Fluid Testing for the Diagnosis of Cytomegalovirus Pneumonitis

Enhancing Influenza Detection through Integrative Machine Learning and Nasopharyngeal Metabolomic Profiling: A Comprehensive Study

Background/Objectives: Nasal and nasopharyngeal swabs are commonly used for detecting respiratory viruses, including influenza, which significantly alters host cell metabolites. This study aimed to develop a machine learning model to identify biomarkers that differentiate between influenza-positive and -negative cases using clinical metabolomics data. Method: A publicly available dataset of 236 nasopharyngeal samples screened via liquid chromatography-quadrupole time-of-flight (LC/Q-TOF) mass spectrometry was used. Among these, 118 samples tested positive for influenza (40 A H1N1, 39 A H3N2, 39 Influenza B), while 118 were negative controls. A stacking-based model was proposed using the top 20 selected features. Thirteen machine learning models were initially trained, and the top three were combined using predicted probabilities to form a stacking classifier. Results: The ExtraTrees stacking model outperformed other models, achieving 97.08% accuracy. External validation on a prospective cohort of 96 symptomatic individuals (48 positive and 48 negatives for influenza) showed 100% accuracy. SHAP values were used to enhance model explainability. Metabolites such as Pyroglutamic Acid (retention time: 0.81 min, m/z: 84.0447) and its in-source fragment ion (retention time: 0.81 min, m/z: 130.0507) showed minimal impact on influenza-positive cases. On the other hand, metabolites with a retention time of 10.34 min and m/z 106.0865, and a retention time of 8.65 min and m/z 211.1376, demonstrated significant positive contributions. Conclusions: This study highlights the effectiveness of integrating metabolomics data with machine learning for accurate influenza diagnosis. The stacking-based model, combined with SHAP analysis, provided robust performance and insights into key metabolites influencing predictions.

Progressive Lung Consolidation in HIV Amidst the COVID-19 Pandemic: Evaluating Probable Cytomegalovirus Pneumonia and the Importance of Early Empirical Treatment

We present the case of a young male who was diagnosed with HIV in 2012. However, his initiation of antiretroviral therapy (ART) was delayed until 2018 due to issues related to his acceptance and acknowledgment of the disease. In April 2021, the patient presented with hemoptysis, shortness of breath, and constitutional symptoms. Initial extensive workup for tuberculosis (TB) and other respiratory pathogens returned negative. Despite this, he was treated for smear-negative pulmonary TB and pneumocystis pneumonia (PCP) and was subsequently discharged. He then had recurrent hospital admissions due to worsening respiratory symptoms, with short intervals between recovery and recurrence. Each admission saw an increase in his oxygen requirements. Throughout these hospitalizations, tests for coronavirus disease 2019 (COVID-19) were consistently negative. TB and PCP treatment continued throughout his admissions. Despite various treatments, his condition continued to deteriorate. A DNA polymerase chain reaction (DNA PCR) test for cytomegalovirus (CMV) was eventually conducted. Unfortunately, the patient succumbed to progressive respiratory failure, and the CMV DNA PCR returned positive a week after his death. In the era of COVID-19, this case underscores the importance of early diagnosis and timely antiviral treatment.

Cytomegalovirus Pneumonia in a Patient with Down Syndrome

Down syndrome (DS) is a chromosomal disorder due to the presence of an additional chromosome 21 that causes intellectual deficit and physical anomalies and predisposes patients to develop infections throughout their lives. Pneumonias are more serious in patients with DS, requiring hospitalization, and they represent an important cause of mortality in this population. Cytomegalovirus (CMV) causes widespread and serious infections in immunocompromised individuals, affecting the respiratory tract and, when causing interstitial pneumonia, associated with a high mortality rate. However, CMV-induced pneumonia is not reported in DS patients. The prevalence and severity of CMV respiratory infections in subjects with DS is unknown. This case describes a 50-year-old female patient with DS who developed extensive bilateral pneumonia with severe respiratory failure which required hospitalization in intensive care, intubation, and mechanical ventilation after approximately 10 days of empiric antibiotic and anitimycotic therapy for fever, cough, and dyspnea. The patient was diagnosed with CMV pneumonia and recovered after treatment with ganciclovir. To the best of our knowledge, this is the first reported case of CMV pneumonia in a patient with DS. This case aims to highlight that CMV pneumonia in individuals with DS can be a life-threatening condition. It also clarifies the importance of early diagnosis of infections from opportunistic pathogens such as CMV to ensure timely and efficient treatment.

Assessment of an automated Cytomegalovirus nucleic acid amplification test using clinical plasma, bronchoalveolar lavage, and tissue specimens

BACKGROUND

Cytomegalovirus (CMV) causes significant morbidity and mortality in immunocompromised patients, particularly transplant recipients. Quantitation of CMV DNA in peripheral blood is used to monitor prophylactic and pre-emptive approaches to prevent CMV disease, whereas CMV DNA testing of non-plasma specimens may aid in the diagnosis of end-organ disease.

METHODS

The analytical performance of the FDA-approved Aptima CMV Quant Assay was evaluated using reference CMV (SeraCare) diluted in defibrinated human plasma, as well as negative bronchoalveolar lavage fluid and tissue. Agreement was determined using 100 clinical acid-citrate-dextrose (ACD) plasma specimens, 77 bronchoalveolar lavage (BAL) fluids, and 101 tissues previously tested using artus CMV qPCR.

RESULTS

Aptima CMV lower limit of detection (LLOD) was 169 IU/mL for ACD plasma, 100 IU/mL for BAL, and 50 IU/mL for tissue. Positive percent agreement (PPA) was 100.0% (50/50; 95% CI: 92.9% - 100.0%) and negative percent agreement (NPA) was 94.0% (47/50; 95% CI: 83.5% - 98.8%) for ACD plasma. Bland-Altman analysis revealed a bias of 0.20 log10 IU/mL (Aptima - artus) with 95% limits of agreement of -0.53 to 0.93. For BAL fluids, PPA was 70.0% (14/20; 95% CI: 45.7% - 88.1%) and NPA was 82.4% (43/51; 95% CI: 69.1% - 91.6%). For tissues, PPA was 90.0% (45/50; 95% CI: 78.2% - 96.7%) and NPA was 94.0% (47/50; 95% CI: 83.5% - 98.8%).

CONCLUSIONS

The Aptima CMV Quant Assay demonstrates high analytical sensitivity and good overall agreement using clinical plasma and tissue specimens.

Detection of cytomegalovirus in bronchoalveolar lavage fluid from immunocompromised patients with pneumonitis by viral culture and DNA quantification

PURPOSE

To compare the detection of human cytomegalovirus (HCMV) in bronchoalveolar lavage (BAL) fluid by viral culture and quantitative polymerase chain reaction (qPCR), and to establish a viral load threshold that can identify cases of HCMV replication indicative of pneumonitis. There is currently no universal viral load cut-off to differentiate between patients with and without pneumonitis, and the interpretation of qPCR results is challenging.

METHODS

176 consecutive BAL samples from immunosuppressed hosts with signs and/or symptoms of respiratory infection were prospectively studied by viral culture and qPCR.

RESULTS

Concordant results were obtained in 81.25% of the BAL samples. The rest were discordant, as only 34% of the qPCR-positive BAL samples were positive by culture. The median HCMV load was significantly higher in culture-positive than in culture-negative BAL samples (5,038 vs 178 IU/mL). Using a cut-off value of 1,258 IU/mL of HCMV in BAL, pneumonia was diagnosed with a sensitivity of 76%, a specificity of 100%, a VPP of 100% and VPN of 98%, and HCMV was isolated in 100% of the BAL cultures.

CONCLUSION

We found that a qPCR-negative was a quick and reliable way of ruling out HCMV pneumonitis, but a positive result did not always indicate clinically significant replication in the lung. However, an HCMV load in BAL fluid of ≥1,258 IU/mL was always associated with disease, whereas <200 IU/mL rarely so.

Quantitative PCR for the Diagnosis of HCMV Pneumonia in HSCT Recipients and Other Immunocompromised Hosts

Pneumonia is among the most serious manifestations of HCMV infection, with high morbidity and mortality. Probable pneumonia is defined as the detection of HCMV in bronchoalveolar lavage (BAL) by viral isolation or DNA quantification (qPCR) combined with symptoms and/or signs of respiratory infection. However, currently, there is no reproducible and well-defined viral load (VL) from BAL that can reliably differentiate patients with pneumonia from the much more common detection of viral DNA in seropositive patients without true HCMV pneumonia. Several studies have been published with the aim of establishing an optimal VL for differentiating pneumonia from viral lung shedding. The aim of this review is to collect and analyze the methodology and the conclusions obtained in studies whose objectives included the correlation between HCMV VL in BAL and/or the plasma and the occurrence of HCMV pneumonia. For this purpose, a total of 14 articles have been included. There are some conclusions on which they all agree. PCR techniques were more sensitive and had a higher NPV than culture techniques but were less specific and had a low PPV. The mean HCMV loads in both BAL and the plasma were significantly higher in patients with pneumonitis than in those without. The HCMV load in patients with pneumonitis was higher in BAL than in the plasma, making qPCR in BAL a better predictor of HCMV pneumonitis than in the plasma. Nevertheless, this review highlights the difficulty of establishing a universal VL value, both in BAL and in the blood, to differentiate patients with HCMV pneumonia from those without. To complete the information available in these studies, prospective multicentre studies would be required. Methodologically, a large number of patients with HCMV pneumonitis would have to be included, and a subclassification of the type of immunosuppression of each patient should be made in order to obtain an optimal VL threshold in different host groups.

Delayed Onset of COVID-19 in an Immunosuppressed Patient

We report on a case of delayed presentation of COVID-19 in a postpartum immunosuppressed patient with the confounding variable of cytomegalovirus viremia. This case highlights the importance of maintaining high suspicion for COVID-19 disease even with delayed onset of symptoms, as this diagnosis as important treatment and public health implications.

A rare case of cytomegalovirus causing respiratory failure and a large pericardial effusion

Cytomegalovirus (CMV) infection is asymptomatic in the majority of immunocompetent patients. However, it can cause severe presentations, particularly in patients who are immunocompromised. We are reporting a rare association between respiratory failure secondary to cavitary pneumonia and a large pericardial effusion due to CMV infection in a patient with human immunodeficiency virus. The patient presented with hypoxic respiratory failure and a large pericardial effusion at risk of tamponade. After extensive investigation, the sole pathogen identified in the patient’s bronchoalveolar lavage and pericardial fluid was CMV.

Nasopharyngeal metabolomics and machine learning approach for the diagnosis of influenza

Background

Respiratory virus infections are significant causes of morbidity and mortality, and may induce host metabolite alterations by infecting respiratory epithelial cells. We investigated the use of liquid chromatography quadrupole time-of-flight mass spectrometry (LC/Q-TOF) combined with machine learning for the diagnosis of influenza infection.

Methods

We analyzed nasopharyngeal swab samples by LC/Q-TOF to identify distinct metabolic signatures for diagnosis of acute illness. Machine learning models were performed for classification, followed by Shapley additive explanation (SHAP) analysis to analyze feature importance and for biomarker discovery.

Findings

A total of 236 samples were tested in the discovery phase by LC/Q-TOF, including 118 positive samples (40 influenza A 2009 H1N1, 39 influenza H3 and 39 influenza B) as well as 118 age and sex-matched negative controls with acute respiratory illness. Analysis showed an area under the receiver operating characteristic curve (AUC) of 1.00 (95% confidence interval [95% CI] 0.99, 1.00), sensitivity of 1.00 (95% CI 0.86, 1.00) and specificity of 0.96 (95% CI 0.81, 0.99). The metabolite most strongly associated with differential classification was pyroglutamic acid. Independent validation of a biomarker signature based on the top 20 differentiating ion features was performed in a prospective cohort of 96 symptomatic individuals including 48 positive samples (24 influenza A 2009 H1N1, 5 influenza H3 and 19 influenza B) and 48 negative samples. Testing performed using a clinically-applicable targeted approach, liquid chromatography triple quadrupole mass spectrometry, showed an AUC of 1.00 (95% CI 0.998, 1.00), sensitivity of 0.94 (95% CI 0.83, 0.98), and specificity of 1.00 (95% CI 0.93, 1.00). Limitations include lack of sample suitability assessment, and need to validate these findings in additional patient populations.

Interpretation

This metabolomic approach has potential for diagnostic applications in infectious diseases testing, including other respiratory viruses, and may eventually be adapted for point-of-care testing.

CMV Infection in Hematopoietic Stem Cell Transplantation: Prevention and Treatment Strategies

Purpose of Review

Cytomegalovirus (CMV) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (Allo-HSCT). New strategies and methods for prevention and management of CMV infection are urgently needed. We aim to review the new developments in diagnostics, prevention, and management strategies of CMV infection in Allo-HSCT recipients.

Recent Findings

The approval of the novel anti-CMV drug letermovir in 2017 has led to an increase in the use of antiviral prophylaxis as a preferred approach for prevention in many centers. Real-world studies have shown efficacy similar to the clinical trial. CMV-specific T cell-mediated immunity assays identify patients with immune reconstitution and predict disease progression. Phase 2 trials of maribavir have shown its efficacy as preemptive therapy and treatment of resistant and refractory CMV infections. Adoptive T cell therapy is an emerging option for treatment of refractory and resistant CMV. Of the different CMV vaccine trials, PepVax has shown promising results in a phase 1 trial.

Summary

CMV cell-mediated immunity assays have potential to be used as an adjunctive test to develop individualized management plan by identifying the patients who develop immune reconstitution; however, further prospective interventional studies are needed. Maribavir and adoptive T cell therapy are promising new therapies for treatment of CMV infections. CMV vaccine trials for prevention are also under way.

Comparing cytomegalovirus diagnostics by cell culture and quantitative nucleic acid testing in broncho-alveolar lavage fluids

Many clinical laboratories have replaced virus isolation in cell-culture (VIC) for cytomegalovirus (CMV) by quantitative-nucleic-acid testing (QNAT), rendering clinically relevant CMV-replication difficult to distinguish from CMV-shedding or latent infection. We compared direct VIC in 1109 consecutive bronchoalveolar lavage fluids (BALFs) and a well-validated CMV-QNAT (Basel-CMV-UL111a-77bp). In the retrospective Group 1 (N = 694) and Group 2 (N = 303), CMV-QNAT was performed within 48 h from 2-fold and 10-fold concentrated total nucleic acid (TNA) eluates, respectively. In Group 3 (N = 112), 2-fold and 10-fold concentrated TNA eluates were prospectively analyzed in parallel to VIC. CMV was detected by VIC in 79 of 694 (11%) and 26 of 303 (9%) of Groups 1 and 2, but in 114 of 694 (16%) and 57 of 303 (17%) by CMV-QNAT, respectively. Median CMV loads were significantly higher in VIC-positive than in VIC-negative BALF. The likelihood for CMV detection by VIC was 85% for BALF CMV- loads >4 log10 copies/ml. In the prospective Group 3, CMV was detected by VIC in 10 of 112 (9%), and in 14 of 112 (13%) and 20 of 112 (18%) by CMV-QNAT, when using 2-fold and 10-fold concentrated TNA eluates, respectively. Notably, CMV was undetectable by CMV-QNAT in 10 VIC-positive cases of Groups 1 and 2, but in none of Group 3. We conclude that CMV-QNAT can be adopted to BALF diagnostics but requires several careful steps in validation. CMV-QNAT loads >10 000 copies/ml in BALF may indicate significant CMV replication as defined by VIC, if short shipment and processing procedures can be guaranteed. Discordance of detecting CMV in time-matched plasma samples emphasises the role of local pulmonary CMV replication, for which histopathology remains the gold standard of proven CMV pneumonia.

Bronchoalveolar lavage as a diagnostic procedure: a review of known cellular and molecular findings in various lung diseases

Bronchoalveolar lavage (BAL) is a commonly used procedure in the evaluation of lung disease as it allows for sampling of the lower respiratory tract. In many circumstances, BAL differential cell counts have been reported to be typical of specific lung disorders. In addition, more specific diagnostic tests including molecular assays such as polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay, special cytopathologic stains, or particular microscopic findings have been described as part of BAL fluid analysis. This review focuses on common cellular and molecular findings of BAL in a wide range of lung diseases. Since the performance of the first lung irrigation in 1927, BAL has become a common and important diagnostic tool. While some pulmonary disorders have a highly characteristic signature of BAL findings, BAL results alone often lack specificity and require interpretation along with other clinical and radiographic details. Development of new diagnostic assays is certain to reinforce the utility of BAL in the future. Our review of the BAL literature is intended to serve as a resource to assist clinicians in the care of patients with lung disorders.

Comparison of different cytomegalovirus diseases following haploidentical hematopoietic stem cell transplantation

Cytomegalovirus (CMV) can cause end-organ diseases including pneumonia, gastroenteritis, retinitis, and encephalitis in hematopoietic stem cell transplantation recipients. Potential differences among different CMV diseases remain uncertain. This study aimed to compare the clinical characteristics, risk factors, and mortality among different CMV diseases. A retrospective nested case-control study was performed based on a cohort of 3862 patients who underwent haploidentical hematopoietic stem cell transplantation at a single-center. CMV diseases occurred in 113 (2.92%) of 3862 haplo-HSCT recipients, including probable CMV pneumonia (CMVP, n = 34), proven CMV gastroenteritis (CMVG, n = 34), CMV retinitis (CMVR, n = 31), probable CMV encephalitis (CMVE, n = 7), and disseminated CMV disease (Di-CMVD, n = 7). Most (91.2%) cases of CMVG developed within 100 days, while most (90.3%) cases of CMVR were late onset. Refractory CMV infection and CMV viral load at different levels were associated with an increased risk of CMVP, CMVG, and CMVR. Compared with patients without CMV diseases, significantly higher non-relapse mortality at 1 year after transplantation was observed in patients with CMVP and CMVR, rather than CMVG. Patients with CMVP, Di-CMVD, and CMVE had higher overall mortality after diagnosis than that of patients with CMVG and CMVR (61.7%, 57.1%, 40.0% vs 27.7%, 18.6%, P = 0.001). In conclusion, the onset time, viral dynamics, and mortality differ among different CMV diseases. The mortality of CMV diseases remains high, especially for CMVP, Di-CMVD, and CMVE.

Comparison of the Panther Fusion respiratory panels to routine methods for detection of viruses in upper and lower respiratory tract specimens

Viral respiratory infections remain a significant cause of morbidity and mortality in pediatric, elderly, and immunocompromised patients. The Panther Fusion respiratory panels consist of 3 separate multiplex assays that test for 1) influenza A, influenza B, and RSV; 2) parainfluenza virus types 1-4; or 3) adenovirus, human metapneumovirus, and rhinovirus. This study evaluated the performance of the Fusion assays for both upper and lower respiratory tract specimens in comparison to routine methods, including viral culture and targeted real-time polymerase chain reaction assays. Following discordant resolution, the Fusion assays demonstrated high overall correlation (98.6% [648/657]) with routine methods. In addition, prospective testing of respiratory specimens (n = 146) submitted for viral culture showed a ~10-fold increase in detection by the Fusion panels compared to viral culture (28.1% versus 2.7% positivity). The Fusion respiratory panels offer a flexible, more targeted approach to respiratory virus testing with a turnaround time comparable to other molecular assays.

Infectious Lung Disease

Infectious diseases are one of the main causes of morbidity and mortality worldwide. With new pathogens continuously emerging, known infectious diseases reemerging, increasing microbial resistance to antimicrobial agents, global environmental change, ease of world travel, and an increasing immunosuppressed population, recognition of infectious diseases plays an ever-important role in surgical pathology. This becomes particularly significant in cases where infectious disease is not suspected clinically and the initial diagnostic workup fails to include samples for culture. As such, it is not uncommon that a lung biopsy becomes the only material available in the diagnostic process of an infectious disease. Once the infectious nature of the pathological process is established, careful search for the causative agent is advised. This can often be achieved by examination of the hematoxylin and eosin-stained sections alone as many organisms or their cytopathic effects are visible on routine staining. However, ancillary studies such as histochemical stains, immunohistochemistry, in situ hybridization, or molecular techniques may be needed to identify the organism in tissue sections or for further characterization, such as speciation.

NKG2C Natural Killer Cells in Bronchoalveolar Lavage Are Associated With Cytomegalovirus Viremia and Poor Outcomes in Lung Allograft Recipients

BACKGROUND

Cytomegalovirus (CMV) infection is a risk factor for chronic lung allograft dysfunction (CLAD), which limits survival in lung allograft recipients. Natural killer (NK) cells that express the NKG2C receptor mediate CMV-specific immune responses. We hypothesized that NKG2C NK cells responding to CMV in the lung allograft would reduce CMV-related inflammation and would improve CLAD-free survival.

METHODS

We prospectively followed 130 subjects who underwent lung transplantation from 2012 to 2016. Bronchoalveolar lavage (BAL) NK cells were immunophenotyped for NKG2C, maturation, and proliferation markers. CMV viral load, serologies, serial spirometry, and mortality were recorded from medical records. Natural killer cell subset association with CMV endpoints were made using generalized estimating equation-adjusted linear models. BAL NKG2C NK cell association with CLAD-free survival was assessed by Cox proportional hazards modeling.

RESULTS

NKG2C NK cells were more mature and proliferative than NKG2C NK cells and represented a median of 7.8% of BAL NK cells. The NKG2C NK cell proportion increased prior to the first detection of viremia and was nearly tripled in subjects with high level viremia (>1000 copies/mL) compared with no detected viremia. Subjects with increased BAL NKG2C NK cells, relative to the median, had a significantly increased risk for CLAD or death (hazard ratio, 4.2; 95% confidence interval, 1.2-13.3).

CONCLUSIONS

The BAL NKG2C NK cell proportion may be a relevant biomarker for assessing risk of CMV viremia and quantifying potential CMV-related graft injury that can lead to CLAD or death.

BAL fluid analysis in the identification of infectious agents in patients with hematological malignancies and pulmonary infiltrates

The present study aims to evaluate the diagnostic yield of bronchoalveolar lavage (BAL) fluid in patients with hematological malignancies and describe the most common pathogens detected in BAL fluid (BALF.) An analysis of 480 BALF samples was performed in patients with hematological malignancies over a period of 7 years. The results of culture methods, PCR, and immunoenzymatic sandwich microplate assays for Aspergillus galactomannan (GM) in BALF were analyzed. Further, the diagnostic thresholds for Aspergillus GM and Pneumocystis jiroveci were also calculated. Microbiological findings were present in 87% of BALF samples. Possible infectious pathogens were detected in 55% of cases; 32% were classified as colonizing. No significant difference in diagnostic yield or pathogen spectrum was found between non-neutropenic and neutropenic patients. There was one significant difference in BALF findings among intensive care units (ICU) versus non-ICU patients for Aspergillus spp. (22% versus 9%, p = 0.03). The most common pathogens were Aspergillus spp. (n = 86, 33% of BAL with causative pathogens) and Streptococcus pneumoniae (n = 46, 18%); polymicrobial etiology was documented in 20% of cases. A quantitative PCR value of > 1860 cp/mL for Pneumocystis jirovecii was set as a diagnostic threshold for pneumocystis pneumonia. The absorbance index of GM in BALF of 0.5 was set as a diagnostic threshold for aspergillosis. The examination of BAL fluid revealed the presence of pathogen in more than 50% of cases and is, therefore, highly useful in this regard when concerning pulmonary infiltrates.

Pulmonary cytomegalovirus (CMV) DNA shedding in allogeneic hematopoietic stem cell transplant recipients: Implications for the diagnosis of CMV pneumonia

OBJECTIVES

To date no definitive cut-off value for cytomegalovirus (CMV) DNA load in bronchoalveolar lavage (BAL) fluid specimens has been established to discriminate between CMV pneumonia and pulmonary CMV DNA shedding in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients.

METHODS

The current retrospective study is aimed at assessing the range of CMV DNA loads quantified in BAL fluid specimens from allo-HSCT patients with pneumonia in which different microorganisms were causally involved.

RESULTS

A total of 144 BAL specimens from 123 patients were included. CMV DNA was detected in 56 out of 144 BAL fluid specimens and the median CMV DNA load from patients in whom CMV pneumonia was unlikely or could be tentatively ruled out was 1210 (31-68, 920) IU/ml. The frequency of CMV DNA detection and median CMV DNA loads were comparable, irrespective of the attributable cause of pneumonia. Detection of CMV DNA loads in BAL fluid specimens >500 IU/ml was independently associated with pneumonia-attributable mortality.

CONCLUSIONS

The current study highlights the difficulty in establishing universal CMV DNA load thresholds in BAL fluid specimens for distinguishing between CMV pneumonia and pulmonary CMV DNA shedding, and suggests that the presence of CMV DNA in BAL fluid specimens beyond a certain level may have a deleterious impact on patient outcome.

Diagnosis of Infectious Diseases in the Lower Respiratory Tract: A Cytopathologist's Perspective

CONTEXT.—

Respiratory cytology continues to play an important role in the diagnosis of lower respiratory tract infections. Prompt, accurate diagnosis of causative organisms is of paramount importance, particularly in immunosuppressed patients. In addition, a rapidly expanding arsenal of ancillary testing is now available, aiding tremendously in organism identification.

OBJECTIVE.—

To provide an updated review on the cytomorphologic features of common organisms in lower respiratory tract infection. Relevant ancillary tests, differential diagnoses, and potential pitfalls of organism identification will also be discussed.

DATA SOURCES.—

Data for this review were gathered from PubMed searches of infectious diseases of the lower respiratory tract, especially related to the diagnoses.

CONCLUSIONS.—

The lower respiratory tract is subject to infection by a wide variety of infectious agents. Pathologists should be familiar with common organisms, including their general clinical characteristics, cytomorphologic features, differential diagnoses, and ancillary methods of detection. Above all, correlation with microbiologic and clinical information is necessary to make a confident diagnosis of infection.

Histopathologic heterogeneity of acute respiratory distress syndrome revealed by surgical lung biopsy and its clinical implications

BACKGROUND/AIMS

Diffuse alveolar damage (DAD) is the histopathologic hallmark of acute respiratory distress syndrome (ARDS). However, there are several non-DAD conditions mimicking ARDS. The purpose of this study was to investigate the histopathologic heterogeneity of ARDS revealed by surgical lung biopsy and its clinical relevance.

METHODS

We retrospectively analyzed 84 patients with ARDS who met the criteria of the Berlin definition and underwent surgical lung biopsy between January 2004 and December 2013 in three academic hospitals in Korea. We evaluated their histopathologic findings and compared the clinical outcomes. Additionally, the impact of surgical lung biopsy on therapeutic alterations was examined.

RESULTS

The histopathologic findings were highly heterogeneous. Of 84 patients undergoing surgical lung biopsy, DAD was observed in 31 patients (36.9%), while 53 patients (63.1%) did not have DAD. Among the non-DAD patients, diffuse interstitial lung diseases and infections were the most frequent histopathologic findings in 19 and 17 patients, respectively. Although the mortality rate was slightly higher in DAD (71.0%) than in non-DAD (62.3%), the difference was not significant. Overall, the biopsy results led to treatment alterations in 40 patients (47.6%). Patients with non-DAD were more likely to change the treatment than those with DAD (58.5% vs. 29.0%), but there were no significant improvements regarding the mortality rate.

CONCLUSIONS

The histopathologic findings of ARDS were highly heterogeneous and classic DAD was observed in one third of the patients who underwent surgical lung biopsy. Although therapeutic alterations were more common in patients with non-DAD-ARDS, there were no significant improvements in the mortality rate.

Detection of Cytomegalovirus in Bronchoalveolar Lavage Fluid from HIV-Positive Individuals with Community Acquired Pneumonia

INTRODUCTION

Cytomegalovirus (CMV) pneumonia is one of the frequent viral pneumonia reported in persons with HIV infection. Knowledge of pulmonary CMV infection is important for deciding appropriate diagnostic strategies. However, there is scanty literature addressing the role of CMV aetiology among HIV positive individuals presenting with Community Acquired Pneumonia (CAP) using Bronchoalveolar Lavage (BAL) samples from India.

AIM

To detect CMV in BAL fluid from HIV-positive individuals presenting with CAP.

MATERIALS AND METHODS

This cross-sectional study was conducted using 107 archival BAL samples collected from consecutive HIV-positive patients presenting with CAP as per the Indian Chest Society and National College of Chest Physicians guidelines at the Department of Chest and Tuberculosis, Sassoon General Hospitals, Pune, India. The samples were tested for CMV by Polymerase Chain Reaction (PCR) targeting the IRL11 region at the National AIDS Research Institute, Pune.

RESULTS

Of the 107 BAL samples tested, 8 (7.4 %) were positive for CMV, while CMV was the sole pathogen in 5 (4.7%) cases. Co-infection with other pathogens was seen in 3 patients and Mycobacterium tuberculosis, Pneumocystis jiroveci and Streptococcus pneumoniae were the co-pathogens. Five patients had fatal clinical outcome of which three had CMV as the sole pathogen.

CONCLUSION

Ours is the first study to detect Cytomegalovirus (CMV) in bronchoalveolar lavage samples from HIV-positive individuals presenting with community acquired pneumonia from India and indicates the need for further multicentre studies to understand pulmonary CMV infection, which will eventually help in designing appropriate diagnostic strategies and therapeutic interventions.

Cytomegalovirus (CMV) DNA Quantitation in Bronchoalveolar Lavage Fluid From Hematopoietic Stem Cell Transplant Recipients With CMV Pneumonia

Background

Quantitative cytomegalovirus (CMV) DNA-specific polymerase chain reaction (PCR) analysis is widely used as a surveillance method for hematopoietic stem cell transplant (HCT) recipients. However, no CMV DNA threshold exists in bronchoalveolar lavage (BAL) to differentiate pneumonia from pulmonary shedding.

Methods

We tested archived BAL fluid samples from 132 HCT recipients with CMV pneumonia and 139 controls (100 patients with non-CMV pneumonia, 18 with idiopathic pneumonia syndrome [IPS], and 21 who were asymptomatic) by quantitative CMV and β-globin DNA-specific PCR.

Results

Patients with CMV pneumonia had higher median viral loads (3.9 log10 IU/mL; interquartile range [IQR], 2.6-6.0 log10 IU/mL) than controls (0 log10 IU/mL [IQR, 0-1.6 log10 IU/mL] for patients with non-CMV pneumonia, 0 log10 IU/mL [IQR, 0-1.6 log10 IU/mL] for patients with IPS, and 1.63 log10 IU/mL [IQR, 0-2.5 log10 IU/mL] for patients who were asymptomatic; P < .001 for all comparisons to patients with CMV pneumonia). Receiver operating characteristic curve analyses and predictive models identified a cutoff CMV DNA level of 500 IU/mL to differentiate between CMV pneumonia and pulmonary shedding, using current CMV pneumonia prevalence figures. However, different levels may be appropriate in settings of very high or low CMV pneumonia prevalence. The presence of pulmonary copathogens, radiographic presentation, or pulmonary hemorrhage did not alter predictive values.

Conclusion

CMV DNA load in BAL can be used to differentiate CMV pneumonia from pulmonary shedding.

CMV viral load in bronchoalveolar lavage for diagnosis of pneumonia in allogeneic hematopoietic stem cell transplantation

The objective of this report is to analyze the value of CMV viral load (VL) in bronchoalveolar lavage (BAL) in recipients of allogeneic hematopoietic stem cell transplantation (AHSCT) and to analyze the concordance between CMV quantification in plasma and BAL samples. Fifty-six patients were included; in 16 (28.6%) patients with symptoms of lung disease a BAL sample was collected, 7 (43.7%) patients had a VL >150 copies/mL (six had probable CMV pneumonia). Patients with CMV pneumonia were female (100%), of median age 53.5 years, and the median time from transplantion to onset of symptoms was 67.5 days. Pneumonia was early in three cases (incidence 5.4%). Median BAL VL was 53 250 copies/mL and plasma VL was 538 copies/mL (in one patient, the plasma VL was negative). Three (50.0%) patients had an improvement in the first week of treatment, and plasma VL became negative; the other 3 (50.0%) patients died with a CMV pneumonia refractory to treatment. Therefore, any value of CMV VL in BAL, especially if it is greater than plasma, with compatible signs or symptoms, should be considered suggestive of CMV pneumonia in recipients of AHSCT and they should receive specific treatment.

Clinical characteristics and outcomes of pediatric patients with CMV DNA detection in bronchoalveolar lavage fluid

INTRODUCTION

Cytomegalovirus (CMV) infection can cause severe pulmonary disease in immunocompromised patients. There are no standard diagnostic criteria for CMV pulmonary disease beyond histopathology findings on lung tissue, which is challenging to obtain in pediatric patients. Bronchoalveolar lavage (BAL) fluid is easier to obtain. Since CMV remains latent after primary infection and can potentially reactivate due to any inflammatory response, CMV detection in BAL specimen may not indicate acute CMV pulmonary disease. Thus, we describe the clinical manifestations and outcomes of pediatric patients with CMV detection in BAL fluid.

METHODS

We reviewed the clinical, radiologic, and laboratory data of patients <19 years old with a BAL specimen positive for CMV during a 5-year period.

RESULTS

Thirty-four encounters in 29 patients were found with CMV detected in their BAL specimen. Half (17/34) of the encounters were in immunocompromised patients. CMV, polymerase chain reaction (PCR) was the most common positive test. Forty-seven percent of the patients had other infections detected in BAL specimens. The majority of patients were never treated for CMV and resolved their acute respiratory illness. Only one patient had probable CMV pulmonary disease.

DISCUSSION

CMV is frequently recovered from BAL specimens but does not usually indicate acute CMV pulmonary disease. We would suggest that other diagnoses be considered first, even if CMV is recovered. Pediatr Pulmonol. 2017;52:112-118. © 2016 Wiley Periodicals, Inc.