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

A rare diagnosis of pulmonary actinomycosis by bronchoalveolar lavage cytology

The role of a bronchoalveolar lavage sample cell block in the diagnosis of pulmonary actinomycosis.

Imaging Approach to Pulmonary Infections in the Immunocompromised Patient

Pulmonary infections are the major cause of morbidity and mortality in immunocompromised patients and almost one-third of intensive care unit patients with pulmonary infections belong to the immunocompromised category. Multiple organisms may simultaneously infect an immunocompromised patient and the overwhelming burden of mixed infections further predisposes critically ill patients to acute hypoxemic respiratory failure. Notwithstanding that lung ultrasound is coming into vogue, the primary imaging investigation is a chest radiograph, followed by thoracic CT scan. This review based on our experience at tertiary care teaching hospitals provides insights into the spectrum of imaging features of various pulmonary infections occurring in immunocompromised patients. This review is unique as, firstly, the imaging spectrum described by us is categorized on basis of the etiological infective agent, comprehensively and emphatically correlated with the clinical setting of the patient. Secondly, a characteristic imaging pattern is emphasized in the clinical setting-imaging-pattern conglomerate, to highlight the most likely diagnosis possible in such a combination. Thirdly, the simulating conditions for a relevant differential diagnosis are discussed in each section. Fourthly, not only are the specific diagnostic and tissue sampling techniques for confirmation of the suspected etiological agent described, but the recommended pharmaco-therapeutic agents are also enumerated, so as to provide a more robust insight to the radiologist. Last but not the least, we summarize and conclude with a diagnostic algorithm, derived by us from the characteristic illustrative cases. The proposed algorithm, illustrated as a flowchart, emphasizes a diagnostic imaging approach comprising: correlation of the imaging pattern with clinical setting and with associated abnormalities in the thorax and in other organs/systems, which is comprehensively analyzed in arriving at the most likely diagnosis. Since a rapid evaluation and emergent management of such patients is of pressing concern not only to the radiologist, but also for the general physicians, pulmonologists, critical care specialists, oncologists and transplant surgery teams, we believe our review is very informative to a wide spectrum reader audience.

Tissue Pathogens and Cancers: A Review of Commonly Seen Manifestations in Histo- and Cytopathology

Tissue pathogens are commonly encountered in histopathology and cytology practice, where they can present as either benign mimickers of malignancy or true malignancies. The aim of this review is to provide a timely synthesis of our understanding of these tissue pathogens, with an emphasis on pertinent diagnostic conundrums associated with the benign mimickers of malignancy that can be seen with viral infections and those which manifest as granulomas. The oncogenic pathogens, including viruses, bacteria, and parasites, are then discussed with relationship to their associated malignancies. Although not exhaustive, the epidemiology, clinical manifestations, pathogenesis, and histological findings are included, along with a short review of emerging therapies.

Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia

Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 10² copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.

Rapid metagenomics for diagnosis of bloodstream and respiratory tract nosocomial infections: current status and future prospects

Introduction: Nosocomial infections represent a major problem for the health-care systems worldwide. Currently, diagnosis relies on microbiological culture, which is slow and has poor sensitivity. While waiting for a diagnosis, patients are treated with empiric broad spectrum antimicrobials, which are often inappropriate for the infecting pathogen. This results in poor patient outcomes, poor antimicrobial stewardship and increased costs for health-care systems.Areas covered: Clinical metagenomics (CMg), the application of metagenomic sequencing for the diagnosis of infection, has the potential to become a viable alternative to culture that can offer rapid results with high accuracy. In this article, we review current CMg methods for the diagnosis of nosocomial bloodstream (BSI) and lower respiratory-tract infections (LRTI).Expert opinion: CMg approaches are more accurate in LRTI compared to BSI. This is because BSIs are caused by low pathogen numbers in a high background of human cells. To overcome this, most approaches focus on cell-free DNA, but, to date, these tests are not accurate enough yet to replace blood culture. The higher pathogen numbers in LRTI samples make this a more suitable for CMg and accurate approaches have been developed, which are likely to be implemented in hospitals within the next 2-5 years.

Role of bronchoalveolar lavage in diagnosing pulmonary infections and malignancies: Experience from a tertiary care center

BACKGROUND

Bronchoalveolar lavage (BAL), is a safe, minimally invasive procedure to sample the terminal airways and the lung parenchyma. Although frequently used, there is lack of contemporary literature regarding the diagnostic utility of BAL for various pulmonary diseases. This study was conducted to evaluate the utility of BAL in diagnosis of various pulmonary pathologies, both infectious and neoplastic.

METHODS

This was a retrospective study performed over a period of 2 years. All the BAL samples reported on cytology were studied, their clinical details were retrieved, and the corresponding smears were reviewed. Cyto-histopathologic correlation was done, wherever possible.

RESULTS

There were a total of 1835 cases (1153 men, 682 women; age, 8 months to 78 years). Of these, 19 (1%) cases were assessed as inadequate for opinion. In 348 (19%) cases, specific infective cause could be identified on BAL cytology alone. Tuberculosis and fungal infections could be diagnosed in 165 (9%) and 178 (9.7%) cases respectively. There were 46 (2.5%) neoplasms, including adenocarcinoma (n = 20), squamous cell carcinoma (n = 5), small cell carcinoma (n = 2), Langerhans cell histiocytosis (n = 1), suspicious for malignancy (n = 15) and metastatic carcinoma (n = 3). Some rare diagnoses were also reported on BAL cytology, including sarcoidosis, actinomycosis, leishmaniasis, pulmonary alveolar proteinosis and metastatic papillary carcinoma of the thyroid.

CONCLUSION

BAL is a safe and useful procedure for primary diagnosis of infections such as tuberculosis and fungal infections, which has special significance in developing nations where prevalence of such infections is high. In addition, BAL has the potential to diagnose both primary as well as secondary malignant lung lesions.

Validation of SARS-CoV-2 detection across multiple specimen types

BACKGROUND

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused considerable disruption across the world, resulting in more than 235,000 deaths since December 2019. SARS-CoV-2 has a wide tropism and detection of the virus has been described in multiple specimen types, including various respiratory secretions, cerebrospinal fluid, and stool.

OBJECTIVE

To evaluate the accuracy and sensitivity of a laboratory modified CDCbased SARS-CoV-2 N1 and N2 assay across a range of sample types. Study Design We compared the matrix effect on the analytical sensitivity of SARS-CoV-2 detection by qRT-PCR in nasal swabs collected in viral transport medium (VTM), bronchoalveolar lavage (BAL), sputum, plasma, cerebral spinal fluid (CSF), stool, VTM, phosphate buffered saline (PBS), and Hanks' Balanced Salt Solution (HBSS). Initial limits of detection (LoD) were subsequently narrowed to confirm an LoD for each specimen type and target gene.

RESULTS

LoDs were established using a modified CDC-based laboratory developed test and ranged from a mean CT cut-off of 33.8-35.7 (10-20 copies/reaction) for the N1 gene target, and 34.0-36.2 (1-10 copies/reaction) for N2. Alternatives to VTM such as PBS and HBSS had comparable LoDs. The N2 gene target was found to be most sensitive in CSF.

CONCLUSION

A modified CDC-based laboratory developed test is able to detect SARSCoV- 2 accurately with similar sensitivity across all sample types tested.

Role of fine-needle aspiration cytology in early diagnosis of fungal infections

BACKGROUND

Fine-needle aspiration (FNA) is an important tool for the diagnosis of infectious diseases. In this study, we assessed the efficacy of FNA cytology in early diagnosis of fungal infections.

METHODS

This was a retrospective study from January 2016 to August 2018. Electronic archives were searched for FNAs from superficial and deep lesions obtained from various sites with the diagnosis of fungal infection. Each case was evaluated for underlying predisposing conditions, FNA source, radiologic findings, culture, and serology results.

RESULTS

A total of 15 cases were identified from the following sites: lung (eight), cervical lymph nodes (four), soft tissue (two), and retroperitoneal lymph node (one). Predisposing conditions were found in 11 patients: HIV (five), malignancy (three), and post-transplant (three). Imaging impression was mostly malignancy vs infection. In all 15 cases, the diagnosis of fungal infection was done by FNA cytology. The presumptive genus specific diagnoses based on yeast morphology was given in 12 cases (five Histoplasma, four Cryptococcus, and three Coccidioides). The diagnosis of fungal infection was provided within 24 h in nine cases, four during onsite evaluation. Microbial cultures were confirmatory in seven cases, and five cases exhibited negative cultures with positive serology. Out of the 15 patients, 14 were discharged in fair condition, and one died with complications of heart graft failure.

CONCLUSION

FNA is a rapid and reliable method for early diagnosis of fungal infections, allowing a prompt and appropriate management, especially in immunocompromised patients. When onsite evaluation indicates infectious process, cultures can be timely done.

Mycobacterium tuberculosis diagnosed promptly by bronchial brushing cytology in an immunocompetent patient

Respiratory cytology plays an important role in the diagnosis of lower respiratory tract infection. The timely diagnosis of pulmonary tuberculosis (TB) can be very challenging due to the nonspecific cytomorphologic features and limited number of organisms, especially in the immunocompetent patients. Here, we reported a case of TB diagnosed promptly by bronchial brushing cytology in a 51-year-old immunocompetent patient. She presented with a 4 cm fungating lesion involving right lower lobe of the lung and mediastinal lymphadenopathy with an initial concern for malignancy. Bronchial brushing showed scattered acute inflammatory cells in the background of necrosis. A cell block was prepared and acid-fast bacilli (AFB)-positive organisms were identified. Subsequent polymerase chain reaction (PCR) performed on the sputum detected Mycobacterium tuberculosis. This case highlights the importance of recognizing the cytomorphology of TB from a bronchial brushing specimen; and also emphasizes the potential utility of the cell block from respiratory cytology in the diagnosis of TB.