1
|
Sun L, Zhang K, Liu Y, Che L, Zhang P, Wang B, Du N. Metagenomic next-generation sequencing targeted and metagenomic next-generation sequencing for pulmonary infection in HIV-infected and non-HIV-infected individuals. Front Cell Infect Microbiol 2024; 14:1438982. [PMID: 39224706 PMCID: PMC11366708 DOI: 10.3389/fcimb.2024.1438982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Background When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals. Methods This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients. Results A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15). Conclusion Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.
Collapse
Affiliation(s)
- Luyao Sun
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Kaiyu Zhang
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Yong Liu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Lihe Che
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Peng Zhang
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Bin Wang
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Na Du
- Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
2
|
Zhang M, Zhang H, Yan B, Ren M, Wang W, Zhang T. Diagnostic performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in bronchoalveolar lavage fluid for pulmonary tuberculosis in HIV-infected patients. J Clin Tuberc Other Mycobact Dis 2024; 36:100459. [PMID: 38983443 PMCID: PMC11231557 DOI: 10.1016/j.jctube.2024.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
Introduction Pulmonary tuberculosis (PTB) remains a significant health concern, particularly in individuals infected with human immunodeficiency virus (HIV) who are more susceptible to developing active TB disease. Early and accurate diagnosis of TB is crucial for effective treatment and prevention of transmission. This study aims to evaluate the potential of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis of bronchoalveolar lavage fluid (BALF) for diagnosis of suspected PTB in HIV-infected patients. Methods This retrospective study recruited 60 HIV-infected patients with suspected PTB presenting with respiratory symptoms and abnormal chest radiographs between January 2022 and June 2023. BALF samples were collected and subjected to analysis using MALDI-TOF MS, GeneXpert, acid-fast bacilli (AFB) smear and culture. And their diagnostic performance was compared. Results The sensitivity of MALDI⁃TOFMS for diagnosing PTB was 83.3 %, which was better than that of smear 11.9 %, culture 40.5 % or Xpert38.1 % (all p < 0.01). The area under the curve (AUC) value of MALDI⁃TOFMS was 0.889, which was better than that of smear 0.532, culture 0.675 or Xpert 0.690 (all p < 0.01). The katG315 and rpoB-RRDR 511 mutations were detected by the MALDI⁃TOFMS in two patients. Conclusion Nucleotide MALDI-TOFMS has a good clinical performance for rapid diagnosis of PTB from BALF samples in HIV infected patients, and detects mutations of TB simultaneously.
Collapse
Affiliation(s)
- Mei Zhang
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Hongwei Zhang
- Clinic of Center for Infection, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Benyong Yan
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Meixin Ren
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Wen Wang
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Tong Zhang
- Department of Infectious Diseases and Medical Immunology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| |
Collapse
|
3
|
Gao W, Yang C, Wang T, Guo Y, Zeng Y. Nanopore-based targeted next-generation sequencing of tissue samples for tuberculosis diagnosis. Front Microbiol 2024; 15:1403619. [PMID: 39027106 PMCID: PMC11256091 DOI: 10.3389/fmicb.2024.1403619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Objective Diagnosing tuberculosis (TB) can be particularly challenging in the absence of sputum for pulmonary tuberculosis cases and extrapulmonary TB (EPTB). This study evaluated the utility of nanopore-based targeted next-generation sequencing (tNGS) for diagnosing TB in tissue samples, and compared its efficacy with other established diagnostic methods. Methods A total of 110 tissue samples from clinical cases were examined. The sensitivity and specificity of tNGS were benchmarked against a range of existing diagnostic approaches including hematoxylin and eosin (HE) staining in conjunction with acid-fast bacilli (AFB) detection, HE staining combined with PCR, HE staining paired with immunohistochemistry (IHC) using anti-MPT64, and the Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) assay. Results The sensitivity and specificity of tNGS were 88.2 and 94.1%, respectively. The respective sensitivities for HE staining combined with AFB, HE staining combined with PCR, HE staining combined with IHC using anti-MPT64, and Xpert MTB/RIF were 30.1, 49.5, 47.3, and 59.1%. The specificities for these methods were 82.4, 88.2, 94.1, and 94.1%, respectively. Analysis of drug resistance based on tNGS results indicated that 10 of 93 TB patients (10.75%) had potential drug resistance. Conclusion Targeted next-generation sequencing achieved higher accuracy than other established diagnostic methods, and can play a crucial role in the rapid and accurate diagnosis of TB, including drug-resistant TB.
Collapse
Affiliation(s)
| | | | | | | | - Yi Zeng
- Department of Tuberculosis, The Second Hospital of Nanjing, Nanjing, China
| |
Collapse
|
4
|
Gai J, Liu L, Zhang X, Guan J, Mao S. Impact of the diseased lung microenvironment on the in vivo fate of inhaled particles. Drug Discov Today 2024; 29:104019. [PMID: 38729235 DOI: 10.1016/j.drudis.2024.104019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Inhalation drug delivery is superior for local lung disease therapy. However, there are several unique absorption barriers for inhaled drugs to overcome, including limited drug deposition at the target site, mucociliary clearance, pulmonary macrophage phagocytosis, and systemic exposure. Moreover, the respiratory disease state can affect or even destroy the physiology of the lung, thus influencing the in vivo fate of inhaled particles compared with that in healthy lungs. Nevertheless, limited information is available on this effect. Thus, in this review, we present pathological changes of the lung microenvironment under varied respiratory diseases and their influence on the in vivo fate of inhaled particles; such insights could provide a basis for rational inhalation particle design based on specific disease states.
Collapse
Affiliation(s)
- Jiayi Gai
- School of Pharmacy, Shenyang Key Laboratory of Intelligent Mucosal Drug Delivery Systems, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Liu Liu
- School of Pharmacy, Shenyang Key Laboratory of Intelligent Mucosal Drug Delivery Systems, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhang
- School of Pharmacy, Shenyang Key Laboratory of Intelligent Mucosal Drug Delivery Systems, Shenyang Pharmaceutical University, Shenyang 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, China
| | - Jian Guan
- School of Pharmacy, Shenyang Key Laboratory of Intelligent Mucosal Drug Delivery Systems, Shenyang Pharmaceutical University, Shenyang 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, China
| | - Shirui Mao
- School of Pharmacy, Shenyang Key Laboratory of Intelligent Mucosal Drug Delivery Systems, Shenyang Pharmaceutical University, Shenyang 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, China.
| |
Collapse
|
5
|
Chan JCK, Boland JM. Granulomatous Lung Diseases: A Practical Approach and Review of Common Entities. Surg Pathol Clin 2024; 17:173-192. [PMID: 38692803 DOI: 10.1016/j.path.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Granulomas are frequently encountered by pathologists in all types of lung specimens and arise from diverse etiologies. They should always be reported as necrotizing or non-necrotizing, with microorganism stains performed to evaluate for infection. With attention to distribution, quality (poorly vs well-formed), associated features, and correlation with clinical, radiologic, and laboratory data, the differential diagnosis for granulomatous lung disease can usually be narrowed to a clinically helpful "short list." This review describes a practical approach to pulmonary granulomas and reviews the clinicopathological aspects of common entities, including infectious (mycobacteria, fungi) and noninfectious (hypersensitivity pneumonitis, sarcoid, and vasculitis) causes.
Collapse
Affiliation(s)
- Jackie Cheuk Ki Chan
- Department of Laboratory Medicine and Pathology, Royal Alexandra and University of Alberta Hospitals, 10240 Kingsway NW, Edmonton, Alberta, Canada, T5H 3V9
| | - Jennifer M Boland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Anatomic Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
| |
Collapse
|
6
|
Dartois V, Dick T. Therapeutic developments for tuberculosis and nontuberculous mycobacterial lung disease. Nat Rev Drug Discov 2024; 23:381-403. [PMID: 38418662 PMCID: PMC11078618 DOI: 10.1038/s41573-024-00897-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Tuberculosis (TB) drug discovery and development has undergone nothing short of a revolution over the past 20 years. Successful public-private partnerships and sustained funding have delivered a much-improved understanding of mycobacterial disease biology and pharmacology and a healthy pipeline that can tolerate inevitable attrition. Preclinical and clinical development has evolved from decade-old concepts to adaptive designs that permit rapid evaluation of regimens that might greatly shorten treatment duration over the next decade. But the past 20 years also saw the rise of a fatal and difficult-to-cure lung disease caused by nontuberculous mycobacteria (NTM), for which the drug development pipeline is nearly empty. Here, we discuss the similarities and differences between TB and NTM lung diseases, compare the preclinical and clinical advances, and identify major knowledge gaps and areas of cross-fertilization. We argue that applying paradigms and networks that have proved successful for TB, from basic research to clinical trials, will help to populate the pipeline and accelerate curative regimen development for NTM disease.
Collapse
Affiliation(s)
- Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA.
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| |
Collapse
|
7
|
Liu Q, Pan X, An H, Du J, Li X, Sun W, Gao Y, Li Y, Niu H, Gong W, Liang J. Building a model for the differential diagnosis of non-tuberculous mycobacterial lung disease and pulmonary tuberculosis: A case-control study based on immunological and radiological features. Int Immunopharmacol 2023; 124:111064. [PMID: 37857122 DOI: 10.1016/j.intimp.2023.111064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Although the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) is increasing annually, it is easily misdiagnosed as pulmonary tuberculosis (PTB). This study aimed to screen and identify the immunological and radiological characteristics that differentiate NTM-PD from PTB and to construct a discriminatory diagnostic model for NTM-PD, providing new tools for its differential diagnosis. METHODS Hospitalised patients diagnosed with NTM-PD or PTB between January 2019 and June 2023 were included in the study. Immunological and radiological characteristics were compared between the two groups. Based on the selected differential features, a logistic regression algorithm was used to construct a discriminatory diagnostic model for NTM-PD, and its diagnostic performance was preliminarily analysed. RESULTS Patients with NTM-PD were significantly older than those with PTB and the tuberculosis-specific interferon-gamma release assay (TB-IGRA) positivity rate was significantly lower in the NTM-PD group. Moreover, the absolute counts of total T lymphocytes, CD4+ T lymphocytes, CD8+ T lymphocytes, NK cells, and B lymphocytes were significantly lower in patients with NTM-PD and PTB than in healthy controls. Additionally, patients with NTM-PD had a significantly lower absolute count of B lymphocytes than the PTB group. Radiological analysis revealed significant differences between patients with NTM-PD and PTB in terms of cavity wall thickness, bronchial dilation, lung consolidation, pulmonary nodule size, pulmonary emphysema, lung bullae, lymph node calcification, pleural effusion, mediastinal and hilar lymphadenopathy, and the tree-in-bud sign. Bronchial dilation was identified as the predominant risk factor of NTM-PD, whereas TB-IGRA positivity, lymph node calcification, pleural effusion, and mediastinal and hilar lymphadenopathies were protective factors. Based on this, we constructed a discriminatory diagnostic model for NTM-PD. Its receiver operating characteristic curve demonstrated good diagnostic performance, with an area under the curve of 0.938. At the maximum Youden index of 0.746, the sensitivity and specificity were 0.835 and 0.911, respectively. CONCLUSIONS Patients with NTM-PD and PTB exhibited impaired humoral and cellular immune functions as well as significant differences in radiological features. The constructed NTM-PD diagnostic model demonstrated good diagnostic performance. This study provides a new tool for the differential diagnosis of NTM-PD.
Collapse
Affiliation(s)
- Qi Liu
- Hebei North University, Zhangjiakou 075000, Hebei, China; Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xiuming Pan
- Hebei North University, Zhangjiakou 075000, Hebei, China
| | - Huiru An
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Jingli Du
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xianan Li
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Wenna Sun
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Yongkun Gao
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Yuxi Li
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Honghong Niu
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Wenping Gong
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China.
| | - Jianqin Liang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital, Beijing 100091, China.
| |
Collapse
|
8
|
Li H, Wei L, Li F. Diagnosis of mycobacterium avium complex infection utilizing metagenomics next-generation sequencing: a case report. Front Med (Lausanne) 2023; 10:1247034. [PMID: 37920597 PMCID: PMC10619715 DOI: 10.3389/fmed.2023.1247034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/25/2023] [Indexed: 11/04/2023] Open
Abstract
Mycobacterium avium-intracellulare complex (MAC) is a type of nontuberculous mycobacteria (NTM) and is associated with underlying pulmonary diseases, such as chronic obstructive pulmonary disease, bronchiectasis, chronic aspiration or recurrent pneumonia, inactive or active tuberculosis, pneumoconiosis, and bronchogenic carcinoma. The risk factors for NTM-PD include host, drug, and environmental factors. In this report, we present the case of a 61-year-old man who developed bilateral lung nodules and was experiencing severe hemoptysis. The repeat acid-fast bacilli test performed on both sputum and bronchoalveolar lavage fluid (BALF) samples showed a negative result, as did the GeneXpert test. We employed metagenomic next-generation sequencing (mNGS) to analyze the lung nodule and BALF samples collected from the patient. Both samples tested positive for MAC within 3 days. In addition, traditional MAC culture, conducted for 2 months, confirmed the growth of MAC in the patient's BALF. Then, the patient was treated accordingly. Following treatment, a high-resolution chest computed tomography scan revealed a significant reduction in lung nodules of the patient after 2 months. These results indicate that MAC-associated lung nodules were responsible for the patient's symptoms, emphasizing the need for vigilance in diagnosing MAC infection in the patient without predisposing conditions. Furthermore, these results highlight the potential utility of mNGS as a promising rapid diagnostic tool for MAC infection and its potential role in the diagnosis of NTM disease.
Collapse
Affiliation(s)
- Hongli Li
- Department of Respiratory, Tianjin Beichen Hospital, Tianjin, China
| | - Luqing Wei
- Department of Respiratory, Tianjin Beichen Hospital, Tianjin, China
| | - Fenge Li
- Department of Respiratory, Tianjin Beichen Hospital, Tianjin, China
- Core Laboratory, Tianjin Beichen Hospital, Tianjin, China
| |
Collapse
|
9
|
Viswanathan VS, Toro P, Corredor G, Mukhopadhyay S, Madabhushi A. The state of the art for artificial intelligence in lung digital pathology. J Pathol 2022; 257:413-429. [PMID: 35579955 PMCID: PMC9254900 DOI: 10.1002/path.5966] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/26/2022] [Accepted: 05/15/2022] [Indexed: 12/03/2022]
Abstract
Lung diseases carry a significant burden of morbidity and mortality worldwide. The advent of digital pathology (DP) and an increase in computational power have led to the development of artificial intelligence (AI)-based tools that can assist pathologists and pulmonologists in improving clinical workflow and patient management. While previous works have explored the advances in computational approaches for breast, prostate, and head and neck cancers, there has been a growing interest in applying these technologies to lung diseases as well. The application of AI tools on radiology images for better characterization of indeterminate lung nodules, fibrotic lung disease, and lung cancer risk stratification has been well documented. In this article, we discuss methodologies used to build AI tools in lung DP, describing the various hand-crafted and deep learning-based unsupervised feature approaches. Next, we review AI tools across a wide spectrum of lung diseases including cancer, tuberculosis, idiopathic pulmonary fibrosis, and COVID-19. We discuss the utility of novel imaging biomarkers for different types of clinical problems including quantification of biomarkers like PD-L1, lung disease diagnosis, risk stratification, and prediction of response to treatments such as immune checkpoint inhibitors. We also look briefly at some emerging applications of AI tools in lung DP such as multimodal data analysis, 3D pathology, and transplant rejection. Lastly, we discuss the future of DP-based AI tools, describing the challenges with regulatory approval, developing reimbursement models, planning clinical deployment, and addressing AI biases. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
| | - Paula Toro
- Department of PathologyCleveland ClinicClevelandOHUSA
| | - Germán Corredor
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
- Louis Stokes Cleveland VA Medical CenterClevelandOHUSA
| | | | - Anant Madabhushi
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
- Louis Stokes Cleveland VA Medical CenterClevelandOHUSA
| |
Collapse
|
10
|
MacLean EL, Kohli M, Köppel L, Schiller I, Sharma SK, Pai M, Denkinger CM, Dendukuri N. Bayesian latent class analysis produced diagnostic accuracy estimates that were more interpretable than composite reference standards for extrapulmonary tuberculosis tests. Diagn Progn Res 2022; 6:11. [PMID: 35706064 PMCID: PMC9202094 DOI: 10.1186/s41512-022-00125-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Evaluating the accuracy of extrapulmonary tuberculosis (TB) tests is challenging due to lack of a gold standard. Latent class analysis (LCA), a statistical modeling approach, can adjust for reference tests' imperfect accuracies to produce less biased test accuracy estimates than those produced by commonly used methods like composite reference standards (CRSs). Our objective is to illustrate how Bayesian LCA can address the problem of an unavailable gold standard and demonstrate how it compares to using CRSs for extrapulmonary TB tests. METHODS We re-analyzed a dataset of presumptive extrapulmonary TB cases in New Delhi, India, for three forms of extrapulmonary TB. Results were available for culture, smear microscopy, Xpert MTB/RIF, and a non-microbiological test, cytopathology/histopathology, or adenosine deaminase (ADA). A diagram was used to define assumed relationships between observed tests and underlying latent variables in the Bayesian LCA with input from an inter-disciplinary team. We compared the results to estimates obtained from a sequence of CRSs defined by increasing numbers of positive reference tests necessary for positive disease status. RESULTS Data were available from 298, 388, and 230 individuals with presumptive TB lymphadenitis, meningitis, and pleuritis, respectively. Using Bayesian LCA, estimates were obtained for accuracy of all tests and for extrapulmonary TB prevalence. Xpert sensitivity neared that of culture for TB lymphadenitis and meningitis but was lower for TB pleuritis, and specificities of all microbiological tests approached 100%. Non-microbiological tests' sensitivities were high, but specificities were only moderate, preventing disease rule-in. CRSs' only provided estimates of Xpert and these varied widely per CRS definition. Accuracy of the CRSs also varied by definition, and no CRS was 100% accurate. CONCLUSION Unlike CRSs, Bayesian LCA takes into account known information about test performance resulting in accuracy estimates that are easier to interpret. LCA should receive greater consideration for evaluating extrapulmonary TB diagnostic tests.
Collapse
Affiliation(s)
- Emily L MacLean
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada
| | | | - Lisa Köppel
- Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University, Heidelberg, Germany
| | - Ian Schiller
- Department of Medicine, McGill University Health Centre, Montréal, Canada
| | - Surendra K Sharma
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhukar Pai
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montréal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada
| | - Claudia M Denkinger
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montréal, Canada
- Division of Tropical Medicine, Center of Infectious Diseases, Heidelberg University, Heidelberg, Germany
| | - Nandini Dendukuri
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montréal, Canada.
- Department of Medicine, McGill University Health Centre, Montréal, Canada.
| |
Collapse
|
11
|
Dartois V, Dick T. Drug development challenges in nontuberculous mycobacterial lung disease: TB to the rescue. J Exp Med 2022; 219:e20220445. [PMID: 35543723 PMCID: PMC9098649 DOI: 10.1084/jem.20220445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nontuberculous mycobacterial pulmonary disease (NTM-PD) is treated with multiple repurposed drugs. Chemotherapy is long and often toxic, includes parenteral drugs, and suffers from poor cure rates. There is an urgent need for more efficacious, tolerated, and oral antibiotics optimized towards the treatment of NTM-PD, adapted to the spectrum of disease. In contrast to the empty NTM pipeline, drug development for the related tuberculosis lung disease has experienced a renaissance. Here, we argue that applying lessons learned from tuberculosis will facilitate the discovery of curative oral regimens for NTM-PD.
Collapse
Affiliation(s)
- Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ
- Department of Microbiology and Immunology, Georgetown University, Washington, DC
| |
Collapse
|
12
|
Mycobacterium avium-intracellulare complex promote release of pro-inflammatory enzymes matrix metalloproteinases by inducing neutrophil extracellular trap formation. Sci Rep 2022; 12:5181. [PMID: 35410994 PMCID: PMC9001666 DOI: 10.1038/s41598-022-09017-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/15/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe prevalence of and mortality from non-tuberculous mycobacteria (NTM) infections have been steadily increasing worldwide. Most NTM infections are caused by Mycobacterium avium-intracellulare complex (MAC). MAC can escape from killing by neutrophils, which are professional phagocytes. However, the involvement of neutrophils in the pathogenesis of MAC infection is poorly understood. The present study assessed the roles of neutrophil extracellular trap (NET) formation in neutrophil defense mechanisms against infection with MAC strains, including M. avium isolated from patients with severe or mild lung tissue destruction. Although all MAC induced NET formation, non-pathogenic mycobacteria (M. gordonae and M. smegmatis) slightly but not significantly induced NET formation. Peptidylarginine deiminase 4 (PAD4) inhibitor reduced MAC-induced NET formation but did not affect MAC escape from neutrophils. PAD4 inhibition attenuated the MAC-induced matrix metalloproteinase (MMP)-8 and 9 release to the levels of MMPs from non-pathogenic mycobacteria. MAC also induced interleukin (IL)-8 release by neutrophils, a process independent of MAC-induced NET formation. Taken together, these findings suggest that MAC induce NET formation, IL-8 release and NETs-dependent release of MMP-8 and -9 from neutrophils, leading to neutrophil accumulation and further inflammation, thereby enhancing the progression of infection in the lungs.
Collapse
|
13
|
A rabbit model to study antibiotic penetration at the site of infection for non-tuberculous mycobacterial lung disease: macrolide case study. Antimicrob Agents Chemother 2022; 66:e0221221. [PMID: 35099272 DOI: 10.1128/aac.02212-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacterial pulmonary disease (NTM-PD) is a potentially fatal infectious disease requiring long treatment duration with multiple antibiotics and against which there is no reliable cure. Among the factors that have hampered the development of adequate drug regimens is the lack of an animal model that reproduces the NTM lung pathology required for studying antibiotic penetration and efficacy. Given the documented similarities between tuberculosis and NTM immunopathology in patients, we first determined that the rabbit model of active tuberculosis reproduces key features of human NTM-PD and provides an acceptable surrogate model to study lesion penetration. We focused on clarithromycin, a macrolide and pillar of NTM-PD treatment, and explored the underlying causes of the disconnect between its favorable potency and pharmacokinetics, and inconsistent clinical outcome. To quantify pharmacokinetic-pharmacodynamic target attainment at the site of disease, we developed a translational model describing clarithromycin distribution from plasma to lung lesions, including the spatial quantitation of clarithromycin and azithromycin in mycobacterial lesions of two patients on long-term macrolide therapy. Through clinical simulations, we visualized the coverage of clarithromycin in plasma and four disease compartments, revealing heterogeneous bacteriostatic and bactericidal target attainment depending on the compartment and the corresponding potency against nontuberculous mycobacteria in clinically relevant assays. Overall, clarithromycin's favorable tissue penetration and lack of bactericidal activity indicated that its clinical activity is limited by pharmacodynamic rather than pharmacokinetic factors. Our results pave the way towards the simulation of lesion pharmacokinetic-pharmacodynamic coverage by multi-drug combinations, to enable the prioritization of promising regimens for clinical trials.
Collapse
|
14
|
Rozmus D, Płomiński J, Augustyn K, Cieślińska A. rs7041 and rs4588 Polymorphisms in Vitamin D Binding Protein Gene (VDBP) and the Risk of Diseases. Int J Mol Sci 2022; 23:ijms23020933. [PMID: 35055118 PMCID: PMC8779119 DOI: 10.3390/ijms23020933] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 02/01/2023] Open
Abstract
The purpose of the study was to investigate the role of vitamin D binding protein (VDBP, DBP) and its polymorphism in the vitamin D pathway and human health. This narrative review shows the latest literature on the most popular diseases that have previously been linked to VDBP. Vitamin D plays a crucial role in human metabolism, controlling phosphorus and calcium homeostasis. Vitamin D binding protein bonds vitamin D and its metabolites and transports them to target tissues. The most common polymorphisms in the VDBP gene are rs4588 and rs7041, which are located in exon 11 in domain III of the VDBP gene. rs4588 and rs7041 may be correlated with differences not only in vitamin D status in serum but also with vitamin D metabolites. This review supports the role of single nucleotide polymorphisms (SNPs) in the VDBP gene and presents the latest data showing correlations between VDBP variants with important human diseases such as obesity, diabetes mellitus, tuberculosis, chronic obstructive pulmonary disease, and others. In this review, we aim to systematize the knowledge regarding the occurrence of diseases and their relationship with vitamin D deficiencies, which may be caused by polymorphisms in the VDBP gene. Further research is required on the possible influence of SNPs, modifications in the structure of the binding protein, and their influence on the organism. It is also important to mention that most studies do not have a specific time of year to measure accurate vitamin D metabolite levels, which can be misleading in conclusions due to the seasonal nature of vitamin D.
Collapse
Affiliation(s)
- Dominika Rozmus
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland;
- Correspondence:
| | - Janusz Płomiński
- Clinical Department of Trauma-Orthopedic Surgery and Spine Surgery of the Provincial Specialist Hospital in Olsztyn, 10-561 Olsztyn, Poland;
- Department and Clinic of Orthopaedics and Traumatology, Collegium Medicum, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Klaudia Augustyn
- Faculty of Medicine, Collegium Medicum, University of Warmia and Mazury, 10-082 Olsztyn, Poland;
| | - Anna Cieślińska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland;
| |
Collapse
|
15
|
Tian B, Sun J, Bai J, Zhang R, Liu J, Shen Y, Li C, Liu L, Chen J, Qi T, Lu H. Cytomegalovirus viremia is associated with poor outcomes in AIDS patients with disseminated nontuberculous mycobacterial disease. Biosci Trends 2021; 15:406-412. [PMID: 34588390 DOI: 10.5582/bst.2021.01279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Both cytomegalovirus (CMV) viremia and disseminated nontuberculous mycobacterial (NTM) disease are common opportunistic infections in AIDS patients. Whether concurrent CMV viremia is associated with mortality in patients with AIDS and disseminated NTM disease is unknown. Subjects were patients with AIDS and disseminated NTM disease seen at a single center from January 2015 to April 2021. Data were retrospectively collected. Differences in demographics and clinical characteristics and hospitalization survival rates were compared between patients with disseminated NTM and with CMV viremia or not. Subjects were 113 AIDS patients with disseminated NTM who were seen at this Hospital from January 2015 to April 2021. Twenty-six of the patients had CMV viremia and 87 did not. The median age was 36 years (interquartile range [IQR] 29-42) and 108 patients were male (96%). The median CD4 count was 7 cells/µL (IQR 3-17). The median plasma CMV viral load was 9,245 IU/mL (IQR 3147-45725). The serum albumin of patients with CMV viremia was significantly lower than that of patients without CMV viremia (P = 0.03). Compared to patients without CMV viremia (81.6%), patients with CMV viremia had a significantly poorer prognosis (P = 0.01). Cox regression analysis indicated that the risk of a poor prognosis in patients with CMV viremia was 4.7 times higher than that in patients without CMV viremia (P = 0.003), and patients with CD8 more than 250/μL had a better prognosis (P = 0.02). CMV viremia increases the risk of a poor prognosis in patients with AIDS and a disseminated NTM infection. A routine CMV DNA test should be performed on patients with AIDS and disseminated NTM disease in order to reduce the risk of death.
Collapse
Affiliation(s)
- Bo Tian
- Department of Infectious Disease, The Third People's Hospital of Kunming, Kunming, Yunnan, China
| | - Jianjun Sun
- Department of Infectious Disease, The Third People's Hospital of Kunming, Kunming, Yunnan, China
| | - Jinsong Bai
- Department of Infectious Disease, The Third People's Hospital of Kunming, Kunming, Yunnan, China
| | - Renfang Zhang
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jun Liu
- Department of Infectious Disease, The Third People's Hospital of Kunming, Kunming, Yunnan, China
| | - Yinzhong Shen
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| | - Chongxi Li
- Department of Infectious Disease, The Third People's Hospital of Kunming, Kunming, Yunnan, China
| | - Li Liu
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| | - Jun Chen
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| | - Tangkai Qi
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hongzhou Lu
- Department of Infection and Immunity, Shanghai Public Health Clinical Center, Shanghai, China
| |
Collapse
|
16
|
Terzi Ö, Öztomurcuk D, Gün S, Kiliçaslan Z. Evaluation of effectiveness of pathology reports in active surveillance of tuberculosis. Cent Eur J Public Health 2021; 29:96-101. [PMID: 34245548 DOI: 10.21101/cejph.a6124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 01/25/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Despite advancing technology, national TB surveillance systems are still inadequate in terms of patient detection around the world. It was aimed to investigate suspicious cases detected by active surveillance method in pathology laboratories and to evaluate the effectiveness of this method in terms of finding new TB cases. METHODS This is a descriptive cross-sectional study. It was administrated in Samsun, Turkey, between January 2012-December 2017. Within the scope of active surveillance, pathology laboratories were regularly visited and reported cases with granulomatous inflammation were assessed. The obtained patient list was compared with the records of the Electronic Tuberculosis Management System (ETMS). Patients who were not included in these records were invited to the dispensary and evaluated for TB. They were also referred to the relevant hospitals for diagnosis if necessary. Frequency values and descriptive statistics were calculated using SPSS method. RESULTS It was found that 35.6% of 703 patients with the diagnosis of granulomatous inflammation were previously diagnosed, treated or currently undergoing treatment in the ETMS registry. As a result of the assessment of remaining 453 cases, 46 patients (10.1%) were newly diagnosed with TB. Newly diagnosed TB patients were reported, and their treatment started. CONCLUSION As a result, active surveillance method conducted in pathology laboratories are used to detect unknown or late reported TB cases and allows to start treatment without further delay.
Collapse
Affiliation(s)
- Özlem Terzi
- Department of Public Health, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | | | - Seda Gün
- Department of Pathology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Zeki Kiliçaslan
- Department of Chest Diseases, Medical Faculty, Istanbul University, Istanbul, Turkey
| |
Collapse
|
17
|
Zhu X, Wu H, Gong X, Li C, Ma J. A luminescent Tb(III)-organic framework: Selective sensing of PO 43– ions and important role on tuberculosis curing. J COORD CHEM 2021. [DOI: 10.1080/00958972.2021.1959560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Xiaodan Zhu
- Department of Respiratory Medicine, Yiwu Central Hospital, Yiwu, China
| | - Hong Wu
- Department of Respiratory Medicine, Yiwu Central Hospital, Yiwu, China
| | - Xinyan Gong
- First Department of Cardiovascular, Yiwu Central Hospital, Yiwu, China
| | - Chun Li
- Department of Medicine, The people's Hospital of Lanzhou, Lanzhou, China
| | - Jianli Ma
- Department of Medicine, The people's Hospital of Lanzhou, Lanzhou, China
| |
Collapse
|
18
|
Abstract
CONTEXT.— Because granulomas are represented in almost every disease category, the number of clinically and pathologically important granulomatous pulmonary diseases is large. Their diagnosis by pathologists is particularly challenging because of their nonspecificity. A specific diagnosis can be achieved only when a granuloma-inciting agent(s) (eg, acid-fast bacilli, fungi, foreign bodies, etc) are identified microscopically or by culture; this does not occur in most cases. Furthermore, a specific diagnosis cannot be reached in a high percentage of cases. Although sarcoidosis and infectious diseases account for approximately half of pulmonary granulomatous diseases worldwide, there is significant geographic variation in their prevalence. OBJECTIVES.— To present updated information to serve as a guide to pathologic diagnosis of pulmonary granulomatous diseases, to address some commonly held misconceptions and to stress the importance of multidisciplinary coordination. Presentation of basic aspects of granulomas is followed by discussion of specific disease entities, such as tuberculous and nontuberculous Mycobacterial infections, fungal, bacterial, and parasitic infections, sarcoidosis, necrotizing sarcoid granulomatosis, berylliosis, hypersensitivity pneumonitis, hot tub lung, rheumatoid nodule, bronchocentric granulomatosis, aspirated, inhaled, and embolized foreign bodies, drug-induced granulomas, chronic granulomatous disease, common variable immunodeficiency, and granulomatous lesions associated with various types of cancer. DATA SOURCES.— Review of pertinent medical literature using the PubMed search engine and the author's practical experience. CONCLUSIONS.— Although the diagnosis of granulomatous lung diseases continues to present significant challenges to pathologists, the information presented in this review can be helpful in overcoming them. The importance of multidisciplinary coordination in cases where morphologic diagnosis is not possible cannot be overstated.
Collapse
Affiliation(s)
- Yale Rosen
- From the Department of Pathology, SUNY Downstate Health Sciences University, Brooklyn, New York
| |
Collapse
|
19
|
Zhou Y, Xiong H, Chen R, Wan L, Kong Y, Rao J, Xie Y, Huang C, Zhang XL. Aptamer Detection of Mycobaterium tuberculosis Mannose-Capped Lipoarabinomannan in Lesion Tissues for Tuberculosis Diagnosis. Front Cell Infect Microbiol 2021; 11:634915. [PMID: 33791241 PMCID: PMC8006938 DOI: 10.3389/fcimb.2021.634915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide. However, the diagnosis of TB, especially extrapulmonary TB (EPTB) diagnosis from lesion tissues, remains a challenge. Nucleic acid aptamers are analogous to antibodies and have advantages of easier modification, high specificity, and affinity. Mannose-capped lipoarabinomannan (ManLAM) is a unique surface lipoglycan component or constantly released from mycobacterium tuberculosis (M.tb) cell wall, which makes it a perfect candidate biomarker for TB diagnosis. Our present study aims to establish M.tb ManLAM aptamer-based immunohistochemistry (IHC) method for TB diagnosis. We performed TB diagnosis using 263 formalin-fixed paraffin-embedded tissue samples including 213 TB samples (pulmonary TB (PTB) and EPTB), and 8 samples from latent TB infection (LTBI) high risk subjects, and 42 samples from other non-TB patients with ManLAM aptamer-based IHC and routine laboratory TB diagnostic methods parallelly. The sensitivity and specificity of the ManLAM aptamer-based IHC were 86.38% and 92.86%, with much higher sensitivity than those of mycobacterial culture (9.66%) and acid-fast staining (AFS) (43.01%) and comparability to Interferon-gamma Release Assay (IGRA) (84.38%) and GeneXpert (79.31%). High agreement between ManLAM based-IHC and IGRA or GeneXpert for TB diagnosis were observed. Furthermore, ManLAM aptamer-based IHC combination with other routine TB laboratory diagnostic methods significantly increased the sensitivity up to 88.64%–97.92%. As our knowledge, this is the first report about aptamer-based IHC for disease diagnosis. Thus, ManLAM aptamer-based IHC has potentials for TB diagnosis, including PTB, and EPTB, and assists the diagnosis of LTBI with high effectiveness, feasibility, and easy production.
Collapse
Affiliation(s)
- Yuanyuan Zhou
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Huan Xiong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Rong Chen
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Lixia Wan
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Ying Kong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jianwei Rao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yan Xie
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Chaolin Huang
- Department of Pathology, Medical Department, Jin Yin-Tan Hospital, Wuhan, China.,Wuhan Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Wuhan, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, China.,Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| |
Collapse
|
20
|
[Histopathology of pulmonary tuberculosis]. DER PATHOLOGE 2021; 42:71-77. [PMID: 33475810 DOI: 10.1007/s00292-021-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Although typical histological findings of tuberculosis are well known, the diagnosis of nonmicrobiologically proven tuberculosis with the instruments available to pathology is challenging. Indeed, necrotizing epithelioid cell granulomatosis is typical for tuberculosis, but it is also seen in a number of different infectious or noninfectious lung diseases. The tools of microscopy and molecular pathology are suitable for confirming the diagnosis or paving the way to a differential diagnosis, but molecular pathology applied to formalin-fixated and paraffin-embedded material is limited. This should be openly communicated to the referring clinician. After interdisciplinary re-evaluation of the findings, an alternative solution to confirm the diagnosis must therefore be found if the additional examinations are negative.
Collapse
|
21
|
Stellmacher F, Perner S. [Overview: granulomatous diseases of the lung]. DER PATHOLOGE 2021; 42:64-70. [PMID: 33475808 DOI: 10.1007/s00292-020-00893-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 11/26/2022]
Abstract
The spectrum of pulmonary granulomatoses is wide and includes infectious and noninfectious entities, each with very different therapeutic consequences. The first step of histological examination discriminates between necrotizing and non-necrotizing granulomatosis. After this, an infectious cause of the granulomatosis has to be excluded by special histological stains and molecular-pathologic methods, if necessary. Diagnosis also includes clinical, radiological, and microbiological findings. The process of pathological examination should be standardized as described.
Collapse
Affiliation(s)
- Florian Stellmacher
- Pathologie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Parkallee 1-40, 23845, Borstel, Deutschland.
| | - Sven Perner
- Pathologie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Parkallee 1-40, 23845, Borstel, Deutschland
- Institut für Pathologie, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Lübeck, Deutschland
- Airwary Research Center North (ARCN), Deutsches Zentrum für Lungenforschung (DZL), Gießen, Deutschland
| |
Collapse
|
22
|
Jin W, Pan J, Miao Q, Ma Y, Zhang Y, Huang Y, Yao Y, Su Y, Wang Q, Wang M, Li B, Bao R, Gao X, Wu H, Hu B. Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1065. [PMID: 33145284 PMCID: PMC7575944 DOI: 10.21037/atm-20-2274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background To evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for active tuberculosis (TB). Methods We retrospectively collected 820 samples at Zhongshan Hospital, Fudan University in Shanghai, China, between 1 April 2017 and 31 March 2018. They were classified into TB cases (125, 15.2%) and NOT TB cases (695, 84.8%) according to the clinical diagnosis. Specimens were evaluated by a regular clinical microbiological assay and mNGS performed in parallel. Results Sixty-one confirmed TB cases and 64 clinical TB cases were included. The overall sensitivity of mNGS was 49.6% [95% confidence interval (95% CI), 40.6–58.6%], and the specificity was 98.3% (95% CI, 96.9–99.1%), with peak sensitivities of 88.9% (95% CI, 50.7–99.4%) for lung tissue, 55.0% (95% CI, 32.0–76.2%) for bronchoalveolar lavage fluid (BALF), and 50.0% (95% CI, 32.8–67.2%) for serous fluids. The overall sensitivity of mNGS was superior to that of the culture assay (35.2%, 95% CI, 27.0–44.3), but no superior sensitivity for sputum was observed in mNGS compared with the culture assay (mNGS: 52.3%, 95% CI, 31.1–72.6%; culture: 60.9%, 95% CI, 38.8–79.5%). In clinical TB cases, mNGS detected additional positive results (40.6%, 26/64). mNGS reduced the turnaround time from 2–6 weeks to 32–36 hours. Conclusions mNGS may be a promising technology for the early auxiliary diagnosis of active TB, especially sputum-negative pulmonary TB (PTB) and tuberculous serous effusion.
Collapse
Affiliation(s)
- Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yao Zhang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yumeng Yao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi Su
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingqing Wang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengran Wang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Li
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rong Bao
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Honglong Wu
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
23
|
Benign Solitary Pulmonary Necrotic Nodules: How Effectively Does Pathological Examination Explain the Cause? Can Respir J 2020; 2020:7850750. [PMID: 32695245 PMCID: PMC7361885 DOI: 10.1155/2020/7850750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022] Open
Abstract
Aims We investigated the histopathological features of solitary pulmonary necrotic nodules (NNs) of undetermined cause. We combined our findings with those obtained using other methods to determine how well the etiological factors were explained. Methods We screened patients who underwent surgery to treat solitary pulmonary granulomatous and nongranulomatous NNs of undetermined cause. The NN sizes and features of both the NNs and adjacent parenchyma were evaluated. Histochemical analyses included Ehrlich-Ziehl-Neelsen (EZN), Grocott, and Gram staining. Polymerase chain reaction (PCR) was used to detect tuberculous and nontuberculous mycobacteria, panfungal DNA, Nocardia, Francisella tularensis types A and B, and actinomycetes. Results The NNs were granulomatous in 78.9% and nongranulomatous in 21% of the 114 patients included. EZN staining or PCR was positive for Mycobacterium in 53.5% of all NNs: 62.2% of granulomatous and 20.8% of nongranulomatous NNs. We found a weak but significant correlation between granulomatous NNs and Bacillus positivity and a significant correlation between granulomas surrounding the NNs and the presence of multiple necroses. The NN etiology was determined via histopathological, histochemical, and PCR analyses in 57% of patients but remained undetermined in 42.9%. Conclusion The causes of both granulomatous and nongranulomatous NNs can be determined by pathological examination. Granulomatous necrosis and granulomas in the adjacent parenchyma are important for differential diagnosis. When both features are present, they strongly support a diagnosis of tuberculosis, even in the absence of bacilli.
Collapse
|
24
|
Host Immune Response and Novel Diagnostic Approach to NTM Infections. Int J Mol Sci 2020; 21:ijms21124351. [PMID: 32570978 PMCID: PMC7352966 DOI: 10.3390/ijms21124351] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
The incidence and prevalence of non-tuberculous mycobacteria (NTM) infections are steadily increasing worldwide, partially due to the increased incidence of immunocompromised conditions, such as the post-transplantation state. The importance of proper diagnosis and management of NTM infection has been recently recognized. Host immunological responses play integral roles in vulnerability to NTM infections, and may contribute to the onset of specific types of NTM infection. Furthermore, distinct NTM species are known to affect and attenuate these host immune responses in unique manners. Therefore, host immune responses must be understood with respect to each causative NTM species. Here, we review innate, cellular-mediated, and humoral immunity to NTM and provide perspectives on novel diagnostic approaches regarding each NTM species.
Collapse
|
25
|
Spectrum of imaging findings in pulmonary infections. Part 2: Fungal, mycobacterial, and parasitic. Pol J Radiol 2019; 84:e214-e223. [PMID: 31481993 PMCID: PMC6717951 DOI: 10.5114/pjr.2019.85813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/11/2019] [Indexed: 01/15/2023] Open
Abstract
Chest radiography is generally the first imaging modality used for the evaluation of pneumonia. It can establish the presence of pneumonia, determine its extent and location, and assess the response to treatment. Computed tomography is not used for the initial evaluation of pneumonia, but it may be used when the response to treatment is unusually slow. It helps to identify complications, detect any underlying chronic pulmonary disease, and characterise complex pneumonias. Although not diagnostic, certain imaging findings may suggest a particular microbial cause over others. Knowledge of whether pneumonia is community-acquired or nosocomial, as well as the age and immune status of the patient, can help to narrow the differential diagnoses. The purpose of this article is to briefly review the various pulmonary imaging manifestations of pathogenic organisms. This knowledge, along with the clinical history and laboratory investigations of the patient, may help to guide the treatment of pneumonia.
Collapse
|
26
|
Kobayashi T, Ford B, Sekar P. Mycobacterium avium- intracellulare (MAI) liver abscess mimicking liver metastasis in a patient with rheumatoid arthritis on adalimumab and methotrexate. BMJ Case Rep 2019; 12:12/6/e230912. [PMID: 31229967 DOI: 10.1136/bcr-2019-230912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Takaaki Kobayashi
- Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Bradley Ford
- Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Poorani Sekar
- Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| |
Collapse
|
27
|
Mukhopadhyay S, Mehta AC. Utility of Core Needle Biopsies and Transbronchial Biopsies for Diagnosing Nonneoplastic Lung Diseases. Arch Pathol Lab Med 2018; 142:1054-1068. [DOI: 10.5858/arpa.2017-0558-ra] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
Small lung biopsies (core needle biopsies and transbronchial biopsies) are the most common—and often the first—lung sample obtained when a radiologic abnormality is detected and tissue diagnosis is required. When a neoplastic diagnosis cannot be made but pathologic abnormalities are present, it is useful for pathologists to have a list (“menu”) of specific nonneoplastic diagnoses that can be made in these samples.
Objective.—
To provide surgical pathologists and pathology trainees with menus of nonneoplastic entities that can be diagnosed in small lung biopsies, and to briefly describe and illustrate some of these entities as they appear in small lung biopsies.
Data Sources.—
Published literature and the authors' experience with small lung biopsies for diagnosis of nonneoplastic lung diseases.
Conclusions.—
Although sampling error imposes some limitations, core needle biopsies and transbronchial lung biopsies can contribute to the diagnosis of a variety of nonneoplastic lung diseases and reduce the need for invasive surgical intervention.
Collapse
Affiliation(s)
| | - Atul C. Mehta
- From the Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute (Dr Mukhopadhyay) and the Department of Pulmonary Medicine, Respiratory Institute (Dr Mehta), Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
28
|
Saffari M, Jolandimi HA, Sehat M, Nejad NV, Hedayati M, Zamani M, Ghasemi A. Smear grading and the Mantoux skin test can be used to predict sputum smear conversion in patients suffering from tuberculosis. GMS HYGIENE AND INFECTION CONTROL 2017; 12:Doc12. [PMID: 28840092 PMCID: PMC5564005 DOI: 10.3205/dgkh000297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Purpose: Smear scores and induration sizes resulting from the PPD (tuberculin purified protein derivative) test can serve as indicators of whether a patient suffering from tuberculosis shows smear conversion or not. Methods: Using microbiological methods smear and sputum tests, patients diagnosed as infected with Mycobacterium tuberculosis between 2002 and 2015 were included in this study. All of the assumed factors that may have a role in smear conversion were studied, in addition to the prolongation of tuberculosis. Results: 398 of 512 patients fulfilled all the inclusion criteria and formed the basis of this study. 215 patients (54%) were females and 183 (46%) were males. The median age for both men and women was 36 years. We found a statistically significant difference between the size of induration resulting from the PPD skin test and the rate of non-conversion (P=0.002). Further univariate analysis also showed that smear grading and an induration size of ≥10 mm were independently associated with delayed smear conversion. Patients with cavitary lesions showed a higher rate of non-conversion after two months, which was not significant. We could not find any association between some of the variables, such as age, sex, weight, smoking, alcoholism, addictions, respiratory diseases, diabetes mellitus, alternative anti-TB treatment, and smear conversion. Conclusion: Intensified treatment and precautions against transmission should be especially considered for TB patients with high smear grading and an induration size of more than 10 mm.
Collapse
Affiliation(s)
- Mahmood Saffari
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hadis Alizadeh Jolandimi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mojtaba Sehat
- Trauma Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Nastarn Vali Nejad
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mehrdad Hedayati
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mahbobeh Zamani
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Amir Ghasemi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran.,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
| |
Collapse
|