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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024:e0045824. [PMID: 38916357 DOI: 10.1128/spectrum.00458-24] [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: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Burgel PR, Southern KW, Addy C, Battezzati A, Berry C, Bouchara JP, Brokaar E, Brown W, Azevedo P, Durieu I, Ekkelenkamp M, Finlayson F, Forton J, Gardecki J, Hodkova P, Hong G, Lowdon J, Madge S, Martin C, McKone E, Munck A, Ooi CY, Perrem L, Piper A, Prayle A, Ratjen F, Rosenfeld M, Sanders DB, Schwarz C, Taccetti G, Wainwright C, West NE, Wilschanski M, Bevan A, Castellani C, Drevinek P, Gartner S, Gramegna A, Lammertyn E, Landau EEC, Plant BJ, Smyth AR, van Koningsbruggen-Rietschel S, Middleton PG. Standards for the care of people with cystic fibrosis (CF); recognising and addressing CF health issues. J Cyst Fibros 2024; 23:187-202. [PMID: 38233247 DOI: 10.1016/j.jcf.2024.01.005] [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: 11/06/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
This is the third in a series of four papers updating the European Cystic Fibrosis Society (ECFS) standards for the care of people with CF. This paper focuses on recognising and addressing CF health issues. The guidance was produced with wide stakeholder engagement, including people from the CF community, using an evidence-based framework. Authors contributed sections, and summary statements which were reviewed by a Delphi consultation. Monitoring and treating airway infection, inflammation and pulmonary exacerbations remains important, despite the widespread availability of CFTR modulators and their accompanying health improvements. Extrapulmonary CF-specific health issues persist, such as diabetes, liver disease, bone disease, stones and other renal issues, and intestinal obstruction. These health issues require multidisciplinary care with input from the relevant specialists. Cancer is more common in people with CF compared to the general population, and requires regular screening. The CF life journey requires mental and emotional adaptation to psychosocial and physical challenges, with support from the CF team and the CF psychologist. This is particularly important when life gets challenging, with disease progression requiring increased treatments, breathing support and potentially transplantation. Planning for end of life remains a necessary aspect of care and should be discussed openly, honestly, with sensitivity and compassion for the person with CF and their family. CF teams should proactively recognise and address CF-specific health issues, and support mental and emotional wellbeing while accompanying people with CF and their families on their life journey.
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Affiliation(s)
- Pierre-Régis Burgel
- Respiratory Medicine and Cystic Fibrosis National Reference Center, Cochin Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Institut Cochin, Inserm U1016, Université Paris-Cité, Paris, France
| | - Kevin W Southern
- Department of Women's and Children's Health, Institute in the Park, Alder Hey Children's Hospital, University of Liverpool, Eaton Road, Liverpool L12 2AP, UK.
| | - Charlotte Addy
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff and Vale University Health Board, Cardiff, UK
| | - Alberto Battezzati
- Clinical Nutrition Unit, Department of Endocrine and Metabolic Medicine, IRCCS Istituto Auxologico Italiano, and ICANS-DIS, Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Claire Berry
- Department of Nutrition and Dietetics, Alder Hey Children's NHS Trust, Liverpool, UK
| | - Jean-Philippe Bouchara
- University of Brest, Fungal Respiratory Infections Research Unit, SFR ICAT, University of Angers, Angers, France
| | - Edwin Brokaar
- Department of Pharmacy, Haga Teaching Hospital, The Hague, the Netherlands
| | - Whitney Brown
- Cystic Fibrosis Foundation, Inova Fairfax Hospital, Bethesda, Maryland, USA, Falls Church, VA, USA
| | - Pilar Azevedo
- Cystic Fibrosis Reference Centre-Centro, Hospitalar Universitário Lisboa Norte, Portugal
| | - Isabelle Durieu
- Cystic Fibrosis Reference Center (Constitutif), Service de médecine interne et de pathologie vasculaire, Hospices Civils de Lyon, Hôpital Lyon Sud, RESearch on HealthcAre PErformance (RESHAPE), INSERM U1290, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69373 Lyon Cedex 08, France; ERN-Lung Cystic Fibrosis Network, Frankfurt, Germany
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Felicity Finlayson
- Department of Respiratory Medicine, The Alfred Hospital, Melbourne, Australia
| | | | - Johanna Gardecki
- CF Centre at Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pavla Hodkova
- CF Center at University Hospital Motol, Prague, Czech Republic
| | - Gina Hong
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jacqueline Lowdon
- Clinical Specialist Paediatric Cystic Fibrosis Dietitian, Leeds Children's Hospital, UK
| | - Su Madge
- Royal Brompton Hospital, Part of Guys and StThomas's Hospital, London, UK
| | - Clémence Martin
- Institut Cochin, Inserm U1016, Université Paris-Cité and National Reference Center for Cystic Fibrosis, Hôpital Cochin AP-HP, ERN-Lung CF Network, Paris 75014, France
| | - Edward McKone
- St.Vincent's University Hospital and University College Dublin School of Medicine, Dublin, Ireland
| | - Anne Munck
- Hospital Necker Enfants-Malades, AP-HP, CF Centre, Université Paris Descartes, Paris, France
| | - Chee Y Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine & Health, Department of Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Lucy Perrem
- Department of Respiratory Medicine, Children's Health Ireland, Dublin, Ireland
| | - Amanda Piper
- Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Andrew Prayle
- Child Health, Lifespan and Population Health & Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Felix Ratjen
- Division of Respiratory Medicine, Department of Pediatrics and Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Margaret Rosenfeld
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Don B Sanders
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Carsten Schwarz
- Division Cystic Fibrosis, CF Center, Clinic Westbrandenburg, HMU-Health and Medical University, Potsdam, Germany
| | - Giovanni Taccetti
- Meyer Children's Hospital IRCCS, Cystic Fibrosis Regional Reference Centre, Italy
| | | | - Natalie E West
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael Wilschanski
- Pediatric Gastroenterology Unit, CF Center, Hadassah Medical Center, Jerusalem, Israel
| | - Amanda Bevan
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Carlo Castellani
- IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, Genova 16147, Italy
| | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Silvia Gartner
- Cystic Fibrosis Unit and Pediatric Pulmonology, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, Respiratory Unit and Adult Cystic Fibrosis Center, Università degli Studi di Milano, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Elise Lammertyn
- Cystic Fibrosis Europe, Brussels, Belgium and the Belgian CF Association, Brussels, Belgium
| | - Eddie Edwina C Landau
- The Graub CF Center, Pulmonary Institute, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Barry J Plant
- Cork Centre for Cystic Fibrosis (3CF), Cork University Hospital, University College Cork, Ireland
| | - Alan R Smyth
- School of Medicine, Dentistry and Biomedical Sciences, Belfast and NIHR Nottingham Biomedical Research Centre, Queens University Belfast, Nottingham, UK
| | | | - Peter G Middleton
- Westmead Clinical School, Department Respiratory & Sleep Medicine, Westmead Hospital, University of Sydney and CITRICA, Westmead, Australia
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Zaporojan N, Negrean RA, Hodișan R, Zaporojan C, Csep A, Zaha DC. Evolution of Laboratory Diagnosis of Tuberculosis. Clin Pract 2024; 14:388-416. [PMID: 38525709 PMCID: PMC10961697 DOI: 10.3390/clinpract14020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
Tuberculosis (TB) is an infectious disease of global public health importance caused by the Mycobacterium tuberculosis complex. Despite advances in diagnosis and treatment, this disease has worsened with the emergence of multidrug-resistant strains of tuberculosis. We aim to present and review the history, progress, and future directions in the diagnosis of tuberculosis by evaluating the current methods of laboratory diagnosis of tuberculosis, with a special emphasis on microscopic examination and cultivation on solid and liquid media, as well as an approach to molecular assays. The microscopic method, although widely used, has its limitations, and the use and evaluation of other techniques are essential for a complete and accurate diagnosis. Bacterial cultures, both in solid and liquid media, are essential methods in the diagnosis of TB. Culture on a solid medium provides specificity and accuracy, while culture on a liquid medium brings rapidity and increased sensitivity. Molecular tests such as LPA and Xpert MTB/RIF have been found to offer significant benefits in the rapid and accurate diagnosis of TB, including drug-resistant forms. These tests allow the identification of resistance mutations and provide essential information for choosing the right treatment. We conclude that combined diagnostic methods, using several techniques and approaches, provide the best result in the laboratory diagnosis of TB. Improving the quality and accessibility of tests, as well as the implementation of advanced technologies, is essential to help improve the sensitivity, efficiency, and accuracy of TB diagnosis.
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Affiliation(s)
- Natalia Zaporojan
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
| | - Rodica Anamaria Negrean
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Ramona Hodișan
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Claudiu Zaporojan
- Emergency County Hospital Bihor, Str. Republicii 37, 410167 Oradea, Romania
| | - Andrei Csep
- Department of Psycho-Neurosciences and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Dana Carmen Zaha
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
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Liu Q, Xu F, Liu Q, Liu X. Comparative analysis of five etiological detecting techniques for the positive rates in the diagnosis of tuberculous granuloma. J Clin Tuberc Other Mycobact Dis 2023; 32:100378. [PMID: 37293271 PMCID: PMC10245093 DOI: 10.1016/j.jctube.2023.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Purpose To examine the relationship between the positive rate and types of necrosis in pathological examinations of tuberculosis granulomas with necrosis, to improve the detection rate of positive cases. Methods Specimens from 381 patients were collected in Wuhan Pulmonary Hospital from Jan 2022 to Feb 2023. The samples were examined using various methods such as AFB smear microscopy, mycobacterial culture, PCR, SAT-TB, and X-pert MTB/RIF rapid molecular detection. Result There were 3 types of necrosis. Including 270 cases of caseous necrosis, 30 cases of coagulation necrosis, and 76 cases of an abscess. Five cases were non-necrotizing granulomas.In the pathological specimen testing for tuberculosis, five detection techniques were used and their positive rates detected in descending order were X-pert, TBDNA, SAT-TB, tuberculosis culture, AFB. Comparison between different examinations in the group: X-pert had the highest positive rate in each group, and it was significantly higher than TBDNA (P < 0.01) in caseous necrosis specimens. Compared with the same examination between the groups, the detection rates of X-pert and TBDNA in abscess and caseous necrosis specimens were significantly higher than in coagulation necrosis specimens (P < 0.01). Conclusion The positive rates of the five etiological detection techniques in tuberculous granuloma with different types of necrosis were quite different. The specimens of caseous necrosis or abscess could be selected for detection, and X-pert had the highest positive rate.
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Affiliation(s)
- Qibin Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Feng Xu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng, Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Qiliang Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng, Road, Qiaokou District, Wuhan City, Hubei Province, China
| | - Xiaoyu Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China
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Yu Q, Wang Y, Gao Z, Yang H, Liu S, Tan J, Yang L. DNA microarray chip assay in new use: early diagnostic value in cutaneous mycobacterial infection. Front Cell Infect Microbiol 2023; 13:1183078. [PMID: 37457951 PMCID: PMC10349391 DOI: 10.3389/fcimb.2023.1183078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The clinical practicability of DNA microarray chip in detecting the presence of mycobacterial species/isolates directly in the skin tissues has not been evaluated, nor the efficacy of DNA microarray chip as a novel diagnostic tool for the early diagnosis of cutaneous mycobacterial infections is known. Methods The present study analyzed the incidence of cutaneous mycobacterial infections in Shanghai and explored the efficacy of a novel DNA microarray chip assay for the clinical diagnosis of the disease from skin tissue specimens compared to traditional detection methods. A total of 60 participants fulfilling the defined diagnostic criteria and confirmed positive for cutaneous mycobacterial infections from 2019 to 2021 were enrolled in the study. Subsequent to recording the participants' medical history and clinical characteristics, the skin tissue specimens were collected for analyses. The specimens underwent histopathological analyses, skin tissue culture, and DNA microarray chip assay. Results Increased incidence of cutaneous mycobacterial infection was detected from 2019 to 2021. The most common infecting pathogen was M. marinum followed by M. abscessus. The sensitivity, specificity and accuracy of the skin tissue culture method were 70%, 100% and 76.62%, respectively, while that of the DNA microarray chip assay were 91.67%, 100% and 93.51%, respectively. The sensitivity and accuracy of the DNA microarray chip assay were significantly higher than those of the skin tissue culture method. The positive likelihood and diagnostic odds ratio were >10 and >1, respectively for both the methods. The negative likelihood ratio was significantly higher (30% vs 8.33%) and the Youden's index was significantly lower (70.00% vs 91.67%) in the skin culture method compared to that of the DNA microarray chip assay. There was a significant association of false negative results with a history of antibiotic use in the skin tissue culture method. Discussion Given the increasing incidence of cutaneous mycobacterial infections, early diagnosis remains a prime clinical focus. The DNA microarray chip assay provides a simple, rapid, high-throughput, and reliable method for the diagnosis of cutaneous mycobacterial infections with potential for clinical application.
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Xiao YH, Liu MF, Wu H, Xu DR, Zhao R. Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital. Infect Drug Resist 2023; 16:1815-1828. [PMID: 37016633 PMCID: PMC10066896 DOI: 10.2147/idr.s401707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice. Patients and Methods In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard. Results There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%). Conclusion Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.
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Affiliation(s)
- Yang-Hua Xiao
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Mei-Fang Liu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Hongwen Wu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Department of Medical Instruments, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - De-Rong Xu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Correspondence: De-Rong Xu; Rui Zhao, Email ;
| | - Rui Zhao
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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Abstract
Nontuberculous mycobacteria (NTM) are important pathogens, with a longitudinal prevalence of up to 20% within the cystic fibrosis (CF) population. Diagnosis of NTM pulmonary disease in people with CF (pwCF) is challenging, as a majority have NTM infection that is transient or indolent, without evidence of clinical consequence. In addition, the radiographic and clinical manifestations of chronic coinfections with typical CF pathogens can overlap those of NTM, making diagnosis difficult. Comprehensive care of pwCF must be optimized to assess the true clinical impact of NTM and to improve response to treatment. Treatment requires prolonged, multidrug therapy that varies depending on NTM species, resistance pattern, and extent of disease. With a widespread use of highly effective modulator therapy (HEMT), clinical signs and symptoms of NTM disease may be less apparent, and sensitivity of sputum cultures further reduced. The development of a disease-specific approach to the diagnosis and treatment of NTM infection in pwCF is a research priority, as a lifelong strategy is needed for this high-risk population.
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Pena MT, Lahiri R, Ebenezer GJ, Wheat SW, Figarola J, Truman RW, Adams LB. The Armadillo as a Model for Leprosy Nerve Function Impairment: Preventative and Therapeutic Interventions. Front Med (Lausanne) 2022; 9:879097. [PMID: 35814754 PMCID: PMC9259846 DOI: 10.3389/fmed.2022.879097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
Mycobacterium leprae infection of peripheral nerves and the subsequent nerve function impairment (NFI), especially in response to reactional episodes, are hallmarks of leprosy. Improved treatments for M. leprae-induced nerve injury are needed, as most if not all of the disability and stigma associated with leprosy arises from the direct or indirect effects of NFI. Nine-banded armadillos (Dasypus novemcinctus), like humans, exhibit the full clinical spectrum of leprosy and extensive involvement of the peripheral nerves. In this study, state-of-the-art technology was used to compare nerve function between uninfected and M. leprae-infected armadillos. Motor nerve conduction velocity (MNCV) and compound muscle action potential (cMAP), which measure changes in the rate of impulse conduction velocity and amplitude, revealed a progression of impairment that was directly correlated with the duration of M. leprae infection and enabled development of an objective nerve impairment scoring system. Ultrasonography accompanied by color Doppler imaging detected enlargement of the M. leprae-infected nerves and increased vascularity, possibly due to inflammation. Assessment of epidermal nerve fiber density (ENFD), which shows a length-dependent innervation in armadillos that is similar to humans, identified small fiber degeneration early after M. leprae infection. Staining for neuromuscular junction (NMJ) integrity, which is an indicator of signal transduction efficiency into skeletal muscle, discerned a markedly lower number and structural integrity of NMJ in M. leprae-infected armadillo footpads. These tools for assessing nerve injury were used to monitor the effects of intervention therapy. Two potential neuro-protective drugs, ethoxyquin (EQ) and 4-aminopyridine (4-AP), were tested for their ability to ameliorate peripheral nerve injury in M. leprae-infected armadillos. 4-AP treatment improved MNCV, cMAP, and EFND compared to untreated animals, while EQ had less effect. These results support the armadillo as a model for M. leprae-induced peripheral nerve injury that can provide insights toward the understanding of NFI progression and contribute to the preclinical investigation of the safety and efficacy of neuro-preventive and neuro-therapeutic interventions for leprosy.
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Affiliation(s)
- Maria Teresa Pena
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen’s Disease Program, Baton Rouge, LA, United States
- *Correspondence: Maria Teresa Pena,
| | - Ramanuj Lahiri
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen’s Disease Program, Baton Rouge, LA, United States
| | - Gigi J. Ebenezer
- Department of Neurology, John Hopkins University, Baltimore, MD, United States
| | - Stephen W. Wheat
- Department of Neurology-Guest Lecturer, Baylor College of Medicine, Houston, TX, United States
| | - John Figarola
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen’s Disease Program, Baton Rouge, LA, United States
| | - Richard W. Truman
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen’s Disease Program, Baton Rouge, LA, United States
| | - Linda B. Adams
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen’s Disease Program, Baton Rouge, LA, United States
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Zhou Z, Pena M, van Hooij A, Pierneef L, de Jong D, Stevenson R, Walley R, Corstjens PLAM, Truman R, Adams L, Geluk A. Detection and Monitoring of Mycobacterium leprae Infection in Nine Banded Armadillos ( Dasypus novemcinctus) Using a Quantitative Rapid Test. Front Microbiol 2021; 12:763289. [PMID: 34777319 PMCID: PMC8581735 DOI: 10.3389/fmicb.2021.763289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Leprosy is an infectious disease caused by Mycobacterium leprae with tropism for skin and peripheral nerves. Incessant transmission in endemic areas is still impeding elimination of leprosy. Although detection of M. leprae infection remains a challenge in asymptomatic individuals, the presence of antibodies specific for phenolglycolipid-I (PGL-I) correlate with bacterial load. Therefore, serosurveillance utilizing field-friendly tests detecting anti-PGL-I antibodies, can be applied to identify those who may transmit bacteria and to study (reduction of) M. leprae transmission. However, serology based on antibody detection cannot discriminate between past and present M. leprae infection in humans, nor can it detect individuals carrying low bacillary loads. In humans, anti-PGL-I IgM levels are long-lasting and usually detected in more individuals than anti-PGL-I IgG levels. Inherent to the characteristically long incubation time of leprosy, IgM/IgG relations (antibody kinetics) in leprosy patients and infected individuals are not completely clear. To investigate the antibody response directly after infection, we have measured antibody levels by ELISA, in longitudinal samples of experimentally M. leprae infected, susceptible nine-banded armadillos (Dasypus novemcinctus). In addition, we assessed the user- and field-friendly, low-cost lateral flow assay (LFA) utilizing upconverting reporter particles (UCP), developed for quantitative detection of human anti-PGL-I IgM (UCP-LFA), to detect treatment- or vaccination-induced changes in viable bacterial load. Our results show that serum levels of anti-PGL-I IgM, and to a lesser extent IgG, significantly increase soon after experimental M. leprae infection in armadillos. In view of leprosy phenotypes in armadillos, this animal model can provide useful insight into antibody kinetics in early infection in the various spectral forms of human leprosy. The UCP-LFA for quantitative detection of anti-PGL-I IgM allows monitoring the efficacy of vaccination and rifampin-treatment in the armadillo leprosy model, thereby providing a convenient tool to evaluate the effects of drugs and vaccines and new diagnostics.
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Affiliation(s)
- Zijie Zhou
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Maria Pena
- U.S. Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen Disease Programme (NHDP), Baton Rouge, LA, United States
| | - Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Louise Pierneef
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Danielle de Jong
- Department Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Roena Stevenson
- U.S. Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen Disease Programme (NHDP), Baton Rouge, LA, United States
| | - Rachel Walley
- U.S. Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen Disease Programme (NHDP), Baton Rouge, LA, United States
| | - Paul L A M Corstjens
- Department Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Richard Truman
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Linda Adams
- U.S. Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen Disease Programme (NHDP), Baton Rouge, LA, United States
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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