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Walker J, Edwards WS, Hall NM, Pappas PG. Challenges in management of invasive fungal infections in stem cell transplant. Transpl Infect Dis 2023; 25 Suppl 1:e14175. [PMID: 37864814 DOI: 10.1111/tid.14175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/23/2023]
Abstract
Invasive fungal infections cause significant morbidity and mortality in hematopoietic stem cell transplant recipients. In order to minimize these infections, prophylaxis has become routine, although the agents used have changed over time. This presents new challenges as we consider an approach to breakthrough infections and recognize the epidemiologic shift toward isolates with higher rates of drug resistance. This review outlines the management of the most common pathogens (Candida, Aspergillus, Mucorales) as well as rarer pathogens that have higher rates of resistance (Trichosporon, Fusarium, Scedosporium, and Lomentospora). We discuss potential approaches to proven or possible breakthrough infections with yeast and pulmonary mold disease. Finally, we outline the role for combination therapy and newer antifungals, acknowledging current knowledge gaps and areas for future exploration.
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Affiliation(s)
- Jeremey Walker
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - W Seth Edwards
- Department of Pharmacy, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nicole M Hall
- Department of Pharmacy, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Peter G Pappas
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Escamilla JE, January SE, Vazquez Guillamet R. Diagnosis and Treatment of Fungal Infections in Lung Transplant Recipients. Pathogens 2023; 12:pathogens12050694. [PMID: 37242364 DOI: 10.3390/pathogens12050694] [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: 03/25/2023] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Fungal infections are a significant source of morbidity in the lung transplant population via direct allograft damage and predisposing patients to the development of chronic lung allograft dysfunction. Prompt diagnosis and treatment are imperative to limit allograft damage. This review article discusses incidence, risk factors, and symptoms with a specific focus on diagnostic and treatment strategies in the lung transplant population for fungal infections caused by Aspergillus, Candida, Coccidioides, Histoplasma, Blastomyces, Scedosporium/Lomentospora, Fusarium, and Pneumocystis jirovecii. Evidence for the use of newer triazole and inhaled antifungals to treat isolated pulmonary fungal infections in lung transplant recipients is also discussed.
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Affiliation(s)
- Jesus E Escamilla
- Department of Pharmacy, Barnes-Jewish Hospital, Saint Louis, MO 63110, USA
| | - Spenser E January
- Department of Pharmacy, Barnes-Jewish Hospital, Saint Louis, MO 63110, USA
| | - Rodrigo Vazquez Guillamet
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Rodrigo Vazquez Guillamet, 4921 Parkview Place, Saint Louis, MO 63110, USA
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Zhao M, Yue R, Wu X, Gao Z, He M, Pan L. The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients. Front Cell Infect Microbiol 2022; 12:1026739. [PMID: 36389151 PMCID: PMC9647189 DOI: 10.3389/fcimb.2022.1026739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring. Method 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People’s Hospital. The clinical performances of mNGS for P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods. Results We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for P. jirovecii in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups. Conclusions An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of P. jirovecii is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.
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Affiliation(s)
- Mengyi Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Xiaoxiao Wu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
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Zhang J, Gao L, Zhu C, Jin J, Song C, Dong H, Li Z, Wang Z, Chen Y, Yang Z, Tan Y, Wang L. Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients. Front Cell Infect Microbiol 2022; 12:1021320. [PMID: 36237436 PMCID: PMC9551279 DOI: 10.3389/fcimb.2022.1021320] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.
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Affiliation(s)
- Jing Zhang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lin Gao
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chi Zhu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Jiajia Jin
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Hang Dong
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zheng Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yubao Chen
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenhua Yang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yan Tan
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Yan Tan, ; Li Wang,
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- *Correspondence: Yan Tan, ; Li Wang,
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Wang D, Wang W, Ding Y, Tang M, Zhang L, Chen J, You H. Metagenomic Next-Generation Sequencing Successfully Detects Pulmonary Infectious Pathogens in Children With Hematologic Malignancy. Front Cell Infect Microbiol 2022; 12:899028. [PMID: 35837477 PMCID: PMC9273861 DOI: 10.3389/fcimb.2022.899028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Pulmonary infection is a leading cause of mortality in pediatric patients with hematologic malignancy (HM). In clinical settings, pulmonary pathogens are frequently undetectable, and empiric therapies may be costly, ineffective and lead to poor outcomes in this vulnerable population. Metagenomic next-generation sequencing (mNGS) enhances pathogen detection, but data on its application in pediatric patients with HM and pulmonary infections are scarce. Methods We retrospectively reviewed 55 pediatric patients with HM and pulmonary infection who were performed mNGS on bronchoalveolar lavage fluid from January 2020 to October 2021. The performances of mNGS methods and conventional microbiological methods in pathogenic diagnosis and subsequently antibiotic adjustment were investigated. Results A definite or probable microbial etiology of pulmonary infection was established for 50 of the 55 patients (90.9%) when mNGS was combined with conventional microbiological tests. The positive rate was 87.3% (48 of 55 patients) for mNGS versus 34.5% (19 of 55 patients) with conventional microbiological methods (P < 0.001). Bacteria, viruses and fungi were detected in 17/55 (30.9%), 25/55 (45.5%) and 19/55 (34.5%) cases using mNGS, respectively. Furthermore, 17 patients (30.9%) were identified as pulmonary mixed infections. Among the 50 pathogen-positive cases, 38% (19/50) were not completely pathogen-covered by empirical antibiotics and all of them were accordingly made an antibiotic adjustment. In the present study, the 30-day mortality rate was 7.3%. Conclusion mNGS is a valuable diagnostic tool to determine the etiology and appropriate treatment in pediatric patients with HM and pulmonary infection. In these vulnerable children with HM, pulmonary infections are life-threatening, so we recommend that mNGS should be considered as a front-line diagnostic test.
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Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance. Microbiol Spectr 2022; 10:e0250221. [PMID: 35171007 PMCID: PMC8849087 DOI: 10.1128/spectrum.02502-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) have high morbidity and mortality rates. However, traditional etiological detection methods have not been able to meet the needs for the clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for the diagnosis and treatment of LRTIs; however, little is known about how to interpret the application of mNGS results in LRTIs. In this study, lower respiratory tract specimens from 46 patients with suspected LRTIs were tested simultaneously using conventional microbiological detection methods and mNGS. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], genomic coverage, and relative abundance of the organism in predicting the true-positive pathogenic bacteria. True-positive viruses were identified according to the lg(RPKM) threshold of bacteria. We also evaluated the ability to predict drug resistance genes using mNGS. Compared to that using conventional detection methods, the false-positive detection rate of pathogenic bacteria was significantly higher using mNGS. It was concluded from the ROC curves that the lg(RPKM) and genomic coverage contributed to the identification of pathogenic bacteria, with the performance of lg(RPKM) being the best (area under the curve [AUC] = 0.99). The corresponding lg(RPKM) threshold for identifying the pathogenic bacteria was −1.35. Thirty-five strains of true-positive virus were identified based on the lg(RPKM) threshold of bacteria, with the detection of human gammaherpesvirus 4 being the highest and prone to coinfection with Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Antimicrobial susceptibility tests (AST) revealed the resistance of bacteria containing drug resistance genes (detected by mNGS). However, the drug resistance genes of some multidrug-resistant bacteria were not detected. As an emerging technology, mNGS has shown many advantages for the unbiased etiological detection and the prediction of antibiotic resistance. However, a correct understanding of mNGS results is a prerequisite for its clinical application, especially for LRTIs. IMPORTANCE LRTIs are caused by hundreds of pathogens, and they have become a great threat to human health due to the limitations of traditional etiological detection methods. As an unbiased approach to detect pathogens, mNGS overcomes such etiological diagnostic challenges. However, there is no unified standard on how to use mNGS indicators (the sequencing reads, genomic coverage, and relative abundance of each organism) to distinguish between pathogens and colonizing microorganisms or contaminant microorganisms. Here, we selected the mNGS indicator with the best identification performance and established a cutoff value for the identification of pathogens in LRTIs using ROC curves. In addition, we also evaluated the accuracy of antibiotic resistance prediction using mNGS.
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Zong F, Gan C, Wang Y, Su D, Deng M, Xiao N, Zhang Z, Zhou D, Gao B, Yang H. Exposure to aerosolized staphylococcal enterotoxin B potentiated by lipopolysaccharide modifies lung transcriptomes and results in lung injury in the mouse model. J Appl Toxicol 2022; 42:1205-1217. [DOI: 10.1002/jat.4289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Fuliang Zong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Changjiao Gan
- Tianjin Key Laboratory of Artificial Cell, Tianjin Institute of Hepatobiliary Disease Nankai University Affiliated Third Center Hospital Tianjin China
| | - Yifeng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Duo Su
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Mengyun Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Nan Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Zhipeng Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Bo Gao
- Institute of Military Cognition and Brain Sciences Beijing China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing China
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The Application of Metagenomic Next-Generation Sequencing in Detection of Pathogen in Bronchoalveolar Lavage Fluid and Sputum Samples of Patients with Pulmonary Infection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:7238495. [PMID: 34790254 PMCID: PMC8592753 DOI: 10.1155/2021/7238495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/12/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022]
Abstract
Objective To uncover the application value of metagenomic next-generation sequencing (mNGS) in the detection of pathogen in bronchoalveolar lavage fluid (BALF) and sputum samples. Methods Totally, 32 patients with pulmonary infection were included. Pathogens in BALF and sputum samples were tested simultaneously by routine microbial culture and mNGS. Main infected pathogens (bacteria, fungi, and viruses) and their distribution in BALF and sputum samples were analyzed. Moreover, the diagnostic performance of mNGS in paired BALF and sputum samples was assessed. Results The pathogen culture results were positive in 9 patients and negative in 13 patients. No statistical differences were recorded on the sensitivity (78.94% vs. 63.15%, p = 0.283) and specificity (62.50% vs. 75.00%, p = 0.375) of mNGS diagnosis in bacteria and fungus in two types of samples. As shown in mNGS detection, 10 patients' two samples were both positive, 13 patients' two samples were both negative, 7 patients were only positive in BALF samples, and 2 patients' sputum samples were positive. Main viruses mNGS detected were EB virus, human adenovirus 5, herpes simplex virus type 1, and human cytomegalovirus. Kappa consensus analysis indicated that mNGS showed significant consistency in detecting pathogens in two samples, no matter bacteria (p < 0.001), fungi (p = 0.026), or viruses (p = 0.008). Conclusion mNGS showed no statistical differences in sensitivity and specificity of pathogen detection in BALF and sputum samples. Under certain conditions, sputum samples might be more suitable for pathogen detection because of invasiveness of BALF samples.
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Astashchanka A, Ryan J, Lin E, Nokes B, Jamieson C, Kligerman S, Malhotra A, Mandel J, Joshua J. Pulmonary Complications in Hematopoietic Stem Cell Transplant Recipients-A Clinician Primer. J Clin Med 2021; 10:3227. [PMID: 34362012 PMCID: PMC8348211 DOI: 10.3390/jcm10153227] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Hematopoietic stem cell transplants (HSCT) are becoming more widespread as a result of optimization of conditioning regimens and prevention of short-term complications with prophylactic antibiotics and antifungals. However, pulmonary complications post-HSCT remain a leading cause of morbidity and mortality and are a challenge to clinicians in both diagnosis and treatment. This comprehensive review provides a primer for non-pulmonary healthcare providers, synthesizing the current evidence behind common infectious and non-infectious post-transplant pulmonary complications based on time (peri-engraftment, early post-transplantation, and late post-transplantation). Utilizing the combination of timing of presentation, clinical symptoms, histopathology, and radiographic findings should increase rates of early diagnosis, treatment, and prognostication of these severe illness states.
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Affiliation(s)
- Anna Astashchanka
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
| | - Joseph Ryan
- Division of Hematology & Oncology, Scripps Clinic, La Jolla, CA 92037, USA;
| | - Erica Lin
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
| | - Brandon Nokes
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
| | - Catriona Jamieson
- Sanford Stem Cell Clinical Center, Moores Cancer Center, Department of Medicine, Division of Regenerative Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Seth Kligerman
- Division of Cardiothoracic Radiology, University of California San Diego, La Jolla, CA 92121, USA;
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
| | - Jess Mandel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
| | - Jisha Joshua
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA 92121, USA; (A.A.); (E.L.); (B.N.); (A.M.); (J.M.)
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Herity LB, Cruz OADL, Aziz MT. Evaluation of a primary antifungal prophylaxis protocol for preventing invasive mold infections after allogeneic hematopoietic stem cell transplantation. J Oncol Pharm Pract 2021; 28:794-804. [PMID: 33906508 DOI: 10.1177/10781552211011221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Invasive mold infections contribute to morbidity and mortality in patients undergoing allogeneic hematopoietic stem cell transplantation. The optimal strategy for primary antifungal prophylaxis in this patient population remains uncertain. METHODS Medical records of patients who underwent allogeneic hematopoietic stem cell transplantation between 1 January 2013 and 31 December 2017 were retrospectively reviewed. Adult patients were included if they received micafungin followed by fluconazole, with the option to escalate to voriconazole, for antifungal prophylaxis. The primary outcome was the incidence rate of proven or probable invasive mold infection. Secondary outcomes were time to invasive mold infection diagnosis, invasive mold infection-related mortality, and risk factors associated with invasive mold infection. RESULTS Two hundred patients were included in the study, a majority of whom underwent matched unrelated (46%) or matched related (33%) donor transplants. The incidence rate of proven or probable invasive mold infection was 18.4 cases per 100 patient-years, with a one-year cumulative incidence of 14%. Median time to proven or probable invasive mold infection was 94 days post-transplant (IQR 26-178), with invasive mold infection-related mortality occurring in 18 (64%) of 28 patients diagnosed with invasive mold infection. Comparison of invasive mold infection-free survival by potential risk factors failed to show any significant differences. CONCLUSIONS In this real-life cohort of allogeneic hematopoietic stem cell transplantation recipients, the incidence of proven or probable invasive mold infection was higher than expected based on previous literature. In the absence of standard guidance on anti-mold prophylaxis in this patient population and given that unique risk factors for invasive mold infection may differ between institutions, it is essential that centers performing allogeneic hematopoietic stem cell transplantation routinely monitor their antifungal prophylaxis strategies for effectiveness.
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Affiliation(s)
- Leah B Herity
- Department of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, NY, USA.,Department of Pharmacy Services, Virginia Commonwealth University Health System, Richmond, VA, USA
| | - Oveimar A De la Cruz
- Department of Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Division of Infectious Diseases, Department of Internal Medicine, Virginia Commonwealth University Health System, Richmond, VA, USA
| | - May T Aziz
- Department of Pharmacy Services, Virginia Commonwealth University Health System, Richmond, VA, USA
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Pulmonary Manifestations of Immunodeficiency and Immunosuppressive Diseases Other than Human Immunodeficiency Virus. Pediatr Clin North Am 2021; 68:103-130. [PMID: 33228927 DOI: 10.1016/j.pcl.2020.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Immune deficiencies may alter normal lung function and protective mechanisms, resulting in a myriad of pulmonary manifestations. Primary immunodeficiencies involve multiple branches of the immune system, and defects may predispose to recurrent upper and lower respiratory infections by common pathogens; opportunistic infections; and autoimmune, inflammatory, and malignant processes that may result in interstitial pneumonias. Secondary immunodeficiencies may result from neoplasms or their treatment, organ transplant and immunosuppression, and from autoimmune diseases and their treatments. Primary and secondary immunodeficiencies and their pulmonary manifestations may be difficult to diagnose and treat. A multidisciplinary approach to evaluation is essential.
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The Added Value of [ 18F]FDG PET/CT in the Management of Invasive Fungal Infections. Diagnostics (Basel) 2021; 11:diagnostics11010137. [PMID: 33477267 PMCID: PMC7830875 DOI: 10.3390/diagnostics11010137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/06/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
Anatomy-based imaging methods are the usual imaging methods used in assessing invasive fungal infections (IFIs). [18F]FDG PET/CT has also been used in the evaluation of IFIs. We assessed the added value of [18F]FDG PET/CT when added to the most frequently used anatomy-based studies in the evaluation of IFIs. The study was conducted in two University Medical Centers in the Netherlands. Reports of [18F]FDG PET/CT and anatomy-based imaging performed within two weeks of the [18F]FDG PET/CT scan were retrieved, and the presence and sites of IFI lesions were documented for each procedure. We included 155 [18F]FDG PET/CT scans performed in 73 patients. A total of 216 anatomy-based studies including 80 chest X-rays, 89 computed tomography studies, 14 magnetic resonance imaging studies, and 33 ultrasound imaging studies were studied. The anatomy-based studies were concordant with the [18F]FDG PET/CT for 94.4% of the scans performed. [18F]FDG PET/CT detected IFI lesions outside of the areas imaged by the anatomy-based studies in 48.6% of the scans. In 74% of the patients, [18F]FDG PET/CT added value in the management of the IFIs.
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The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions. Can Respir J 2020; 2020:2367505. [PMID: 32322324 PMCID: PMC7165338 DOI: 10.1155/2020/2367505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/18/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a new technology that allows for unbiased detection of pathogens. However, there are few reports on mNGS of lung biopsy tissues for pulmonary infection diagnosis. In addition, radial endobronchial ultrasound (R-EBUS) is widely used to detect peripheral pulmonary lesions (PPLs), but it is rarely used in the diagnosis of peripheral lung infection. Objective The present study aims to evaluate the combined application of R-EBUS-guided transbronchial lung biopsy (TBLB) and mNGS for the diagnosis of peripheral pulmonary infectious lesions. Methods From July 2018 to April 2019, 121 patients from Tianjin Medical University General Hospital diagnosed with PPLs and lung infection were enrolled in this prospective randomized study . Once the lesion was located, either TBLB or R-EBUS-guided-TBLB was performed in randomly selected patients, and mNGS was applied for pathogen detection in lung biopsy tissues. The results of mNGS were compared between the TBLB group and R-EBUS-guided TBLB group. In addition, the clinical characteristics and EBUS images from 61 patients receiving bronchoscopy for peripheral lung infectious detection were analyzed and compared with the results of mNGS. Results The positivity rate of mNGS in R-EBUS-guided TBLB was (78.7%, 48/61) that was significantly higher than (60.0%, 36/60) in the TBLB group. Difference in the position of R-EBUS probe and image characteristics of peripheral lung infectious lesions affected the positivity rate of mNGS. Tissue collected by R-EBUS within the lesion produced higher positivity rate than samples collected adjacent to the lesion (P=0.030, odds ratio 17.742; 95% confidence interval, from 1.325 to 237.645). Anechoic areas and luminant areas of ultrasonic image characteristics were correlated with lower positivity rate of mNGS (respectively, P=0.019, odds ratio 17.878; 95% confidence interval, from 1.595 to 200.399; P=0.042, odds ratio 16.745; 95% confidence interval, from 1.106 to 253.479). Conclusions R-EBUS-guided TBLB is a safe and effective technique in the diagnosis of peripheral lung infectious lesions. R-EBUS significantly facilitates the accurate insertion of bronchoscope into the lesions, which improves positivity rate of mNGS analysis in pathogen detection. The R-EBUS probe position within lesion produced a higher positivity rate of mNGS analysis. Nevertheless, the presence of anechoic and luminant areas on ultrasonic image was correlated with poor mNGS positivity rate.
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Zarei F, Hashemi SJ, Salehi M, Mahmoudi S, Zibafar E, Ahmadinejad Z, Rahimi Foroushani A, Ardi P, Daie Ghazvini R. Molecular characterization of fungi causing colonization and infection in organ transplant recipients: A one-year prospective study. Curr Med Mycol 2020; 6:30-35. [PMID: 32420505 PMCID: PMC7217253 DOI: 10.18502/cmm.6.1.2505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background and Purpose: Organ transplant recipients are vulnerable to fungal infections. The aim of this study was to determine the prevalence of fungal colonization and infections among patients who underwent various transplantations and molecularly characterize the etiological agents. Materials and Methods: This study was conducted on candidates for transplantation in Imam Khomeini Hospital, Tehran, Iran, from April 2017 to April 2018. All patients were monitored for fungal colonization or infections before and after transplantation. Isolated fungi were identified using molecular methods. Results: A total of 125 patients, including 86 males and 39 females, with the mean age of 52.2 years participated in the study (age range: 15-75 years). Out of 125 patients, 84 (67.2%) cases had fungal colonization that appeared pre- and post-transplantation in 21 and 63 cases, respectively (alone or concurrent with another infection in 55 and 29 cases, respectively). In addition, a total of 39 episodes of fungal infections were diagnosed in 36 (28.8%) recipients (alone or concurrent with colonization in 7 and 29 cases, respectively). Out of the 39 fungal infections, 9 cases appeared pre-transplantation, while the other 30 cases occurred post-transplantation. However, no fungal colonization or infection was observed in 34 (27.2%) patients. Oral candidiasis (n=20) was the most common type of infection, followed by funguria (n=7), onychomycosis (n=5), candidemia (n=3), rhinocerebral mucormycosis (n=1), cutaneous mucormycosis (n=1), cutaneous aspergillosis (n=1), and peritonitis (n=1). Six yeast species were recovered from colonization cases with the dominance of Candida albicans both before and after transplantation. The observed fungal infections were caused by 11 distinct species, including the members of Candida (i.e., C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and C. krusei), Aspergillus (i.e., A. oryzae and A. candidus), Rhizopus (i.e., R. oryzae and R. microsporus), Trichosporon asahii, and Trichophyton interdigitale. The results also indicated that the development of a fungal infection post-transplantation was associated with fungal colonization (r=0.0184; P=0.043). Conclusion: Based on the results, fungal colonization was a common finding in transplant recipients at Imam Khomeini Hospital. However, the incidence of fungal infections was comparable with those of other centers. As the oral cavity was the most common site of colonization and infection, it might be beneficial to take further care about the oral health of patients using effective mouthwash.
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Affiliation(s)
- Fereshteh Zarei
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Jamal Hashemi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Salehi
- Department of Infectious Diseases, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Mahmoudi
- Department of Medical Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ensieh Zibafar
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Ahmadinejad
- Liver Transplantation Research Center, Department of Infectious Diseases, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Ardi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Roshanak Daie Ghazvini
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Huang J, Jiang E, Yang D, Wei J, Zhao M, Feng J, Cao J. Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions. Infect Drug Resist 2020; 13:567-576. [PMID: 32110067 PMCID: PMC7036976 DOI: 10.2147/idr.s235182] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose The aim of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) in peripheral pulmonary infection management by comparing the diagnostic yield of mNGS and traditional pathogen detection methods on interventional specimens obtained by bronchoscopy. Patients and Methods This study enrolled patients suspected with pulmonary infection who were admitted to Tianjin Medical University General Hospital from June 2018 to August 2019. Specimens were obtained from bronchoscopy for mNGS analysis and traditional pathogen detection (including bronchoalveolar lavage fluid microbial culture, smear microscopy, and lung biopsy histopathology), and the diagnostic yields were compared between mNGS and traditional methods to evaluate the diagnostic value of mNGS in peripheral pulmonary infection diagnosis. Results In this study, by comparing mNGS with traditional pathogen detection, the results indicated that, first, mNGS identified at least one microbial species in almost 89% of the patients with pulmonary infection; second, mNGS detected microbes related to human diseases in 94.49% of samples from pulmonary infection patients who had received negative results from traditional pathogen detection; third, the accuracy and sensitivity of mNGS are higher than those of traditional pathogen detection; and, finally, mNGS could simultaneously detect and identify a large variety of pathogens. Conclusion Metagenomic NGS analysis provided fast and precise pathogen detection and identification, contributing to prompt and accurate treatment of peripheral pulmonary infection.
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Affiliation(s)
- Jie Huang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Graduate School, Tianjin Medical University, Tianjin, People's Republic of China
| | - Erlie Jiang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Donglin Yang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Jialin Wei
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, People's Republic of China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, People's Republic of China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
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Bronchoalveolar lavage to evaluate new pulmonary infiltrates in allogeneic hematopoietic stem cell transplant recipients: impact on antimicrobial optimization. Infect Prev Pract 2019; 1:100029. [PMID: 34316554 PMCID: PMC7148605 DOI: 10.1016/j.infpip.2019.100029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/26/2019] [Indexed: 12/01/2022] Open
Abstract
Background Pulmonary complications cause significant morbidity and mortality after allogeneic hematopoietic stem cell transplant (AHSCT). Bronchoscopy with targeted bronchoalveolar lavage (BAL) is often used in AHSCT patients with suspected lower respiratory tract infection (LRTI) to help guide management. Aim To evaluate how positive BAL results change antimicrobial management of AHSCT recipients with suspected LRTI. Methods We performed a retrospective review of BAL results from January 2014 to July 2016 for 54 AHSCT recipients. A positive BAL was determined by culture, multiplex polymerase chain reaction (PCR), Aspergillus galactomannan antigen (AGA), and cytology. Findings BAL was positive for infectious etiologies in 63%, and antimicrobials were adjusted in 48/54 (89%) of patients. Antibacterial escalation was predicted by a positive BAL bacterial culture (OR 7.61, P=0.017). Antibiotic de-escalation was more likely with an elevated AGA (OR 3.86, P=0.035). Antiviral initiation was more likely with positive BAL multiplex PCR (OR 17.33, P=0.010). Antifungals were more likely to be escalated or changed with an elevated AGA (OR 4.33, P=0.020). The patients with a negative BAL were more likely to be started on steroids (OR 0.19, P= 0.043). Conclusions BAL was helpful to determine the etiology of pulmonary complications and optimize antimicrobials. The addition of AGA and multiplex PCR to standard BAL significantly impacted de-escalating antibiotics and adjusting antifungals to provide adequate coverage. The association with an elevated AGA with antibacterial de-escalation highlights a new role for BAL in antimicrobial optimization.
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Abstract
Lung transplantation is an appropriate therapeutic option for select patients with end-stage lung diseases and offers the possibility of improved quality of life and longer survival. Unfortunately, the transplant recipient is at risk for numerous immunologic, infectious, and medical complications that threaten both of these goals. Median survival after lung transplantation is approximately 6 years. Optimizing outcomes requires close partnership between the patient, transplant center, and primary medical team. Early referral to a transplant center should be considered for patients with idiopathic pulmonary fibrosis and related interstitial lung diseases due to risk of acute exacerbation and accelerated development of respiratory failure.
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Affiliation(s)
- Vivek N Ahya
- Division of Pulmonary, Allergy and Critical Care Division, Paul F. Harron Jr. Lung Center, Penn Medicine, Perelman School of Medicine, University of Pennsylvania, 9035 Gates Building, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Joshua M Diamond
- Lung Transplantation Program, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, 9039 Gates Building, 3400 Spruce Street, Philadelphia, PA 19104, USA
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18
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Abstract
The emergency department (ED) is an increasingly important site of care for patients who have undergone solid organ transplantation or hematopoietic cell transplantation. It is paramount for emergency physicians to recognize infections early on, obtain appropriate diagnostic testing, initiate empirical antimicrobial therapy, and consider specialty consultation and inpatient admission when caring for these patients. This review provides emergency physicians with an approach to the assessment of transplant patients' underlying risk for infection, formulation of a broad differential diagnosis, and initial management of transplant infectious disease emergencies in the ED.
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Voriconazole exposure and risk of cutaneous squamous cell carcinoma among lung or hematopoietic cell transplant patients: A systematic review and meta-analysis. J Am Acad Dermatol 2018; 80:500-507.e10. [PMID: 30130598 DOI: 10.1016/j.jaad.2018.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/11/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Current evidence about the association between voriconazole and risk of cutaneous squamous cell carcinoma (SCC) remains inconsistent. OBJECTIVE To assess the association between voriconazole use and risk of SCC. METHODS We systematically searched PubMed and Embase and performed a random effects model meta-analysis to calculate the pooled relative risk (RR) with a 95% confidence interval (CI). RESULTS Of the 8 studies involving a total of 3710 individuals with a lung transplant or hematopoietic cell transplant that were included in the qualitative analysis, 5 were included in the meta-analysis. Use of voriconazole was significantly associated with increased risk of SCC (RR, 1.86; 95% CI, 1.36-2.55). The increased risk did not differ according to type of transplantation or adjustment for sun exposure. Longer duration of voriconazole use was found to be positively associated with risk of SCC (RR, 1.72; 95% CI, 1.09-2.72). Voriconazole use was not associated with increased risk of basal cell carcinoma (RR, 0.84; 95% CI, 0.41-1.71). LIMITATIONS There were some heterogeneities in the retrospective observational studies. CONCLUSIONS Our findings support an increased risk of SCC associated with voriconazole in individuals with a lung transplant or hematopoietic cell transplant. Routine dermatologic surveillance should be performed, especially among individuals at high risk of developing SCC.
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20
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Li H, Gao H, Meng H, Wang Q, Li S, Chen H, Li Y, Wang H. Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing. Front Cell Infect Microbiol 2018; 8:205. [PMID: 29988504 PMCID: PMC6026637 DOI: 10.3389/fcimb.2018.00205] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/05/2018] [Indexed: 01/26/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. However, reports on the use of mNGS in pulmonary infection applied to lung biopsy tissues remain scarce. In this study, we applied mNGS to detect the presence of pathogenic microbes in lung biopsy tissues from 20 patients with pulmonary disorders indicating possible infection. We applied a new data management for identifying pathogen species based on mNGS data. We determined the thresholds for the unique reads and relative abundance required to identify the infectious pathogens. Potential pathogens of pulmonary infections in 15 patients were identified by mNGS. The comparison between mNGS and culture method resulted that the sensitivity and specificity were 100.0% (95% CI: 31.0–100.0%) and 76.5% (95% CI: 49.8–92.2%) for bacteria, 57.1% (95% CI: 20.2–88.2%) and 61.5% (95% CI: 32.2–84.9%) for fungi. The positive predictive value (PPV) (42.9% for bacteria, 44.4% for fungi) was much lower than negative predictive value (NPV) (100% for bacteria, 72.7% for fungi) in mNGS vs. culture method. The mNGS showed the highest specificity (100.0 and 94.1%) and PPV (100.0 and 75.0%) in the evaluation of fungi and MTBC respectively, when compared with histopathology method. The study indicated that mNGS of lung biopsy tissues can be used to detect the presence (or absence) of pulmonary pathogens in patients, with potential benefits in speed and sensitivity. However, accurate data management and interpretation of mNGS are required, and should be combined with observations of clinical manifestations and conventional laboratory-based diagnostic methods.
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Affiliation(s)
- Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hua Gao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Han Meng
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuguang Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yongjun Li
- BGI Genomics, Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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Chandrika NT, Shrestha SK, Ranjan N, Sharma A, Arya DP, Garneau-Tsodikova S. New Application of Neomycin B-Bisbenzimidazole Hybrids as Antifungal Agents. ACS Infect Dis 2018; 4:196-207. [PMID: 29227087 PMCID: PMC5971066 DOI: 10.1021/acsinfecdis.7b00254] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alkylated aminoglycosides and bisbenzimidazoles have previously been shown to individually display antifungal activity. Herein, we explore for the first time the antifungal activity (in liquid cultures and in biofilms) of ten alkylated aminoglycosides covalently linked to either mono- or bisbenzimidazoles. We also investigate their toxicity against mammalian cells, their hemolytic activity, and their potential mechanism(s) of action (inhibition of fungal ergosterol biosynthetic pathway and/or reactive oxygen species (ROS) production). Overall, many of our hybrids exhibited broad-spectrum antifungal activity. We also found them to be less cytotoxic to mammalian cells and less hemolytic than the FDA-approved antifungal agents amphotericin B and voriconazole, respectively. Finally, we show with our best derivative (8) that the mechanism of action of our compounds is not the inhibition of ergosterol biosynthesis, but that it involves ROS production in yeast cells.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sanjib K. Shrestha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Nihar Ranjan
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Anindra Sharma
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Dev P. Arya
- Department of Chemistry, Clemson University, 219 Hunter Laboratories, Clemson, South Carolina 29634, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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22
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Li H, Gao H, Meng H, Wang Q, Li S, Chen H, Li Y, Wang H. Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing. Front Cell Infect Microbiol 2018. [PMID: 29988504 DOI: 10.3389/fcimb.2018.00205.ecollection2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. However, reports on the use of mNGS in pulmonary infection applied to lung biopsy tissues remain scarce. In this study, we applied mNGS to detect the presence of pathogenic microbes in lung biopsy tissues from 20 patients with pulmonary disorders indicating possible infection. We applied a new data management for identifying pathogen species based on mNGS data. We determined the thresholds for the unique reads and relative abundance required to identify the infectious pathogens. Potential pathogens of pulmonary infections in 15 patients were identified by mNGS. The comparison between mNGS and culture method resulted that the sensitivity and specificity were 100.0% (95% CI: 31.0-100.0%) and 76.5% (95% CI: 49.8-92.2%) for bacteria, 57.1% (95% CI: 20.2-88.2%) and 61.5% (95% CI: 32.2-84.9%) for fungi. The positive predictive value (PPV) (42.9% for bacteria, 44.4% for fungi) was much lower than negative predictive value (NPV) (100% for bacteria, 72.7% for fungi) in mNGS vs. culture method. The mNGS showed the highest specificity (100.0 and 94.1%) and PPV (100.0 and 75.0%) in the evaluation of fungi and MTBC respectively, when compared with histopathology method. The study indicated that mNGS of lung biopsy tissues can be used to detect the presence (or absence) of pulmonary pathogens in patients, with potential benefits in speed and sensitivity. However, accurate data management and interpretation of mNGS are required, and should be combined with observations of clinical manifestations and conventional laboratory-based diagnostic methods.
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Affiliation(s)
- Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hua Gao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Han Meng
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuguang Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yongjun Li
- BGI Genomics, Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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