1
|
Katsoulis O, Pitts OR, Singanayagam A. The airway mycobiome and interactions with immunity in health and chronic lung disease. OXFORD OPEN IMMUNOLOGY 2024; 5:iqae009. [PMID: 39206335 PMCID: PMC11357796 DOI: 10.1093/oxfimm/iqae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
The existence of commensal fungi that reside within the respiratory tract, termed the airway mycobiome, has only recently been discovered. Studies are beginning to characterize the spectrum of fungi that inhabit the human upper and lower respiratory tract but heterogeneous sampling and analysis techniques have limited the generalizability of findings to date. In this review, we discuss existing studies that have examined the respiratory mycobiota in healthy individuals and in those with inflammatory lung conditions such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. Associations between specific fungi and features of disease pathogenesis are emerging but the precise functional consequences imparted by mycobiota upon the immune system remain poorly understood. It is imperative that further research is conducted in this important area as a more detailed understanding could facilitate the development of novel approaches to manipulating the mycobiome for therapeutic benefit.
Collapse
Affiliation(s)
- Orestis Katsoulis
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Oliver R Pitts
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Aran Singanayagam
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
- National Heart and Lung Institute, Imperial College London, London SW7 2DD, UK
| |
Collapse
|
2
|
Feng Q, Tong Z. Clinical Characteristics and Prognostic Predictors of Pneumocystis Jirovecii Pneumonia in Patients with and without Chronic Pulmonary Disease: A Retrospective Cohort Study. Infect Drug Resist 2024; 17:2169-2182. [PMID: 38832106 PMCID: PMC11146626 DOI: 10.2147/idr.s456716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Objective Pneumocystis jirovecii pneumonia (PJP) is a severe respiratory infection caused by Pneumocystis jirovecii in immunocompromised hosts. The role of P. jirovecii colonization in the development or progression of various pulmonary diseases has been reported. Our aim was to explore serial change in serum biomarkers and the independent risk factors for mortality in patients with and without chronic pulmonary diseases who developed PJP. Methods We performed a retrospective study to select patients with Pneumocystis jirovecii pneumonia between January 1, 2012, and December 31, 2021. Information regarding demographics, clinical characteristics, underlying diseases, laboratory tests, treatment, and outcomes was collected. Univariate and multivariate logistic regression analyses were used to identify independent predictors of in-hospital mortality. Results A total of 167 patients diagnosed with PJP were included in the study: 53 in the CPD-PJP group and 114 in the NCPD-PJP group. The number of patients with PJP showed an increasing trend over the 10-year period. A similar trend was observed for in-hospital mortality. Independent risk factors associated with death in the NCPD-PJP group were procalcitonin level (adjusted OR 1.08, 95% CI 1.01-1.16, P=0.01), pneumothorax (adjusted OR 0.07, 95% CI 0.01-0.38, P=0.002), neutrophil count (adjusted OR 1.27, 95% CI 1.05-1.53, P=0.01) at 14 days, and hemoglobin level (adjusted OR 0.94, 95% CI 0.91-0.98; P=0.002) at 14 days after admission. The risk factor associated with death in the CPD-PJP group was neutrophil count (adjusted OR 1.19, 95% CI 0.99-1.43; P=0.05) at 14 days after admission. Conclusion The risk factors for death were different between patients with PJP with and without chronic pulmonary disease. Early identification of these factors in patients with PJP and other underlying diseases may improve prognosis.
Collapse
Affiliation(s)
- Qiuyue Feng
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Beijing Huairou Hospital, Beijing, 101400, People’s Republic of China
| | - Zhaohui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People’s Republic of China
| |
Collapse
|
3
|
Lian Q, Song X, Yang J, Wang L, Xu P, Wang X, Xu X, Yang B, He J, Ju C. Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia. Respir Res 2024; 25:125. [PMID: 38486264 PMCID: PMC10941442 DOI: 10.1186/s12931-024-02755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Increasing evidence revealed that lung microbiota dysbiosis was associated with pulmonary infection in lung transplant recipients (LTRs). Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungal pathogen that frequently causes lethal pneumonia in LTRs. However, the lung microbiota in LTRs with P. jirovecii pneumonia (PJP) remains unknow. METHODS In this prospective observational study, we performed metagenomic next-generation sequencing (mNGS) on 72 bronchoalveolar lavage fluid (BALF) samples from 61 LTRs (20 with PJP, 22 with PJC, 19 time-matched stable LTRs, and 11 from LTRs after PJP recovery). We compared the lung microbiota composition of LTRs with and without P. jirovecii, and analyzed the related clinical variables. RESULTS BALFs collected at the episode of PJP showed a more discrete distribution with a lower species diversity, and microbiota composition differed significantly compared to P. jirovecii colonization (PJC) and control group. Human gammaherpesvirus 4, Phreatobacter oligotrophus, and Pseudomonas balearica were the differential microbiota species between the PJP and the other two groups. The network analysis revealed that most species had a positive correlation, while P. jirovecii was correlated negatively with 10 species including Acinetobacter venetianus, Pseudomonas guariconensis, Paracandidimonas soli, Acinetobacter colistiniresistens, and Castellaniella defragrans, which were enriched in the control group. The microbiota composition and diversity of BALF after PJP recovery were also different from the PJP and control groups, while the main components of the PJP recovery similar to control group. Clinical variables including age, creatinine, total protein, albumin, IgG, neutrophil, lymphocyte, CD3+CD45+, CD3+CD4+ and CD3+CD8+ T cells were deeply implicated in the alterations of lung microbiota in LTRs. CONCLUSIONS This study suggests that LTRs with PJP had altered lung microbiota compared to PJC, control, and after recovery groups. Furthermore, lung microbiota is related to age, renal function, nutritional and immune status in LTRs.
Collapse
Affiliation(s)
- Qiaoyan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xiuling Song
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Juhua Yang
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Lulin Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Peihang Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xiaohua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
- Department of Thoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China
| | - Bin Yang
- Vision Medicals Co., Ltd, 510700, Guangzhou, Guangdong, P.R. China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
- Department of Thoracic Surgery, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
| | - Chunrong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Organ transplantation, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, Guangdong, P.R. China.
| |
Collapse
|
4
|
Kobayashi T, Tsuyuguchi K, Shimatani Y, Matsuda Y, Kagawa T, Takimoto T, Takeuchi N, Arai T, Inoue Y. Utility of a loop-mediated isothermal amplification detection kit to diagnose chronic pulmonary aspergillosis. J Infect Chemother 2024; 30:7-11. [PMID: 37660734 DOI: 10.1016/j.jiac.2023.08.018] [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: 03/19/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Diagnosing chronic pulmonary aspergillosis (CPA) is still challenging, and infection with Aspergillus spp. must be detected early. The aim of this study was to evaluate, for the first time, the usefulness of a new loop-mediated isothermal amplification (LAMP) test kit in diagnosing CPA. METHODS This cross-sectional study was performed at the National Hospital Organization Kinki-Chuo Chest Medical Center. We prospectively enrolled patients with and without CPA. The primary outcomes of this study were the sensitivity and specificity of LAMP for the diagnosis of CPA. RESULTS In total, 34 patients with CPA and 21 without CPA (the control group) were enrolled between October 2019 and December 2021. Among the 34 patients with CPA, cultures were positive for CPA in 16 and negative for 18. The majority of fungi isolated in sputum were A. fumigatus in 15 specimens; Aspergillus flavus was isolated in 1) LAMP demonstrated 55.9% sensitivity (95% confidence interval [CI] 37.9-72.8) and 100.0% specificity (95% CI 77.2-100.0). CONCLUSION LAMP is an acceptable tool for diagnosing CPA, and its application in clinical practice necessitates more studies.
Collapse
Affiliation(s)
- Takehiko Kobayashi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan.
| | - Yasuaki Shimatani
- Department of Clinical Microbiology, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshinobu Matsuda
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Tomoko Kagawa
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Takayuki Takimoto
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Naoko Takeuchi
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Toru Arai
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| |
Collapse
|
5
|
Kianipour S, Dehghan P, Emami Ardestani M. Detection of Opportunistic Fungi from the Bronchoalveolar Lavage Specimens of Patients with Pulmonary Diseases. Adv Biomed Res 2023; 12:176. [PMID: 37694245 PMCID: PMC10492593 DOI: 10.4103/abr.abr_297_22] [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: 09/05/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 09/12/2023] Open
Abstract
Background Opportunistic fungi are a constantly evolving group of pathogens that become active when the immune system is compromised, begin to multiply, and soon overwhelm the weakened immune system. This study was performed to evaluate the number of opportunistic fungi in bronchoalveolar lavage (BAL) samples of patients with pulmonary diseases. Materials and Methods After receiving patients' consent and demographic forms, a total of 120 BAL samples were taken by a pulmonary physician. The etiologic agents were identified by standard morphological and molecular methods. Yeast cells were counted on culture media, and direct smears were precisely examined for the presence of yeasts elements, Pneumocystis, and filamentous fungi. Results In this study, 29 (24.1%) patients showed positive direct smears for yeast elements in their BAL samples. The mean colony count of yeasts was 42,000 (CFU/mL) on culture media. Six (5%) species of filamentous fungi, including three (2.5%) isolates of Penicillium species (P. variabile, P. glabrum, and P. thomii), two (1.67%) Aspergillus species (A. flavus and A. fumigatus), 1 case (0.83%) Pseudallescheria boydii were detected. Seven cases (5.83%) of Pneumocystis cysts were observed in the direct smears stained with Giemsa. Identification of all fungi confirmed by molecular or sequencing methods. Conclusions Due to the presence of a large number of fungi in the BAL samples and possible physical interference with the selected drugs for treatment, we draw the attention of pulmonologists to this important issue. Rapid diagnosis of fungal infections is essential to optimize treatments and outcomes.
Collapse
Affiliation(s)
- Sahar Kianipour
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parvin Dehghan
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Emami Ardestani
- Department of Internal Medicine, School of Medicine, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
6
|
Harizanov R, Tsvetkova N, Ivanova A, Enikova R, Videnova M, Rainova I, Kaneva E, Kaftandjiev I, Strashimirov D, Yancheva-Petrova N, Simeonovski I, Levterova V, Yanev N. Study on the Prevalence of Pneumocystis jirovecii as a Causative Agent of Lung Pathology in People with Different Immune Status. Biomedicines 2023; 11:1851. [PMID: 37509491 PMCID: PMC10376562 DOI: 10.3390/biomedicines11071851] [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: 06/02/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) commonly affects immunocompromised individuals, whereas in immunocompetent persons, it occurs relatively rarely, and in most cases, the Pneumocystis infection is detected as an asymptomatic colonization. The present study aimed to establish the prevalence of Pneumocystis jirovecii infection in human hosts with different immune status (immunocompromised and immunocompetent), using molecular diagnostic methods, and to compare their diagnostic value with that of classical staining methods. METHODS We used the collected-to-this-moment data from a prospective study on the prevalence of pneumocystosis among the Bulgarian population. Clinical specimens (including throat secretions, induced sputum, tracheal aspirates, and bronchoalveolar lavage) collected from 220 patients suspected of PCP (153 immunocompetent and 67 immunocompromised patients) were examined with microscopic staining methods and real-time PCR for detection of P. jirovecii. Results: DNA of the pathogen was detected in 38 (17%) specimens (32 immunocompromised patients and 6 immunocompetent subjects). From all 220 clinical samples examined by staining methods, only five (2%) P. jirovecii cysts were detected by the Gomori stain. All patients with PCP were treated with trimethoprim-sulfamethoxazole, but in ten of them (HIV-positive patients), the disease had a fatal outcome. CONCLUSIONS This study is the first in Bulgaria including the main available laboratory methods for diagnosis of human pneumocystosis. Regarding the etiological diagnosis of PCP, in our study the sensitivity of real-time PCR was higher compared to the staining methods. The choice of a method for sample collection and examination has an important role in the efficiency of the laboratory diagnostics.
Collapse
Affiliation(s)
- Rumen Harizanov
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nina Tsvetkova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Aleksandra Ivanova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Raina Enikova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Mihaela Videnova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Iskra Rainova
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Eleonora Kaneva
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Iskren Kaftandjiev
- Department of Parasitology and Tropical Medicine, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Dimitar Strashimirov
- Department for AIDS, Specialized Hospital for Active Treatment of Infectious and Parasitic Diseases, Ivan Geshev Blvd. 17, 1431 Sofia, Bulgaria
| | - Nina Yancheva-Petrova
- Department for AIDS, Specialized Hospital for Active Treatment of Infectious and Parasitic Diseases, Ivan Geshev Blvd. 17, 1431 Sofia, Bulgaria
| | - Ivan Simeonovski
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Nikolay Yanev
- Department of Bronchology, University Multi-Profile Hospital (UMBAL) for Active Treatment of Lung Diseases "Sveti Ivan Rilski" EAD, Ivan Geshev Blvd. 19, 1431 Sofia, Bulgaria
| |
Collapse
|
7
|
Niamatullah H, Nasir N, Jabeen K, Rattani S, Farooqi J, Ghanchi N, Irfan M. Post-COVID-19 Pneumocystis pneumonia cases from Pakistan: an observational study. Access Microbiol 2023; 5:acmi000406. [PMID: 36860506 PMCID: PMC9968954 DOI: 10.1099/acmi.0.000406] [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: 01/21/2022] [Accepted: 11/29/2022] [Indexed: 01/07/2023] Open
Abstract
Background. Concurrent coronavirus disease 2019 (COVID-19) and Pneumocystis jirovecii pneumonia (PJP) has been described in various reports, with a recent study describing a 9.3 % P. jirovecii detection rate in critically ill COVID-19 patients. Methods. Patients with PCR-confirmed PJP following COVID-19 infection who were admitted to Aga Khan University Hospital, Karachi, Pakistan from March 2020-June 2021 were identified through a laboratory database. Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus was performed by RT-PCR Cobas SARS-CoV-2 qualitative assay. P. jirovecii PCR was performed using the RealStar Pneumocystis jirovecii PCR kit. Clinical, radiological and laboratory data for PJP patients were recorded. Results. During the study period, 3707 patients were admitted with COVID-19 at our hospital. P. jirovecii PCR was requested for 90 patients and was positive in 10 (11 %). Five out of 10 patients were discharged from the hospital and later developed cough and dyspnoea. Five patients remained hospitalized with severe COVID-19 and developed PJP. Eight patients in our study received systemic steroids. The trends of lymphocyte counts of all patients showed a lymphocyte count of <1000 mm-3 (<1.0×106 cells µl-1) in the week of PJP diagnosis. Four patients did not survive; one of these patients did not receive co-trimoxazole due to late diagnosis, one patient had concomitant nosocomial pneumonia and bacteraemia with multidrug-resistant Acinetobacter species, and two patients had concomitant aspergillosis. Conclusion. In summary, invasive fungal infections such as PJP should be considered as a complication in COVID-19 patients, with prompt evaluation and management.
Collapse
Affiliation(s)
| | - Nosheen Nasir
- Department of Medicine, Aga Khan University, Karachi, Pakistan
| | - Kauser Jabeen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan,*Correspondence: Kauser Jabeen,
| | - Salima Rattani
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Joveria Farooqi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Najia Ghanchi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Muhammad Irfan
- Department of Medicine, Aga Khan University, Karachi, Pakistan
| |
Collapse
|
8
|
Papiris SA, Kolilekas L, Kagouridis K, Maniati M, Manali ED. IPF-Acute Exacerbations: Advances and Future Perspectives. Front Pharmacol 2022; 13:836553. [PMID: 35496286 PMCID: PMC9047939 DOI: 10.3389/fphar.2022.836553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/15/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Spyros A. Papiris
- 2ndPulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- *Correspondence: Spyros A. Papiris,
| | | | - Konstantinos Kagouridis
- 2ndPulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Maniati
- 2ndPulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Effrosyni D. Manali
- 2ndPulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
9
|
Xue T, Du WQ, Dai WJ, Li YS, Wang SF, Wang JL, Zhang XR. Genetic Polymorphisms of Pneumocystis jirovecii in HIV-Positive and HIV-Negative Patients in Northern China. Pol J Microbiol 2022; 71:27-34. [PMID: 35635165 PMCID: PMC9152919 DOI: 10.33073/pjm-2022-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic fungus that can cause severe and potentially fatal Pneumocystis pneumonia (PCP) in immunodeficient patients. In this study, we investigated the genetic polymorphisms of P. jirovecii at eight different loci, including six nuclear genes (ITS, 26S rRNA, sod, dhps, dhfr and β-Tub) and two mitochondrial genes (mtLSU-rRNA and cyb) in three PCP cases, including two patients with HIV infection and one without HIV infection in Shanxi Province, P.R. China. The gene targets were amplified by PCR followed by sequencing of plasmid clones. The HIV-negative patient showed a coinfection with two genotypes of P. jirovecii at six of the eight loci sequenced. Of the two HIV-positive patients, one showed a coinfection with two genotypes of P. jirovecii at the same two of the six loci as in the HIV-negative patient, while the other showed a single infection at all eight loci sequenced. None of the three drug target genes (dhfr, dhps and cyb) showed mutations known to be potentially associated with drug resistance. This is the first report of genetic polymorphisms of P. jirovecii in PCP patients in Shanxi Province, China. Our findings expand our understanding of the genetic diversity of P. jirovecii in China. ![]()
Collapse
Affiliation(s)
- Ting Xue
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Wei-Qin Du
- Department of clinical inspection , Eleventh Affiliated Hospital of Shanxi Medical University , Lvliang , P.R. China
| | - Wen-Juan Dai
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Yi-Shan Li
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Shu-Feng Wang
- Department of Clinical Inspection , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| | - Jun-Ling Wang
- Department of Translation Medicine , Jinzhou Medical University , Jinzhou , P.R. China
| | - Xin-Ri Zhang
- NHC Key Laboratory of Pneumoconiosis, Key Laboratory of Prophylaxis and Treatment and Basic Research of Respiratory Diseases of Shanxi Province , Department of Respiratory and Critical Care Medicine , First Affiliated Hospital of Shanxi Medical University , Taiyuan , P.R. China
| |
Collapse
|
10
|
Glasgow HL, Cruz K, Murphy SC. Reverse-transcription PCR increases sensitivity of broad-range fungal detection in bronchoalveolar lavage fluid. Med Mycol 2021; 60:6433194. [PMID: 34878120 DOI: 10.1093/mmy/myab061] [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: 07/22/2021] [Revised: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Broad-range PCR targeting 28S D1-D2 ribosomal DNA (rDNA) identifies numerous fungi but has limited sensitivity in clinical specimens. Ribosomal RNA (rRNA) vastly outnumbers rDNA, suggesting reverse transcription (RT)-PCR could improve detection. Among contrived samples, RT-PCR decreased 28S PCR cycle threshold values by 10--12 cycles and lowered the limit of detection > 2000-fold. Among 32 bronchoalveolar lavage specimens, RT-PCR detected 12/15 (80%) fungal PCR- or culture-positive specimens, versus 6/12 (50%) by 28S PCR, 9/12 (75%) by any fungal PCR, and 13/15 (87%) by culture. RT-PCR newly identified fungi in 4/17 (24%) PCR- and culture-negative specimens. RT substantially increased 28S PCR sensitivity overall. LAY SUMMARY Fungal infection remains difficult to diagnose in the laboratory. Here, we have shown that detecting ribosomal RNA and DNA, rather than only ribosomal DNA, in a broad range fungal assay results in a significant enhancement in the ability to detect and identify fungal pathogens in clinical samples.
Collapse
Affiliation(s)
- Heather L Glasgow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Kurtis Cruz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA.,Department of Microbiology, University of Washington, Seattle, Washington, 98195, USA
| |
Collapse
|
11
|
Sabbagh SE, Neely J, Chow A, DeGuzman M, Lai J, Lvovich S, McGrath T, Pereira M, Pinal-Fernandez I, Roberts J, Rouster-Stevens K, Schmeling H, Sura A, Tarshish G, Tucker L, Rider LG, Kim S. Risk factors associated with Pneumocystis jirovecii pneumonia in juvenile myositis in North America. Rheumatology (Oxford) 2021; 60:829-836. [PMID: 32889531 DOI: 10.1093/rheumatology/keaa436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Pneumocystis jirovecii pneumonia (PJP) is associated with significant morbidity and mortality in adult myositis patients; however, there are few studies examining PJP in juvenile myositis [juvenile idiopathic inflammatory myopathy (JIIM)]. The purpose of this study was to determine the risk factors and clinical phenotypes associated with PJP in JIIM. METHODS An research electronic data capture (REDCap) questionnaire regarding myositis features, disease course, medications and PJP infection characteristics was completed by treating physicians for 13 JIIM patients who developed PJP (PJP+) from the USA and Canada. Myositis features and medications were compared with 147 JIIM patients without PJP (PJP-) from similar geographic regions who enrolled in National Institutes of Health natural history studies. RESULTS PJP+ patients were more often of Asian ancestry than PJP- patients [odds ratio (OR) 8.7; 95% CI 1.3, 57.9]. Anti- melanoma differentiation associated protein 5 (MDA5) autoantibodies (OR 12.5; 95% CI 3.0, 52.4), digital infarcts (OR 43.8; 95% CI 4.2, 460.2), skin ulcerations (OR 12.0; 95% CI 3.5, 41.2) and interstitial lung disease (OR 10.6; 95% CI 2.1, 53.9) were more frequent in PJP+ patients. Before PJP diagnosis, patients more frequently received pulse steroids, rituximab and more immunosuppressive therapy compared with PJP- patients. Seven PJP+ patients were admitted to the intensive care unit and four patients died due to PJP or its complications. CONCLUSIONS PJP is a severe infection in JIIM that can be associated with mortality. Having PJP was associated with more immunosuppressive therapy, anti-MDA5 autoantibodies, Asian race and certain clinical features, including digital infarcts, cutaneous ulcerations and interstitial lung disease. Prophylaxis for PJP should be considered in juvenile myositis patients with these features.
Collapse
Affiliation(s)
- Sara E Sabbagh
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD, USA.,Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jessica Neely
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Chow
- Division of Pediatric Rheumatology, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA.,Division of Pediatric Rheumatology, Department of Pediatrics, Loma Linda University Children's Hospital, Loma Linda, CA, USA
| | - Marietta DeGuzman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Division of Rheumatology, Texas Children's Hospital, Houston, TX, USA
| | - Jamie Lai
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Division of Rheumatology, Texas Children's Hospital, Houston, TX, USA.,University of Colorado School of Medicine, Division of Pediatric Rheumatology, Children's Hospital Colorado, Aurora, CO, USA
| | - Svetlana Lvovich
- Section of Rheumatology, Department of Pediatrics, St Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Tara McGrath
- Division of Rheumatology, Department of Pediatrics, University of British Columbia, Vancouver, BC, USA.,BC Children's Hospital, Vancouver, BC, Canada
| | - Maria Pereira
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Division of Rheumatology, Texas Children's Hospital, Houston, TX, USA
| | - Iago Pinal-Fernandez
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Jordan Roberts
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kelly Rouster-Stevens
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Heinrike Schmeling
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Anjali Sura
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.,Department of Pediatrics, Upstate University Hospital, Syracuse, NY, USA
| | - Gabriel Tarshish
- Division of Pediatric Rheumatology, Department of Pediatrics, Children's Hospital at Montefiore, Bronx, NY, USA
| | - Lori Tucker
- Division of Rheumatology, Department of Pediatrics, University of British Columbia, Vancouver, BC, USA.,BC Children's Hospital, Vancouver, BC, Canada
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Susan Kim
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | |
Collapse
|
12
|
Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
Collapse
|
13
|
Scharmann U, Kirchhoff L, Schmidt D, Buer J, Steinmann J, Rath PM. Evaluation of a commercial Loop-mediated Isothermal Amplification (LAMP) assay for rapid detection of Pneumocystis jirovecii. Mycoses 2020; 63:1107-1114. [PMID: 32738076 DOI: 10.1111/myc.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Various tools are obtainable for the detection of Pneumocystis jirovecii, among them qPCR promising highest sensitivity. A novel molecular method is commercially available, the loop-mediated isothermal amplification (LAMP) assay. OBJECTIVES We compared the performance of the LAMP eazyplex® Pneumocystis jirovecii with the RealStar Pneumocystis jirovecii PCR 1.0 qPCR. MATERIAL/METHODS Overall, 162 lower respiratory tract specimens from 146 critically ill patients were investigated. LAMP assay and qPCR were carried out according to the manufacturer's recommendations. Positive results of the LAMP were described as time to positivity (TTP). The limit of detection (LOD) of the LAMP was analysed using 10-fold serial dilutions of a high positive P jirovecii respiratory sample. For each serial dilution, TTP of the LAMP was plotted against cycle threshold (Ct) values of the qPCR. RESULTS The LOD of the LAMP was determined to be approximately 4 × 103 copies/mL. While the LAMP revealed 28 (17%) positive signals from 20 patients, by using qPCR 41 (25%) positive samples from 28 patients were identified. Overall agreement with qPCR was 92%. Five false-negative, one false-positive and nine invalid results were detected by the LAMP. Positive and negative predictive values were 96% each, and sensitivity and specificity were 84% and 99%, respectively. There was a low correlation between the TTP and the fungal load. CONCLUSION The LAMP is a time-saving and easy-to-perform method. It can be used as an alternative diagnostic method. However, for quantification purposes the qPCR is still the gold standard.
Collapse
Affiliation(s)
- Ulrike Scharmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Klinikum Nürnberg, Paracelsus Medical University, Nuremberg, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|