1
|
Zhu Z, Wang Y, Ning W, Liu C, Chen C. Torquetenovirus from bronchoalveolar lavage fluid as a biomarker for lung infection among immunocompromised hosts. Biomark Med 2024:1-11. [PMID: 38982729 DOI: 10.1080/17520363.2024.2366148] [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: 01/01/2024] [Accepted: 05/08/2024] [Indexed: 07/11/2024] Open
Abstract
Aim: Torquetenovirus (TTV) was a promising biomarker for immunity, while lung regional TTV for evaluating the opportunistic infection among immunocompromised hosts (ICH) was unclear. Materials & methods: In the ICH and non-ICH populations, we compared the susceptibility to opportunistic infections, clinical severity and the prognosis between subgroups, respectively. Results: ICH with detectable bronchoalveolar lavage fluid (BALF)-TTV were more susceptible to lung aspergillosis and Mycobacterium infections. Furthermore, our data demonstrated that the ICH cohort with detectable BALF-TTV represented a higher clinical severity and a worse prognosis, while the above findings were not found in the non-ICH population. Conclusion: Our findings demonstrated that the BALF-TTV could act as an effective predictor for opportunistic infection for ICH that complemented the CD4+ T cell counts.
Collapse
Affiliation(s)
- Ziwen Zhu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Yang Wang
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Weiwei Ning
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Chao Liu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| | - Cheng Chen
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou 215006, China
| |
Collapse
|
2
|
Rucar A, Totet A, Le Govic Y, Demey B, Damiani C. Pulmonary co-infections by Pneumocystis jirovecii and Herpesviridae: a seven-year retrospective study. Ann Clin Microbiol Antimicrob 2024; 23:8. [PMID: 38245721 PMCID: PMC10800065 DOI: 10.1186/s12941-023-00663-2] [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: 06/26/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungus responsible for Pneumocystis pneumonia (PCP) in deeply immunocompromised patients and for pulmonary colonization in individuals with mild immunosuppression or impaired respiratory function. PCP and Cytomegalovirus (CMV) co-infections have been widely described whereas those involving other Herpesviruses (HVs) such as Epstein-Barr virus (EBV), Herpes simplex virus type 1 and type 2 (HSV-1 and -2), and Varicella zoster virus (VZV) remain scarce. To date, no data are available concerning HVs co-infections in P. jirovecii colonization. METHODS Our main objective was to evaluate the frequency of HVs in bronchoalveolar lavage fluid (BALF) samples from patients with PCP or with pulmonary colonization. The secondary objective was to assess the relationship between HVs and the mortality rate in PCP patients. A retrospective single-center study over a seven-year period was conducted. All patients with P. jirovecii detected using PCR in a BALF sample and for whom a PCR assay for HVs detection was performed were included in the study. RESULTS One hundred and twenty-five patients were included, corresponding to 77 patients with PCP and 48 colonized patients. At least one HV was detected in 54/77 (70.1%) PCP patients and in 28/48 (58.3%) colonized patients. EBV was the most frequent in both groups. Furthermore, the 30-day survival rate in PCP patients was significantly lower with [EBV + CMV] co-infection than that with EBV co-infection, [EBV + HSV-1] co-infection and without HV co-infection. CONCLUSION Our results show that the frequency of HV, alone or in combination is similar in PCP and colonization. They also suggest that [EBV + CMV] detection in BALF samples from PCP patients is associated with an increased mortality rate, underlying the significance to detect HVs in the course of PCP.
Collapse
Affiliation(s)
- Alan Rucar
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens-Picardie, 1 rond-point du Pr Cabrol, 80054, Amiens Cedex 1, France
| | - Anne Totet
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens-Picardie, 1 rond-point du Pr Cabrol, 80054, Amiens Cedex 1, France
- Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, 1 rue des Louvels, 80037, Amiens Cedex 1, France
| | - Yohann Le Govic
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens-Picardie, 1 rond-point du Pr Cabrol, 80054, Amiens Cedex 1, France
- Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, 1 rue des Louvels, 80037, Amiens Cedex 1, France
| | - Baptiste Demey
- Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, 1 rue des Louvels, 80037, Amiens Cedex 1, France
- Laboratoire de Virologie, Centre de Biologie Humaine, CHU Amiens-Picardie, 1 rond-point du Pr Cabrol, 80054, Amiens Cedex 1, France
| | - Céline Damiani
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens-Picardie, 1 rond-point du Pr Cabrol, 80054, Amiens Cedex 1, France.
- Agents Infectieux, Résistance et Chimiothérapie (AGIR), UR 4294, Université de Picardie Jules Verne, 1 rue des Louvels, 80037, Amiens Cedex 1, France.
| |
Collapse
|
3
|
Liu Y, Wen Z, Fang Y, Wang T, Wu F, Zhang H, Chen D, Liu J. Herpesvirus reactivation in respiratory tract is associated with increased mortality of severe pneumonia patients and their respiratory microbiome dysbiosis. Front Cell Infect Microbiol 2023; 13:1294142. [PMID: 38188628 PMCID: PMC10771827 DOI: 10.3389/fcimb.2023.1294142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Severe pneumonia (SP) is a respiratory tract disease that seriously threatens human health. The herpesvirus detected in patients, especially with severe and immunodeficient diseases, is gradually attracting the attention of clinical doctors. However, little is known about the effect of herpesvirus on the prognosis of SP patients and the pulmonary microbial community. Here, we retrospectively analyzed respiratory samples from 45 SP patients detected by metagenomic next-generation sequencing (mNGS). A total of five types of herpesviruses were detected, with Human alphaherpesvirus 1 (HHV-1) in 19 patients, Human betaherpesvirus 5 (CMV) in 7 patients, Human betaherpesvirus 7 (HHV-7) in 6 patients, Human alphaherpesvirus 2 (HHV-2) in 5 patients, and Human gammaherpesvirus 4 (EBV) in 4 patients. Further analysis showed that the mortality of the herpesvirus-positive group was significantly higher than that of the negative group. The results also showed that HHV-1 was significantly associated with the prognosis of SP patients, while the other herpesviruses did not have a significant difference in patient mortality. A comparison of the microbial community characteristics of SP patients showed a significant difference in beta-diversity between herpesvirus-positive and negative groups. Species difference analysis showed that the herpesvirus-positive group was related to more conditional pathogens, such as Pneumocystis jirovecii and Burkholderia cepacia. In summary, our results suggest that the presence of herpesvirus is associated with the mortality of SP patients. Furthermore, enrichment of conditional pathogens in the respiratory tract of herpesvirus-positive SP patients may be a potential reason for the increased mortality.
Collapse
Affiliation(s)
- Yongan Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhenliang Wen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuan Fang
- Department of Medicine, Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Tao Wang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fengsheng Wu
- Department of Medicine, Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Hongming Zhang
- Department of Medicine, Genoxor Medical Science and Technology Inc., Zhejiang, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| |
Collapse
|
4
|
Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [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: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
Collapse
Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| |
Collapse
|
5
|
Burzio C, Balzani E, Corcione S, Montrucchio G, Trompeo AC, Brazzi L. Pneumocystis jirovecii Pneumonia after Heart Transplantation: Two Case Reports and a Review of the Literature. Pathogens 2023; 12:1265. [PMID: 37887781 PMCID: PMC10610317 DOI: 10.3390/pathogens12101265] [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: 09/16/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Post-transplant Pneumocystis jirovecii pneumonia (PcP) is an uncommon but increasingly reported disease among solid organ transplantation (SOT) recipients, associated with significant morbidity and mortality. Although the introduction of PcP prophylaxis has reduced its overall incidence, its prevalence continues to be high, especially during the second year after transplant, the period following prophylaxis discontinuation. We recently described two cases of PcP occurring more than one year after heart transplantation (HT) in patients who were no longer receiving PcP prophylaxis according to the local protocol. In both cases, the disease was diagnosed following the diagnosis of a viral illness, resulting in a significantly increased risk for PcP. While current heart transplantation guidelines recommend Pneumocystis jirovecii prophylaxis for up to 6-12 months after transplantation, after that period they only suggest an extended prophylaxis regimen in high-risk patients. Recent studies have identified several new risk factors that may be linked to an increased risk of PcP infection, including medication regimens and patient characteristics. Similarly, the indication for PcP prophylaxis in non-HIV patients has been expanded in relation to the introduction of new medications and therapeutic regimens for immune-mediated diseases. In our experience, the first patient was successfully treated with non-invasive ventilation, while the second required tracheal intubation, invasive ventilation, and extracorporeal CO2 removal due to severe respiratory failure. The aim of this double case report is to review the current timing of PcP prophylaxis after HT, the specific potential risk factors for PcP after HT, and the determinants of a prompt diagnosis and therapeutic approach in critically ill patients. We will also present a possible proposal for future investigations on indications for long-term prophylaxis.
Collapse
Affiliation(s)
- Carlo Burzio
- Department of Anesthesia, Intensive Care and Emergency, Città della Salute e della Scienza di Torino Hospital, 10126 Torino, Italy; (C.B.); (G.M.); (A.C.T.); (L.B.)
| | - Eleonora Balzani
- Department of Surgical Science, University of Turin, 10124 Torino, Italy
| | - Silvia Corcione
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10124 Turin, Italy;
- School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Giorgia Montrucchio
- Department of Anesthesia, Intensive Care and Emergency, Città della Salute e della Scienza di Torino Hospital, 10126 Torino, Italy; (C.B.); (G.M.); (A.C.T.); (L.B.)
- Department of Surgical Science, University of Turin, 10124 Torino, Italy
| | - Anna Chiara Trompeo
- Department of Anesthesia, Intensive Care and Emergency, Città della Salute e della Scienza di Torino Hospital, 10126 Torino, Italy; (C.B.); (G.M.); (A.C.T.); (L.B.)
| | - Luca Brazzi
- Department of Anesthesia, Intensive Care and Emergency, Città della Salute e della Scienza di Torino Hospital, 10126 Torino, Italy; (C.B.); (G.M.); (A.C.T.); (L.B.)
- Department of Surgical Science, University of Turin, 10124 Torino, Italy
| |
Collapse
|
6
|
Zhang X, Tang X, Yi X, Lei Y, Lu S, Li T, Yue R, Pan L, Feng G, Huang X, Wang Y, Cheng D. Etiologic characteristics revealed by mNGS-mediated ultra-early and early microbiological identification in airway secretions from lung transplant recipients. Front Immunol 2023; 14:1271919. [PMID: 37809079 PMCID: PMC10551139 DOI: 10.3389/fimmu.2023.1271919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background Post-operative etiological studies are critical for infection prevention in lung transplant recipients within the first year. In this study, mNGS combined with microbial culture was applied to reveal the etiological characteristics within one week (ultra-early) and one month (early) in lung transplant recipients, and the epidemiology of infection occurred within one month. Methods In 38 lung transplant recipients, deep airway secretions were collected through bronchofiberscope within two hours after the operation and were subjected to microbial identification by mNGS and microbial culture. The etiologic characteristics of lung transplant recipients were explored. Within one month, the infection status of recipients was monitored. The microbial species detected by mNGS were compared with the etiological agents causing infection within one month. Results The detection rate of mNGS in the 38 airway secretions specimens was significantly higher than that of the microbial culture (P<0.0001). MNGS identified 143 kinds of pathogenic microorganisms; bacterial pathogens account for more than half (72.73%), with gram-positive and -negative bacteria occupying large proportions. Fungi such as Candida are also frequently detected. 5 (50%) microbial species identified by microbial culture had multiple drug resistance (MDR). Within one month, 26 (68.42%) recipients got infected (with a median time of 9 days), among which 10 (38.46%) cases were infected within one week. In the infected recipients, causative agents were detected in advance by mNGS in 9 (34.62%) cases, and most of them (6, 66.67%) were infected within one week (ultra-early). In the infection that occurred after one week, the consistency between mNGS results and the etiological agents was decreased. Conclusion Based on the mNGS-reported pathogens in airway secretions samples collected within two hours, the initial empirical anti-infection regimes covering the bacteria and fungi are reasonable. The existence of bacteria with MDR forecasts the high risk of infection within 48 hours after transplant, reminding us of the necessity to adjust the antimicrobial strategy. The predictive role of mNGS performed within two hours in etiological agents is time-limited, suggesting continuous pathogenic identification is needed after lung transplant.
Collapse
Affiliation(s)
- Xiaoqin Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuemei Tang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoli Yi
- Medical Department, Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yu Lei
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Sen Lu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Tianlong Li
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Gang Feng
- Department of Thoracic Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaobo Huang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Wang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Deyun Cheng
- Department of Respiratory and Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
| |
Collapse
|
7
|
Aghbash PS, Rasizadeh R, Arefi V, Nahand JS, Baghi HB. Immune-checkpoint expression in antigen-presenting cells (APCs) of cytomegaloviruses infection after transplantation: as a diagnostic biomarker. Arch Microbiol 2023; 205:280. [PMID: 37430000 DOI: 10.1007/s00203-023-03623-8] [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: 05/25/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/12/2023]
Abstract
Cytomegalovirus (CMV), a member of the Herpesviridae family, mostly causes only slight feverish symptoms or can be asymptomatic in immunocompetent individuals. However, it is known to be particularly a significant cause of morbidity in immunocompromised patients, including transplant recipients, whose immune system has been weakened due to the consumption of immunosuppressor drugs. Therefore, the diagnosis of CMV infection after transplantation is crucial. New diagnostic methods for the quick detection of CMV have been developed as a result of understanding the clinical importance of invasive CMV. Antigen-presenting cells (APCs) and T cells are important components of the immune system and it may be possible to diagnose viral infections using immunological markers, such as lymphocytosis, cytotoxic T lymphocytes (CTL), and serum cytokine levels. Moreover, PD-1, CTLA 4, and TIGIT, which are expressed on certain T cells and antigen-presenting cells, are over-expressed during the infection. The assessment of CMV infection based on T cell and APC activity, and the expression of immunological checkpoints, can be helpful for the diagnosis of transplant patients at risk for CMV infection. In this review, we will investigate how immune checkpoints affect immune cells and how they impair organ transplantation after CMV infection.
Collapse
Affiliation(s)
- Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reyhaneh Rasizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Arefi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran.
| |
Collapse
|
8
|
Li S, Qin J, Zhou P, Peng M, Qian J, Cai Y, Shi Q, Tung TH, Shen B, Yu S. The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections. Front Cell Infect Microbiol 2022; 12:961746. [PMID: 36590589 PMCID: PMC9801411 DOI: 10.3389/fcimb.2022.961746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Objective Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce. Methods A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms. Results The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group. Conclusion In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.
Collapse
Affiliation(s)
- Shixiao Li
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiajia Qin
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Peng Zhou
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Minfei Peng
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiao Qian
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Yingying Cai
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Qingxin Shi
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Bo Shen
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Sufei Yu
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China,*Correspondence: Sufei Yu,
| |
Collapse
|
9
|
Guohui J, Kun W, Dong T, Ji Z, Dong L, Dong W, Jingyu C. Microbiosis in lung allotransplantation and xenotransplantation: State of the art and future perspective. HEALTH CARE SCIENCE 2022; 1:119-128. [PMID: 38938886 PMCID: PMC11080722 DOI: 10.1002/hcs2.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 06/29/2024]
Abstract
The respiratory tract is known to harbor a microbial community including bacteria, viruses, and fungi. New techniques contribute enormously to the identification of unknown or culture-independent species and reveal the interaction of the community with the host immune system. The existing respiratory microbiome and substantial equilibrium of the transplanted microbiome from donor lung grafts provide an extreme bloom of dynamic changes in the microenvironment in lung transplantation (LT) recipients. Dysbiosis in grafts are not only related to the modified microbial components but also involve the kinetics of the host-graft "talk," which signifies the destination of graft allograft injury, acute rejection, infection, and chronic allograft dysfunction development in short- and long-term survival. Microbiome-derived factors may contribute to lung xenograft survival when using genetically multimodified pig-derived organs. Here, we review the most advanced knowledge of the dynamics and resilience of microbial communities in transplanted lungs with various pretransplant indications. Conceptual and analytical points of view have been illustrated along the time series, gaining insight into the microbiome and lung grafts. Future endeavors on precise tools, sophisticated models, and novel targeted regimens are needed to improve the long-term survival in these patients.
Collapse
Affiliation(s)
- Jiao Guohui
- Center for Medical Device Evaluation, NMPABeijingChina
| | - Wu Kun
- Center for Medical Device Evaluation, NMPABeijingChina
| | - Tian Dong
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduChina
| | - Zhang Ji
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Liu Dong
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Wei Dong
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| | - Chen Jingyu
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical UniversityWuxiChina
| |
Collapse
|