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Sumon MSI, Hossain MSA, Al-Sulaiti H, Yassine HM, Chowdhury MEH. Enhancing Influenza Detection through Integrative Machine Learning and Nasopharyngeal Metabolomic Profiling: A Comprehensive Study. Diagnostics (Basel) 2024; 14:2214. [PMID: 39410618 PMCID: PMC11476346 DOI: 10.3390/diagnostics14192214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/24/2024] [Accepted: 09/27/2024] [Indexed: 10/20/2024] Open
Abstract
Background/Objectives: Nasal and nasopharyngeal swabs are commonly used for detecting respiratory viruses, including influenza, which significantly alters host cell metabolites. This study aimed to develop a machine learning model to identify biomarkers that differentiate between influenza-positive and -negative cases using clinical metabolomics data. Method: A publicly available dataset of 236 nasopharyngeal samples screened via liquid chromatography-quadrupole time-of-flight (LC/Q-TOF) mass spectrometry was used. Among these, 118 samples tested positive for influenza (40 A H1N1, 39 A H3N2, 39 Influenza B), while 118 were negative controls. A stacking-based model was proposed using the top 20 selected features. Thirteen machine learning models were initially trained, and the top three were combined using predicted probabilities to form a stacking classifier. Results: The ExtraTrees stacking model outperformed other models, achieving 97.08% accuracy. External validation on a prospective cohort of 96 symptomatic individuals (48 positive and 48 negatives for influenza) showed 100% accuracy. SHAP values were used to enhance model explainability. Metabolites such as Pyroglutamic Acid (retention time: 0.81 min, m/z: 84.0447) and its in-source fragment ion (retention time: 0.81 min, m/z: 130.0507) showed minimal impact on influenza-positive cases. On the other hand, metabolites with a retention time of 10.34 min and m/z 106.0865, and a retention time of 8.65 min and m/z 211.1376, demonstrated significant positive contributions. Conclusions: This study highlights the effectiveness of integrating metabolomics data with machine learning for accurate influenza diagnosis. The stacking-based model, combined with SHAP analysis, provided robust performance and insights into key metabolites influencing predictions.
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Affiliation(s)
| | - Md Sakib Abrar Hossain
- Department of Electrical Engineering, Qatar University, Doha 2713, Qatar; (M.S.I.S.); (M.S.A.H.)
| | - Haya Al-Sulaiti
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Muhammad E. H. Chowdhury
- Department of Electrical Engineering, Qatar University, Doha 2713, Qatar; (M.S.I.S.); (M.S.A.H.)
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2
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Duggal N, Gupta P, Ambalavanan N, Gupta N, Muthu V. The need for "eagle-eyed screening": Owl's eyes in bronchoalveolar lavage cytology. Diagn Cytopathol 2024; 52:533-537. [PMID: 39031526 DOI: 10.1002/dc.25384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/22/2024]
Affiliation(s)
- Nisha Duggal
- Department of Cytology and Gynecologic Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Parikshaa Gupta
- Department of Cytology and Gynecologic Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nivetha Ambalavanan
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nalini Gupta
- Department of Cytology and Gynecologic Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Valliappan Muthu
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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3
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Bhide M, Singh O, Nasa P, Juneja D. Cytomegalovirus infection in non-immunocompromised critically ill patients: A management perspective. World J Virol 2024; 13:89135. [PMID: 38616856 PMCID: PMC11008403 DOI: 10.5501/wjv.v13.i1.89135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 03/11/2024] Open
Abstract
Critically ill patients are a vulnerable group at high risk of developing secondary infections. High disease severity, prolonged intensive care unit (ICU) stay, sepsis, and multiple drugs with immunosuppressive activity make these patients prone to immuneparesis and increase the risk of various opportunistic infections, including cytomegalovirus (CMV). CMV seroconversion has been reported in up to 33% of ICU patients, but its impact on patient outcomes remains a matter of debate. Even though there are guidelines regarding the management of CMV infection in immunosuppressive patients with human immunodeficiency virus/ acquired immuno deficiency syndrome, the need for treatment and therapeutic approaches in immunocompetent critically ill patients is still ambiguous. Even the diagnosis of CMV infection may be challenging in such patients due to non-specific symptoms and multiorgan involvement. Hence, a better understanding of the symptomatology, diagnostics, and treatment options may aid intensive care physicians in ensuring accurate diagnoses and instituting therapeutic interventions.
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Affiliation(s)
- Madhura Bhide
- Institute of Critical Care Medicine, Max Super Speciality Hospital, Saket, New Delhi 110017, India
| | - Omender Singh
- Institute of Critical Care Medicine, Max Super Speciality Hospital, Saket, New Delhi 110017, India
| | - Prashant Nasa
- Department of Critical Care Medicine, NMC Specialty Hospital, Dubai 7832, United Arab Emirates
| | - Deven Juneja
- Institute of Critical Care Medicine, Max Super Speciality Hospital, Saket, New Delhi 110017, India
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Diaz-Decaro J, Myers E, Mucha J, Neumann M, Lewandowski W, Kaczanowska M, Schmidt E, Natenshon A, Talarico C, Buck PO. A systematic literature review of the economic and healthcare resource burden of cytomegalovirus. Curr Med Res Opin 2023; 39:973-986. [PMID: 37395088 DOI: 10.1080/03007995.2023.2222583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 05/22/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
OBJECTIVE Cytomegalovirus (CMV) can infect individuals at any age, including infants, who may contract it from infected mothers (congenital CMV [cCMV]). Whereas CMV infection is typically asymptomatic or causes mild illness in healthy individuals, infection can result in severe outcomes in immunocompromised individuals and in infants with cCMV. This systematic review aims to characterize the economic impact of CMV and cCMV infections. METHODS Medline, Embase, and LILACS databases were searched for publications reporting the economic impact of cCMV and CMV infections across all age groups. Manuscripts published between 2010 and 2020 from Australia, Latin America, Canada, Europe, Israel, Japan, the United States, and global (international, worldwide) studies were included; congress materials were excluded. Outcomes of interest included cCMV- and CMV-attributable direct costs/charges, resource utilization, and indirect/societal costs. RESULTS Of 751 records identified, 518 were excluded based on duplication, population, outcome, study design, or country. Overall, 55 articles were eligible for full-text review; 25 were further excluded due to population, outcome, study design, or congress abstract. Two publications were additionally identified, resulting in economic impact data compiled from 32 publications. Of these, 24 publications reported cost studies of cCMV or CMV, including evaluation of direct costs/charges, healthcare resource utilization, and indirect/societal costs, and 7 publications reported economic evaluations of interventions. The populations, methods and outcomes used across these studies varied widely. CONCLUSIONS CMV and cCMV infections impose a considerable economic impact on different countries, populations, and outcomes. There are substantial evidence gaps where further research is warranted.
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Affiliation(s)
| | - Evan Myers
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
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5
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Cilloniz C, Luna CM, Hurtado JC, Marcos MÁ, Torres A. Respiratory viruses: their importance and lessons learned from COVID-19. Eur Respir Rev 2022; 31:220051. [PMID: 36261158 PMCID: PMC9724808 DOI: 10.1183/16000617.0051-2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 01/08/2023] Open
Abstract
Respiratory virus infection can cause severe illnesses capable of inducing acute respiratory failure that can progress rapidly to acute respiratory distress syndrome (ARDS). ARDS is related to poor outcomes, especially in individuals with a higher risk of infection, such as the elderly and those with comorbidities, i.e. obesity, asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. Despite this, effective antiviral treatments available for severe viral lung infections are scarce. The coronavirus disease 2019 (COVID-19) pandemic demonstrated that there is also a need to understand the role of airborne transmission of respiratory viruses. Robust evidence supporting this exists, but better comprehension could help implement adequate measures to mitigate respiratory viral infections. In severe viral lung infections, early diagnosis, risk stratification and prognosis are essential in managing patients. Biomarkers can provide reliable, timely and accessible information possibly helpful for clinicians in managing severe lung viral infections. Although respiratory viruses highly impact global health, more research is needed to improve care and prognosis of severe lung viral infections. In this review, we discuss the epidemiology, diagnosis, clinical characteristics, management and prognosis of patients with severe infections due to respiratory viruses.
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Affiliation(s)
- Catia Cilloniz
- Pneumology Dept, Respiratory Institute, Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
- Faculty of Health Sciences, Continental University, Huancayo, Peru
| | - Carlos M Luna
- Pneumology Division, Hospital of Clínicas, Faculty of Medicine, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan Carlos Hurtado
- Dept of Microbiology, Hospital Clinic, Universitat de Barcelona, ISGlobal, Barcelona, Spain
| | - María Ángeles Marcos
- Dept of Microbiology, Hospital Clinic, Universitat de Barcelona, ISGlobal, Barcelona, Spain
| | - Antoni Torres
- Pneumology Dept, Respiratory Institute, Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
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6
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Zhang Z, Li R, Chen Y, Zhang J, Zheng Y, Xu M, Liang J, Li J, Huang Y, Xu Y, He W, Liu X, Li Y. Association between active cytomegalovirus infection and lung fibroproliferation in adult patients with acute respiratory distress syndrome: a retrospective study. BMC Infect Dis 2022; 22:788. [PMID: 36241980 PMCID: PMC9562065 DOI: 10.1186/s12879-022-07747-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 09/20/2022] [Indexed: 12/05/2022] Open
Abstract
Background Cytomegalovirus (CMV) has high seroprevalence, and its active infection is associated with several adverse prognoses in adult patients with acute respiratory distress syndrome (ARDS). However, the role of active CMV infection in ARDS-associated fibroproliferation is unknown. This study aimed at determining the association between active CMV infection and lung fibroproliferation in adult patients with ARDS. Methods We retrospectively reviewed the medical records of all adult patients with ARDS who were admitted to the intensive care unit (ICU) from January 2018 to December 2020 at a national university-affiliated hospital in China. Study subjects were divided into active and non-active CMV infection groups based on CMV DNAemia within a 28-day ICU hospitalization. Lung fibroproliferation was measured using chest high-resolution computed tomography (HRCT) and N-terminal peptide of serum procollagen III (NT-PCP-III) within the first 28 days of ICU admission. Pulmonary fibrosis, clinical features, laboratory findings, treatment measures, and clinical outcomes were compared between the two groups. Results Among the 87 ARDS patients included in this study, the incidence of active CMV infection was 16.1% within the 28-day ICU admission period. In logistic regression analyze, active CMV infection was found to be associated with higher pulmonary fibrogenesis, pulmonary fibrosis score, and NT-PCP-III level (P < 0.05). The duration of ICU stay in ARDS patients with active CMV infection was significantly higher than in those without active CMV infection (P < 0.05). Conclusions Among adult patients with ARDS, active CMV infection was related to poor clinical outcomes. Active CMV infection was associated with ARDS-associated fibroproliferation. Prophylactic and preemptive use of anti-CMV agents on pulmonary fibrosis should be assessed to determine a consensus therapeutic strategy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07747-y.
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Affiliation(s)
- Zhihui Zhang
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Rujian Li
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Yubiao Chen
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Jierong Zhang
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Yongxin Zheng
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Minmin Xu
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Jiaqi Liang
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Jiahui Li
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.,Guangzhou Medical University, Guangzhou, 511436, Guangdong, People's Republic of China
| | - Yongbo Huang
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Yonghao Xu
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Weiqun He
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Xiaoqing Liu
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.
| | - Yimin Li
- Department of Critical Care Medicine, State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, People's Republic of China.
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7
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Jiang W, Chen S, Xu L, Xu X, Huang L, Wang Y, Hao C. Presence of Cytomegalovirus Infection Is Associated With an Unfavorable Outcome in Immunocompetent Infants With Pertussis. Front Cell Infect Microbiol 2022; 12:800452. [PMID: 35252027 PMCID: PMC8895427 DOI: 10.3389/fcimb.2022.800452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background We aimed to examine cytomegalovirus (CMV) infection in immunocompetent infants with pertussis, based on polymerase chain reaction in plasma and broncho alveolar lavage (BAL), and to assess the clinical characteristics and outcomes for these patients. Methods We performed a prospective observational cohort study of consecutive infants with pertussis in Children’s Hospital of Soochow University between Jan 2017 and Jan 2020. We report the burden of CMV PCR in plasma and BAL within this patient group, and evaluate associations between CMV infection and pertussis in these hospitalized infants. Results During the study period, 1,867 infants <1 years were evaluated for pertussis, 190 infants were diagnosed as pertussis. For the 190 pertussis patients, 38 (20.0%) patients had positive CMV PCR in plasma. CMV PCR in plasma had high sensitivity and specificity for CMV PCR in BAL (81.3% and 94.4%, respectively). Children with positive CMV PCR in plasma were 3.67 times more likely to present with severe disease (OR 3.67; CI 1.61-8.36). Comparisons of duration of hospital stay curves using the log-rank test statistic demonstrated that the relative risk of longer hospital stay of positive CMV PCR relative to negative CMV was 1.51 (95% CI: 1.05 to 2.14, P = 0.01). Conclusions Our study reported a high prevalence of CMV reactivation in immunocompetent infants with lower respiratory tract infection. The presence of CMV in plasma may be associated with an unfavorable outcome in infants with pertussis.
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Affiliation(s)
| | | | | | | | | | - Yuqing Wang
- *Correspondence: Yuqing Wang, ; Chuangli Hao,
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8
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Cillóniz C, Pericàs JM, Rojas JR, Torres A. Severe Infections Due to Respiratory Viruses. Semin Respir Crit Care Med 2022; 43:60-74. [PMID: 35172359 DOI: 10.1055/s-0041-1740982] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.
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Affiliation(s)
- Catia Cillóniz
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
| | - Juan M Pericàs
- Department of Infectious Diseases, Hospital Clinic of Barcelona, Barcelona, Spain.,Internal Medicine Department, Vall d'Hebron Institute for Research, Barcelona, Spain
| | - Jorge R Rojas
- Department of Pneumology, Hospital Regional Docente Clínico Quirúrgico Daniel Alcides Carrión, Huancayo, Perú
| | - Antoni Torres
- Department of Pneumology, Institut Clinic del Tórax, Hospital Clinic of Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Ciber de Enfermedades Respiratorias (Ciberes), Barcelona, Spain
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9
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Lécuyer R, Issa N, Tessoulin B, Lavergne RA, Morio F, Gabriel F, Canet E, Bressollette-Bodin C, Guillouzouic A, Boutoille D, Raffi F, Lecomte R, Le Turnier P, Deschanvres C, Camou F, Gaborit BJ. Epidemiology and clinical impact of respiratory co-infections at diagnosis of Pneumocystis jirovecii Pneumonia. J Infect Dis 2021; 225:868-880. [PMID: 34604908 DOI: 10.1093/infdis/jiab460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES To describe the epidemiology and clinical impact of respiratory co-infections at diagnosis of Pneumocystis jirovecii Pneumonia (PcP). METHODS A retrospective observational study was conducted between January 2011 and April 2019 to evaluate respiratory co-infections at diagnosis of PcP patients, in two tertiary care hospitals. Respiratory co-infection was defined by the identification of pathogens from P. jirovecii-positive samples. RESULTS Of the 7 882 respiratory samples tested for P. jirovecii during the 8-year study period, 328 patients with final diagnosis of PcP were included in this study. Mean age was 56.7 ± 14.9 years, 193 (58.8%) were male, 74 (22.6%) had a positive HIV serology, 125 (38.1%) had a viral co-infections, 76 (23.2%) a bacterial co-infections and 90-day mortality was 25.3%. In overall population, 90-Day mortality was independently associated with a solid tumor underlying disease (OR 11.8, 1.90-78, p=0.008), SOFA score at admission (OR 1.62, 1.34-2.05; p<0.001) and CMV respiratory co-infection (OR 3.44, 1.24-2.90; p=0.02). Among HIV-negative patients, respiratory CMV co-infection was associated with a worse prognosis, especially when treated with adjunctive corticosteroid therapy. CONCLUSIONS Respiratory CMV co-infection at diagnosis of PcP was independently associated with increased 90-day mortality, specifically in HIV-negative patients.
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Affiliation(s)
- Romain Lécuyer
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France.,EA 1155, Laboratory of targets and drugs for infections and cancer, IRS2-Nantes Biotech, Nantes, France
| | - Nahema Issa
- Intensive Care and Infectious Disease Unit, Groupe Saint-André, University Hospital, Bordeaux, France
| | - Benoit Tessoulin
- INSERM, U1232, Université de Nantes, Service d'Hématologie, University Hospital, Nantes, France
| | - Rose-Anne Lavergne
- EA 1155, Laboratory of targets and drugs for infections and cancer, IRS2-Nantes Biotech, Nantes, France.,Laboratoire de Parasitologie-Mycologie, Institut de Biologie, University Hospital, Nantes, France
| | - Florent Morio
- EA 1155, Laboratory of targets and drugs for infections and cancer, IRS2-Nantes Biotech, Nantes, France.,Laboratoire de Parasitologie-Mycologie, Institut de Biologie, University Hospital, Nantes, France
| | - Frederic Gabriel
- Centre Hospitalier Universitaire de Bordeaux, Service de Parasitologie Mycologie, F-33000, Bordeaux, France
| | - Emmanuel Canet
- Medical Intensive Care, University Hospital, Nantes, France
| | | | | | - David Boutoille
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France.,EA 3826, Laboratory of clinical and experimental therapeutics of infections, IRS2-Nantes Biotech, Nantes, France
| | - François Raffi
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France
| | - Raphael Lecomte
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France
| | - Paul Le Turnier
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France
| | - Colin Deschanvres
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France
| | - Fabrice Camou
- Intensive Care and Infectious Disease Unit, Groupe Saint-André, University Hospital, Bordeaux, France
| | - Benjamin Jean Gaborit
- Department of Infectious Diseases, University Hospital of Nantes and CIC 1413, INSERM, Nantes, France.,EA 3826, Laboratory of clinical and experimental therapeutics of infections, IRS2-Nantes Biotech, Nantes, France
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10
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Pacitti D, Scotton CJ, Kumar V, Khan H, Wark PAB, Torregrossa R, Hansbro PM, Whiteman M. Gasping for Sulfide: A Critical Appraisal of Hydrogen Sulfide in Lung Disease and Accelerated Aging. Antioxid Redox Signal 2021; 35:551-579. [PMID: 33736455 DOI: 10.1089/ars.2021.0039] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hydrogen sulfide (H2S) is a gaseous signaling molecule involved in a plethora of physiological and pathological processes. It is primarily synthesized by cystathionine-β-synthase, cystathionine-γ-lyase, and 3-mercaptopyruvate sulfurtransferase as a metabolite of the transsulfuration pathway. H2S has been shown to exert beneficial roles in lung disease acting as an anti-inflammatory and antiviral and to ameliorate cell metabolism and protect from oxidative stress. H2S interacts with transcription factors, ion channels, and a multitude of proteins via post-translational modifications through S-persulfidation ("sulfhydration"). Perturbation of endogenous H2S synthesis and/or levels have been implicated in the development of accelerated lung aging and diseases, including asthma, chronic obstructive pulmonary disease, and fibrosis. Furthermore, evidence indicates that persulfidation is decreased with aging. Here, we review the use of H2S as a biomarker of lung pathologies and discuss the potential of using H2S-generating molecules and synthesis inhibitors to treat respiratory diseases. Furthermore, we provide a critical appraisal of methods of detection used to quantify H2S concentration in biological samples and discuss the challenges of characterizing physiological and pathological levels. Considerations and caveats of using H2S delivery molecules, the choice of generating molecules, and concentrations are also reviewed. Antioxid. Redox Signal. 35, 551-579.
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Affiliation(s)
- Dario Pacitti
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Chris J Scotton
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Vinod Kumar
- Priority Research Centre for Healthy Lungs and Hunter Medical Research Institute, The University of Newcastle, Newcastle, Australia
| | - Haroon Khan
- Priority Research Centre for Healthy Lungs and Hunter Medical Research Institute, The University of Newcastle, Newcastle, Australia
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs and Hunter Medical Research Institute, The University of Newcastle, Newcastle, Australia
| | - Roberta Torregrossa
- Priority Research Centre for Healthy Lungs and Hunter Medical Research Institute, The University of Newcastle, Newcastle, Australia
| | - Philip M Hansbro
- Faculty of Science, Centre for Inflammation, Centenary Institute, University of Technology Sydney, Sydney, Australia
| | - Matthew Whiteman
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Nasopharyngeal metabolomics and machine learning approach for the diagnosis of influenza. EBioMedicine 2021; 71:103546. [PMID: 34419924 PMCID: PMC8385175 DOI: 10.1016/j.ebiom.2021.103546] [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: 03/26/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Background Respiratory virus infections are significant causes of morbidity and mortality, and may induce host metabolite alterations by infecting respiratory epithelial cells. We investigated the use of liquid chromatography quadrupole time-of-flight mass spectrometry (LC/Q-TOF) combined with machine learning for the diagnosis of influenza infection. Methods We analyzed nasopharyngeal swab samples by LC/Q-TOF to identify distinct metabolic signatures for diagnosis of acute illness. Machine learning models were performed for classification, followed by Shapley additive explanation (SHAP) analysis to analyze feature importance and for biomarker discovery. Findings A total of 236 samples were tested in the discovery phase by LC/Q-TOF, including 118 positive samples (40 influenza A 2009 H1N1, 39 influenza H3 and 39 influenza B) as well as 118 age and sex-matched negative controls with acute respiratory illness. Analysis showed an area under the receiver operating characteristic curve (AUC) of 1.00 (95% confidence interval [95% CI] 0.99, 1.00), sensitivity of 1.00 (95% CI 0.86, 1.00) and specificity of 0.96 (95% CI 0.81, 0.99). The metabolite most strongly associated with differential classification was pyroglutamic acid. Independent validation of a biomarker signature based on the top 20 differentiating ion features was performed in a prospective cohort of 96 symptomatic individuals including 48 positive samples (24 influenza A 2009 H1N1, 5 influenza H3 and 19 influenza B) and 48 negative samples. Testing performed using a clinically-applicable targeted approach, liquid chromatography triple quadrupole mass spectrometry, showed an AUC of 1.00 (95% CI 0.998, 1.00), sensitivity of 0.94 (95% CI 0.83, 0.98), and specificity of 1.00 (95% CI 0.93, 1.00). Limitations include lack of sample suitability assessment, and need to validate these findings in additional patient populations. Interpretation This metabolomic approach has potential for diagnostic applications in infectious diseases testing, including other respiratory viruses, and may eventually be adapted for point-of-care testing.
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Zhang Y, Huang Q, Zhou Z, Xie Y, Li X, Jin W, Wang R. Prognosis of severe lower respiratory tract infected patients with virus detected: a retrospective observational study. Infect Dis (Lond) 2021; 53:600-606. [PMID: 33826440 DOI: 10.1080/23744235.2021.1905874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES To compare the prognosis of severe lower respiratory tract infected patients with virus detected and patients with virus undetected by using metagenomic sequencing technology and a series of traditional serological tests. METHODS A total of 51 consecutive lower respiratory tract infected patients were enrolled in this study and samples were obtained to perform metagenomic next-generation sequencing (mNGS) and other traditional tests for virus detection. According to the results, patients were divided into a virus-detected (VD) group and a virus-undetected (VUD) group. Meanwhile, patients' demographic information, relevant baseline indicators and outcome indicators were also collected. RESULTS There were 27 patients in the VD group and 24 patients in the VUD group. Patients in the VD group had a longer mechanical ventilation (MV) supporting time [528.0 h (216.0, 997.0) vs 235.5 h (119.3, 421.3), p = .003], a higher tracheotomy rate [(63.0 vs. 29.2%), p = .016] and red blood cell (RBC) transfusion rate [(66.7 vs. 33.3%), p = .017] compared to the VUD group. The two groups had no significant difference in mortality rate, hospital length of stay (HLOS) or ICU length of stay (ICULOS). CONCLUSIONS Virus detected in patients with severe lower respiratory tract infection (LRTI) was not related to a poorer prognosis, but patients in the VD group did need more clinical resources, such as more MV support and RBC transfusion.
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Affiliation(s)
- Yuan Zhang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Qiuping Huang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Zhigang Zhou
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Yun Xie
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Xianchen Li
- Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Wei Jin
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Songjiang, China
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Hogea SP, Tudorache E, Pescaru C, Marc M, Oancea C. Bronchoalveolar lavage: role in the evaluation of pulmonary interstitial disease. Expert Rev Respir Med 2020; 14:1117-1130. [PMID: 32847429 DOI: 10.1080/17476348.2020.1806063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Bronchoalveolar lavage (BAL), a noninvasive, well-tolerated procedure is an important diagnostic tool that can facilitate the diagnosis of various lung diseases. This procedure allows the assessment of large alveolar compartments, by providing cells as well as non-cellular constituents from the lower respiratory tract. Alterations in BAL fluid and cells ratio reflects pathological changes in the lung parenchyma. In some cases, clinicians use BAL as a differential diagnosis guide for interstitial lung disease. AREAS COVERED In this review, we summarized the diagnostic criteria for BAL in interstitial lung diseases, pulmonary infections, lung cancer and other pathologies such as fat embolism, gastroesophageal reflux and collagen vascular disease. For this review, we have selected scientific papers published in the PubMed database in our area of interest. We aimed to highlight the usefulness of BAL in respiratory pathology. EXPERT OPINION Although BAL fluid analyzes has an essential role in the diagnostic work-up of many lung pathologies, it should be performed in selected patients. For accurate results, the BAL technique is very important to be standardized.
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Affiliation(s)
- Stanca-Patricia Hogea
- Department of Pulmonology, University of Medicine and Pharmacy "Victor Babeș" , Timișoara, Romania
| | - Emanuela Tudorache
- Department of Pulmonology, University of Medicine and Pharmacy "Victor Babeș" , Timișoara, Romania
| | - Camelia Pescaru
- Department of Pulmonology, University of Medicine and Pharmacy "Victor Babeș" , Timișoara, Romania
| | - Monica Marc
- Department of Pulmonology, University of Medicine and Pharmacy "Victor Babeș" , Timișoara, Romania
| | - Cristian Oancea
- Department of Pulmonology, University of Medicine and Pharmacy "Victor Babeș" , Timișoara, Romania
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