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Cilloniz C, Dy-Agra G, Pagcatipunan RS, Torres A. Viral Pneumonia: From Influenza to COVID-19. Semin Respir Crit Care Med 2024; 45:207-224. [PMID: 38228165 DOI: 10.1055/s-0043-1777796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Respiratory viruses are increasingly recognized as a cause of community-acquired pneumonia (CAP). The implementation of new diagnostic technologies has facilitated their identification, especially in vulnerable population such as immunocompromised and elderly patients and those with severe cases of pneumonia. In terms of severity and outcomes, viral pneumonia caused by influenza viruses appears similar to that caused by non-influenza viruses. Although several respiratory viruses may cause CAP, antiviral therapy is available only in cases of CAP caused by influenza virus or respiratory syncytial virus. Currently, evidence-based supportive care is key to managing severe viral pneumonia. We discuss the evidence surrounding epidemiology, diagnosis, management, treatment, and prevention of viral pneumonia.
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Affiliation(s)
- Catia Cilloniz
- Hospital Clinic of Barcelona, IDIBAPS, CIBERESA, Barcelona, Spain
- Faculty of Health Sciences, Continental University, Huancayo, Peru
| | - Guinevere Dy-Agra
- Institute of Pulmonary Medicine, St Luke's Medical Center-Global City, Taguig, Metro Manila, Philippines
| | - Rodolfo S Pagcatipunan
- Institute of Pulmonary Medicine, St Luke's Medical Center-Global City, Taguig, Metro Manila, Philippines
| | - Antoni Torres
- Hospital Clinic of Barcelona, IDIBAPS, CIBERESA, Barcelona, Spain
- School of Medicine, University of Barcelona, Barcelona, Spain
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2
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Chai R, Zhou C, Hu Z, Hu J. Diagnostic predictability of serum miR-4793-3p and miR-1180-3p expression in community-acquired pneumonia. Biomark Med 2024; 18:231-241. [PMID: 38456294 PMCID: PMC11216277 DOI: 10.2217/bmm-2023-0463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/07/2023] [Indexed: 03/09/2024] Open
Abstract
Background: Early identification of community-acquired pneumonia (CAP) is crucial to prevent severe progression. Methods: The authors enrolled 150 hospitalized CAP patients and collected clinicopathologic features and blood indicators. Plasma miRNA profiling was conducted using microarray detection, and selected miRNAs were tested with reverse transcription quantitative PCR. Predictive models were built using least shrinkage and selection operator regression. Results: Least shrinkage and selection operator regression identified two miRNAs (miR-4793-3p and miR-1180-3p) that distinguished mild from severe CAP patients (area under the curve = 0.948). The miRNA model outperformed D-dimer, platelet and procalcitonin (max area under the curve = 0.729). Conclusion: Increased levels of miR-4793-3p and miR-1180-3p may indicate severe pneumonia development. Plasma miRNA profiling enables early prediction of severe CAP, aiding therapeutic decisions.
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Affiliation(s)
- Rong Chai
- Department of Respiratory & Critical Care Medicine, Changhai Hospital, Navy Military Medical University, No. 168 Changhai RD, Yangpu District, Shanghai, P.R. China
| | - Cihang Zhou
- Department of General Practice Teaching & Research Office, Changhai Hospital, Navy Military Medical University, No. 168 Changhai RD, Yangpu District, Shanghai, P.R. China
| | - Zhenli Hu
- Department of Respiratory & Critical Care Medicine, Changhai Hospital, Navy Military Medical University, No. 168 Changhai RD, Yangpu District, Shanghai, P.R. China
| | - Jingjing Hu
- Department of Clinical Laboratory, Changhai Hospital, Navy Military Medical University, No. 168 Changhai RD, Yangpu District, Shanghai, P.R. China
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Gress C, Litzenburger T, Schmid R, Xiao K, Heissig F, Muller M, Gupta A, Hohlfeld JM. Transcriptomic characterization of the human segmental endotoxin challenge model. Sci Rep 2024; 14:1721. [PMID: 38242945 PMCID: PMC10798985 DOI: 10.1038/s41598-024-51547-0] [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: 10/04/2023] [Accepted: 01/06/2024] [Indexed: 01/21/2024] Open
Abstract
Segmental instillation of lipopolysaccharide (LPS) by bronchoscopy safely induces transient airway inflammation in human lungs. This model enables investigation of pulmonary inflammatory mechanisms as well as pharmacodynamic analysis of investigational drugs. The aim of this work was to describe the transcriptomic profile of human segmental LPS challenge with contextualization to major respiratory diseases. Pre-challenge bronchoalveolar lavage (BAL) fluid and biopsies were sampled from 28 smoking, healthy participants, followed by segmental instillation of LPS and saline as control. Twenty-four hours post instillation, BAL and biopsies were collected from challenged lung segments. Total RNA of cells from BAL and biopsy samples were sequenced and analysed for differentially expressed genes (DEGs). After challenge with LPS compared with saline, 6316 DEGs were upregulated and 241 were downregulated in BAL, but only one DEG was downregulated in biopsy samples. Upregulated DEGs in BAL were related to molecular functions such as "Inflammatory response" or "chemokine receptor activity", and upregulated pro-inflammatory pathways such as "Wnt-"/"Ras-"/"JAK-STAT" "-signaling pathway". Furthermore, the segmental LPS challenge model resembled aspects of the five most prevalent respiratory diseases chronic obstructive pulmonary disease (COPD), asthma, pneumonia, tuberculosis and lung cancer and featured similarities with acute exacerbations in COPD (AECOPD) and community-acquired pneumonia. Overall, our study provides extensive information about the transcriptomic profile from BAL cells and mucosal biopsies following LPS challenge in healthy smokers. It expands the knowledge about the LPS challenge model providing potential overlap with respiratory diseases in general and infection-triggered respiratory insults such as AECOPD in particular.
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Affiliation(s)
- Christina Gress
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Clinical Airway Research, 30625, Hannover, Germany
- German Center for Lung Research (DZL-BREATH), Hannover, Germany
| | | | - Ramona Schmid
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ke Xiao
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Clinical Airway Research, 30625, Hannover, Germany
| | - Florian Heissig
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Meike Muller
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Clinical Airway Research, 30625, Hannover, Germany
- German Center for Lung Research (DZL-BREATH), Hannover, Germany
| | - Abhya Gupta
- Boehringer Ingelheim International GmbH, Biberach an der Riss, Germany
| | - Jens M Hohlfeld
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Clinical Airway Research, 30625, Hannover, Germany.
- German Center for Lung Research (DZL-BREATH), Hannover, Germany.
- Hannover Medical School, Department of Respiratory Medicine and Infectious Disease, Hannover, Germany.
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4
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Adukauskiene D, Ciginskiene A, Adukauskaite A, Koulenti D, Rello J. Clinical Features and Outcomes of VAP Due to Multidrug-Resistant Klebsiella spp.: A Retrospective Study Comparing Monobacterial and Polybacterial Episodes. Antibiotics (Basel) 2023; 12:1056. [PMID: 37370375 DOI: 10.3390/antibiotics12061056] [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: 05/10/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
VAP due to multidrug-resistant (MDR) bacteria is a frequent infection among patients in ICUs. Patient characteristics and mortality in mono- and polybacterial cases of VAP may differ. A single-centre, retrospective 3-year study was conducted in the four ICUs of a Lithuanian referral university hospital, aiming to compare both the clinical features and the 60-day ICU all-cause mortality of monobacterial and polybacterial MDR Klebsiella spp. VAP episodes. Of the 86 MDR Klebsiella spp. VAP episodes analyzed, 50 (58.1%) were polybacterial. The 60-day mortality was higher (p < 0.05) in polybacterial episodes: overall (50.0 vs. 27.8%), in the sub-group with less-severe disease (SOFA < 8) at VAP onset (45.5 vs. 15.0%), even with appropriate treatment (41.7 vs. 12.5%), and the sub-group of extended drug-resistant (XDR) Klebsiella spp. (46.4 vs. 17.6%). The ICU mortality (44.0 vs. 22.5%) was also higher in the polybacterial episodes. The monobacterial MDR Klebsiella spp. VAP was associated (p < 0.05) with prior hospitalization (61.1 vs. 40.0%), diabetes mellitus (30.6 vs. 5.8%), obesity (30.6 vs. 4.7%), prior antibiotic therapy (77.8 vs. 52.0%), prior treatment with cephalosporins (66.7 vs. 36.0%), and SOFA cardiovascular ≥ 3 (44.4 vs. 10.0%) at VAP onset. Patients with polybacterial VAP were more likely (p < 0.05) to be comatose (22.2 vs. 52.0%) and had a higher SAPS II score (median [IQR] 45.0 [35.25-51.1] vs. 50.0 [40.5-60.75]) at VAP onset. Polybacterial MDR Klebsiella spp. VAP had distinct demographic and clinical characteristics compared to monobacterial, and was associated with poorer outcomes.
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Affiliation(s)
- Dalia Adukauskiene
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Ausra Ciginskiene
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Agne Adukauskaite
- Department of Cardiology and Angiology, University Hospital of Innsbruck, 6020 Innsbruck, Austria
| | - Despoina Koulenti
- Second Critical Care Department, Attikon University Hospital, 12462 Athens, Greece
- UQ Centre for Clinical Research (UQCCR), Faculty of Medicine, The Univesrity of Queensland, 4029 Brisbane, Australia
| | - Jordi Rello
- Vall d'Hebron Institute of Research, Vall d'Hebron Campus Hospital, 08035 Barcelona, Spain
- Clinical Research, CHU Nîmes, 30900 Nîmes, France
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5
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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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6
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Abstract
Severe pneumonia is associated with high mortality (short and long term), as well as pulmonary and extrapulmonary complications. Appropriate diagnosis and early initiation of adequate antimicrobial treatment for severe pneumonia are crucial in improving survival among critically ill patients. Identifying the underlying causative pathogen is also critical for antimicrobial stewardship. However, establishing an etiological diagnosis is challenging in most patients, especially in those with chronic underlying disease; those who received previous antibiotic treatment; and those treated with mechanical ventilation. Furthermore, as antimicrobial therapy must be empiric, national and international guidelines recommend initial antimicrobial treatment according to the location's epidemiology; for patients admitted to the intensive care unit, specific recommendations on disease management are available. Adherence to pneumonia guidelines is associated with better outcomes in severe pneumonia. Yet, the continuing and necessary research on severe pneumonia is expansive, inviting different perspectives on host immunological responses, assessment of illness severity, microbial causes, risk factors for multidrug resistant pathogens, diagnostic tests, and therapeutic options.
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Affiliation(s)
- Catia Cillóniz
- Department of pneumology, Hospital Clinic of Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Centers in Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Antoni Torres
- Department of pneumology, Hospital Clinic of Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- Biomedical Research Networking Centers in Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Michael S Niederman
- Weill Cornell Medical College, Department of Pulmonary Critical Care Medicine, New York, NY, USA
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7
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Paukner S, Mariano D, Das AF, Moran GJ, Sandrock C, Waites KB, File TM. Lefamulin in Patients with Community-Acquired Bacterial Pneumonia Caused by Atypical Respiratory Pathogens: Pooled Results from Two Phase 3 Trials. Antibiotics (Basel) 2021; 10:antibiotics10121489. [PMID: 34943700 PMCID: PMC8698636 DOI: 10.3390/antibiotics10121489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/08/2023] Open
Abstract
Lefamulin was the first systemic pleuromutilin antibiotic approved for intravenous and oral use in adults with community-acquired bacterial pneumonia based on two phase 3 trials (Lefamulin Evaluation Against Pneumonia [LEAP]-1 and LEAP-2). This pooled analysis evaluated lefamulin efficacy and safety in adults with community-acquired bacterial pneumonia caused by atypical pathogens (Mycoplasma pneumoniae, Legionella pneumophila, and Chlamydia pneumoniae). In LEAP-1, participants received intravenous lefamulin 150 mg every 12 h for 5–7 days or moxifloxacin 400 mg every 24 h for 7 days, with optional intravenous-to-oral switch. In LEAP-2, participants received oral lefamulin 600 mg every 12 h for 5 days or moxifloxacin 400 mg every 24 h for 7 days. Primary outcomes were early clinical response at 96 ± 24 h after first dose and investigator assessment of clinical response at test of cure (5–10 days after last dose). Atypical pathogens were identified in 25.0% (91/364) of lefamulin-treated patients and 25.2% (87/345) of moxifloxacin-treated patients; most were identified by ≥1 standard diagnostic modality (M. pneumoniae 71.2% [52/73]; L. pneumophila 96.9% [63/65]; C. pneumoniae 79.3% [46/58]); the most common standard diagnostic modality was serology. In terms of disease severity, more than 90% of patients had CURB-65 (confusion of new onset, blood urea nitrogen > 19 mg/dL, respiratory rate ≥ 30 breaths/min, blood pressure <90 mm Hg systolic or ≤60 mm Hg diastolic, and age ≥ 65 years) scores of 0–2; approximately 50% of patients had PORT (Pneumonia Outcomes Research Team) risk class of III, and the remaining patients were more likely to have PORT risk class of II or IV versus V. In patients with atypical pathogens, early clinical response (lefamulin 84.4–96.6%; moxifloxacin 90.3–96.8%) and investigator assessment of clinical response at test of cure (lefamulin 74.1–89.7%; moxifloxacin 74.2–97.1%) were high and similar between arms. Treatment-emergent adverse event rates were similar in the lefamulin (34.1% [31/91]) and moxifloxacin (32.2% [28/87]) groups. Limitations to this analysis include its post hoc nature, the small numbers of patients infected with atypical pathogens, the possibility of PCR-based diagnostic methods to identify non-etiologically relevant pathogens, and the possibility that these findings may not be generalizable to all patients. Lefamulin as short-course empiric monotherapy, including 5-day oral therapy, was well tolerated in adults with community-acquired bacterial pneumonia and demonstrated high clinical response rates against atypical pathogens.
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Affiliation(s)
- Susanne Paukner
- Nabriva Therapeutics GmbH, Leberstrasse 20, 1110 Vienna, Austria
- Correspondence: ; Tel.: +43-1-74093-1224
| | - David Mariano
- Nabriva Therapeutics US, Inc., Fort Washington, PA 19034, USA;
| | | | | | - Christian Sandrock
- Department of Internal Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA;
| | - Ken B. Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
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8
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Menéndez R, Méndez R, Torres A. Respuesta a «Dual antibiotic therapy for outpatient management of community-acquired pneumonia?». Arch Bronconeumol 2020; 56:766-767. [DOI: 10.1016/j.arbres.2020.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/29/2022]
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9
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Defining Community-Acquired Pneumonia as a Public Health Threat: Arguments in Favor from Spanish Investigators. Med Sci (Basel) 2020; 8:medsci8010006. [PMID: 31991843 PMCID: PMC7151587 DOI: 10.3390/medsci8010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/18/2023] Open
Abstract
Despite advances in its prevention, pneumonia remains associated with high morbidity, mortality, and health costs worldwide. Studies carried out in the last decade have indicated that more patients with community-acquired pneumonia (CAP) now require hospitalization. In addition, pneumonia management poses many challenges, especially due to the increase in the number of elderly patients with multiple comorbidities, antibiotic-resistant pathogens, and the difficulty of rapid diagnosis. In this new call to action, we present a wide-ranging review of the information currently available on CAP and offer some reflections on ways to raise awareness of this disease among the general public. We discuss the burden of CAP and the importance of attaining better, faster microbiological diagnosis and initiating appropriate treatment. We also suggest that closer cooperation between health professionals and the population at large could improve the management of this largely preventable infectious disease that takes many lives each year.
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10
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Bertrams W, Griss K, Han M, Seidel K, Klemmer A, Sittka-Stark A, Hippenstiel S, Suttorp N, Finkernagel F, Wilhelm J, Greulich T, Vogelmeier CF, Vera J, Schmeck B. Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation. Sci Rep 2020; 10:241. [PMID: 31937830 PMCID: PMC6959367 DOI: 10.1038/s41598-019-57108-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023] Open
Abstract
Lower respiratory infections, such as community-acquired pneumonia (CAP), and chronic obstructive pulmonary disease (COPD) rank among the most frequent causes of death worldwide. Improved diagnostics and profound pathophysiological insights are urgent clinical needs. In our cohort, we analysed transcriptional networks of peripheral blood mononuclear cells (PBMCs) to identify central regulators and potential biomarkers. We investigated the mRNA- and miRNA-transcriptome of PBMCs of healthy subjects and patients suffering from CAP or AECOPD by microarray and Taqman Low Density Array. Genes that correlated with PBMC composition were eliminated, and remaining differentially expressed genes were grouped into modules. One selected module (120 genes) was particularly suitable to discriminate AECOPD and CAP and most notably contained a subset of five biologically relevant mRNAs that differentiated between CAP and AECOPD with an AUC of 86.1%. Likewise, we identified several microRNAs, e.g. miR-545-3p and miR-519c-3p, which separated AECOPD and CAP. We furthermore retrieved an integrated network of differentially regulated mRNAs and microRNAs and identified HNF4A, MCC and MUC1 as central network regulators or most important discriminatory markers. In summary, transcriptional analysis retrieved potential biomarkers and central molecular features of CAP and AECOPD.
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Affiliation(s)
- Wilhelm Bertrams
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Kathrin Griss
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Maria Han
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Kerstin Seidel
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Andreas Klemmer
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Alexandra Sittka-Stark
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany
| | - Stefan Hippenstiel
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - University Medicine Berlin, Berlin, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Genomics Core Facility, Philipps-University of Marburg, Marburg, Germany
| | - Jochen Wilhelm
- Justus-Liebig-University, Universities Giessen & Marburg Lung Center, German Center for Lung Research (DZL), Giessen, Germany
| | - Timm Greulich
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Claus F Vogelmeier
- Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center, German Center for Lung Research (DZL), Marburg, Germany. .,Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, German Center for Lung Research (DZL), Marburg, Germany. .,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University of Marburg, Marburg, Germany. .,German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Marburg, Germany.
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11
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Multidrug Resistant Gram-Negative Bacteria in Community-Acquired Pneumonia. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:79. [PMID: 30850010 PMCID: PMC6408800 DOI: 10.1186/s13054-019-2371-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2019. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2019. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.
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12
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Civljak R, Tot T, Falsey AR, Huljev E, Vranes J, Ljubin-Sternak S. Viral pathogens associated with acute respiratory illness in hospitalized adults and elderly from Zagreb, Croatia, 2016 to 2018. J Med Virol 2019; 91:1202-1209. [PMID: 30801727 PMCID: PMC7166480 DOI: 10.1002/jmv.25437] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
Aims To investigate the viral etiology of acute respiratory infection (ARI) in hospitalized adults and elderly patients in Croatia, compare the prevalence of detected viruses, and to determine clinical characteristics and seasonal occurrence of investigated infections. Methods From January 2016 to June 2018, a total of 182 adult patients presented with symptoms of ARI and admitted to the hospital were tested for 15 respiratory viruses by multiplex reverse‐transcription polymerase chain reaction. Clinical data were collected by retrospective analysis of the patient's chart. Results A virus was identified in 106 (58.5%) of the patients. The most commonly detected virus was influenza virus (41.5%), followed by respiratory syncytial virus (13.8%), human metapneumovirus (13.0%), parainfluenza viruses (12.2%), rhinoviruses (11.4%), adenovirus and coronaviruses with equal frequencies (3.3%), and enterovirus (1.6%). The serum level of C‐reactive protein and white blood cell count were significantly lower in patients with respiratory viruses identified when compared with those in whom no virus was detected (P < 0.001 and
P = 0.007, respectively). There were no differences in clinical symptoms according to the type of the detected virus, except for more frequent illness exposure recall for influenza infection (
P = 0.010). Influenza, parainfluenza, and pneumoviruses were detected mostly in winter months, while rhinoviruses in autumn and spring. Conclusions In addition to influenza, pneumoviruses, rhinoviruses, and parainfluenza viruses play an important role in etiology of ARIs in adults. Fast and accurate laboratory diagnosis for respiratory viruses in routine practice is needed for clinicians optimally manage patients with ARI and potentially avoid the unnecessary use of antimicrobial drugs.
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Affiliation(s)
- Rok Civljak
- Department of Respiratory Tract Infections, Dr Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tatjana Tot
- Department of Microbiology, General Hospital Karlovac, Karlovac, Croatia
| | - Ann R Falsey
- Department of Medicine, Rochester General Hospital and University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Eva Huljev
- Department of Respiratory Tract Infections, Dr Fran Mihaljevic University Hospital for Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jasmina Vranes
- Department of Clinical Microbiology, Dr Andrija Stampar Teaching Institute of Public Health, Zagreb, Croatia.,Department of Medical Microbiology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Suncanica Ljubin-Sternak
- Department of Clinical Microbiology, Dr Andrija Stampar Teaching Institute of Public Health, Zagreb, Croatia.,Department of Medical Microbiology, University of Zagreb School of Medicine, Zagreb, Croatia
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Huang T, Zhang M, Tong X, Chen J, Yan G, Fang S, Guo Y, Yang B, Xiao S, Chen C, Huang L, Ai H. Microbial communities in swine lungs and their association with lung lesions. Microb Biotechnol 2019; 12:289-304. [PMID: 30556308 PMCID: PMC6389860 DOI: 10.1111/1751-7915.13353] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung-lesion phenotype and investigated lung microbial communities by sequencing the V3-V4 region of 16S rRNA gene for each individual. We found reduced microbial diversity but more biomass in the severe-lesion lungs. Methylotenera, Prevotella, Sphingobium and Lactobacillus were the prominent bacteria in the healthy lungs, while Mycoplasma, Ureaplasma, Sphingobium, Haemophilus and Phyllobacterium were the most abundant microbes in the severe-lesion lungs. Notably, we identified 64 lung-lesion-associated OTUs, of which two classified to Mycoplasma were positively associated with lung lesions and 62 showed negative association including thirteen classified to Prevotella and six to Ruminococcus. Cross-validation analysis showed that lung microbiota explained 23.7% phenotypic variance of lung lesions, suggesting that lung microbiota had large effects on promoting lung healthy. Furthermore, 22 KEGG pathways correlated with lung lesions were predicted. Altogether, our findings improve the knowledge about swine lung microbial communities and give insights into the relationship between lung microbiota and lung lesions.
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Affiliation(s)
- Tao Huang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Mingpeng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Xinkai Tong
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Jiaqi Chen
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Guorong Yan
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Shaoming Fang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Yuanmei Guo
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Bin Yang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Congying Chen
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Lusheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Huashui Ai
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
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14
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Abstract
A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.
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15
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Vincent JL. Multidrug Resistant Gram-Negative Bacteria in Community-Acquired Pneumonia. ANNUAL UPDATE IN INTENSIVE CARE AND EMERGENCY MEDICINE 2019 2019. [PMCID: PMC7119995 DOI: 10.1007/978-3-030-06067-1_36] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Community-acquired pneumonia (CAP) is associated with high morbidity and mortality worldwide [1]. Although several different bacteria and respiratory viruses can be responsible for CAP, Streptococcus pneumoniae (pneumococcus) remains the most common causative pathogen. A small proportion of CAP cases are caused by Gram-negative bacteria, especially Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii and Stenotrophomona maltophilia [2, 3]. The main problem concerning the treatment of Gram-negative bacterial infections is their related antibiotic resistance, reported as multidrug resistant (MDR = resistant to at least one agent in three or more groups of antibiotics), extensively drug resistant (XDR = resistant to at least one agent in all but two or fewer groups of antibiotics) and pan-drug resistant (PDR = resistant to all groups of antibiotics) [4]. This makes the clinical management of pneumonia caused by such pathogens a challenge for physicians. Taking into account the clinical severity that may be associated with CAP caused by Gram-negative bacteria (respiratory failure, bacteremia, shock, acute respiratory distress syndrome [ARDS]) the magnitude of the global health problem is tremendous.
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Affiliation(s)
- Jean-Louis Vincent
- Dept. of Intensive Care, Erasme Hospital, Université libre de Bruxelles, Brussels, Belgium
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16
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Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A 2018; 115:E12353-E12362. [PMID: 30482864 PMCID: PMC6310811 DOI: 10.1073/pnas.1809700115] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In critically ill patients, noninfectious respiratory syndromes that resemble LRTIs further complicate diagnosis and confound targeted treatment. To address this, we developed a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response. We studied this approach in a prospective cohort of critically ill patients with acute respiratory failure and found that combining pathogen, microbiome, and host gene expression metrics achieved accurate LRTI diagnosis and identified etiologic pathogens in patients with clinically identified infections but otherwise negative testing. Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86–1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63–0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75–1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.
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Okumura J, Shindo Y, Takahashi K, Sano M, Sugino Y, Yagi T, Taniguchi H, Saka H, Matsui S, Hasegawa Y. Mortality in patients with community-onset pneumonia at low risk of drug-resistant pathogens: Impact of β-lactam plus macrolide combination therapy. Respirology 2017; 23:526-534. [PMID: 29239493 DOI: 10.1111/resp.13232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/01/2017] [Accepted: 11/07/2017] [Indexed: 01/14/2023]
Abstract
BACKGROUND AND OBJECTIVE Drug-resistant pathogen (DRP) risk stratification is important for choosing a treatment strategy for community-onset pneumonia. Evidence for benefits of non-antipseudomonal β-lactam plus macrolide combination therapy (BLM) on mortality is limited in patients at low DRP risk. Risk factors for mortality remain to be clarified. METHODS Post hoc analysis using a prospective multicentre study cohort of community-onset pneumonia was performed to assess 30-day differences in mortality between non-antipseudomonal β-lactam monotherapy (BL) and BLM groups. Logistic regression analysis was performed to assess the therapeutic effect and risk factors for mortality in patients at low DRP risk. RESULTS In total, 594 patients with community-onset pneumonia at low DRP risk (369 BL and 225 BLM) were analysed. The 30-day mortality in BL and BLM was 13.8% and 1.8%, respectively (P < 0.001). Multivariate analysis showed that BLM reduced the 30-day mortality (adjusted odds ratio: 0.28, 95% CI: 0.09-0.87) compared with BL. Independent prognostic factors for 30-day mortality included arterial partial pressure of carbon dioxide (PaCO2 ) > 50 mm Hg, white blood cell count < 4000/mm3 , non-ambulatory status, albumin < 3.0 g/dL, haematocrit < 30%, age ≥ 80 years, respiratory rate > 25/min and body temperature < 36°C. CONCLUSION In patients with community-onset pneumonia at low DRP risk, BLM treatment reduced 30-day mortality compared with BL. Independent risk factors for mortality are potential confounding factors when assessing antibiotic effects in randomized clinical trials.
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Affiliation(s)
- Junya Okumura
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Shindo
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kunihiko Takahashi
- Department of Biostatistics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Sano
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuteru Sugino
- Department of Respiratory Medicine, Toyota Memorial Hospital, Toyota, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya, Japan
| | - Hiroyuki Taniguchi
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Japan
| | - Hideo Saka
- Department of Respiratory Medicine, National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
| | - Shigeyuki Matsui
- Department of Biostatistics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Development of an Extended-Specificity Multiplex Immunoassay for Detection of Streptococcus pneumoniae Serotype-Specific Antigen in Urine by Use of Human Monoclonal Antibodies. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00262-17. [PMID: 28978509 DOI: 10.1128/cvi.00262-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/30/2017] [Indexed: 11/20/2022]
Abstract
Current pneumococcal vaccines cover the 10 to 23 most common serotypes of the 92 presently described. However, with the increased usage of pneumococcal-serotype-based vaccines, the risk of serotype replacement and an increase in disease caused by nonvaccine serotypes remains. Serotype surveillance of pneumococcal infections relies heavily on culture techniques, which are known to be insensitive, particularly in cases of noninvasive disease. Pneumococcal-serotype-specific urine assays offer an alternative method of serotyping for both invasive and noninvasive disease. However, the assays described previously cover mainly conjugate vaccine serotypes, give little information about circulating nonvaccine serotypes, and are currently available only in one or two specialist laboratories. Our laboratory has developed a Luminex-based extended-range antigen capture assay to detect pneumococcal-serotype-specific antigens in urine samples. The assay targets 24 distinct serotypes/serogroups plus the cell wall polysaccharide (CWP) and some cross-reactive serotypes. We report that the assay is capable of detecting all the targeted serotypes and the CWP at 0.1 ng/ml, while some serotypes are detected at concentrations as low as 0.3 pg/ml. The analytical serotype specificity was determined to be 98.4% using a panel of polysaccharide-negative urine specimens spiked with nonpneumococcal bacterial antigens. We also report clinical sensitivities of 96.2% and specificities of 89.9% established using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease. This assay can be extended for testing other clinical samples and has the potential to greatly improve serotype-specific surveillance in the many cases of pneumococcal disease in which a culture is never obtained.
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19
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Nasopharyngeal polymicrobial colonization during health, viral upper respiratory infection and upper respiratory bacterial infection. J Infect 2017; 75:26-34. [PMID: 28412081 DOI: 10.1016/j.jinf.2017.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVES We sought to understand how polymicrobial colonization varies during health, viral upper respiratory infection (URI) and acute upper respiratory bacterial infection to understand differences in infection-prone vs. non-prone patients. METHODS Nasopharyngeal (NP) samples were collected from 74 acute otitis media (AOM) infection-prone and 754 non-prone children during 2094 healthy visits, 673 viral URI visits and 631 AOM visits. Three otopathogens Streptococcus pneumoniae (Spn), Nontypeable Haemophilus influenzae (NTHi), and Moraxella catarrhalis (Mcat) were identified by culture. RESULTS NP colonization rates of multiple otopathogens during health were significantly lower than during viral URI, and during URI they were lower than at onset of upper respiratory bacterial infection in both AOM infection-prone and non-prone children. AOM infection-prone children had higher polymicrobial colonization rates than non-prone children during health, viral URI and AOM. Polymicrobial colonization rates of AOM infection-prone children during health were equivalent to that of non-prone children during viral URI, and during viral URI were equivalent to that of non-prone during AOM infection. Spn colonization was positively associated with NTHi and Mcat colonization during health, but negatively during AOM infection. CONCLUSION The infection-prone patients more frequently have multiple potential bacterial pathogens in the NP than the non-prone patients. Polymicrobial interaction in the NP differs during health and at onset of infection.
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20
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Restrepo MI, Chalmers JD, Song Y, Mallow C, Hewlett J, Maldonado F, Yarmus L. Year in review 2016: Respiratory infections, acute respiratory distress syndrome, pleural diseases, lung cancer and interventional pulmonology. Respirology 2017; 22:602-611. [PMID: 28244617 PMCID: PMC5889848 DOI: 10.1111/resp.13016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Marcos I Restrepo
- South Texas Veterans Health Care System and University of Texas Health, San Antonio, TX, USA
| | - James D Chalmers
- Scottish Centre for Respiratory Research, Dundee, UK
- School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Justin Hewlett
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Lonny Yarmus
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
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21
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Sahuquillo-Arce JM, Menéndez R, Méndez R, Amara-Elori I, Zalacain R, Capelastegui A, Aspa J, Borderías L, Martín-Villasclaras JJ, Bello S, Alfageme I, de Castro FR, Rello J, Molinos L, Ruiz-Manzano J, Torres A. Age-related risk factors for bacterial aetiology in community-acquired pneumonia. Respirology 2016; 21:1472-1479. [PMID: 27417291 DOI: 10.1111/resp.12851] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/01/2016] [Accepted: 05/09/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND OBJECTIVE The objective of this study was to evaluate the effect of age and comorbidities, smoking and alcohol use on microorganisms in patients with community-acquired pneumonia (CAP). METHODS A prospective multicentre study was performed with 4304 patients. We compared microbiological results, bacterial aetiology, smoking, alcohol abuse and comorbidities in three age groups: young adults (<45 years), adults (45-64 years) and seniors (>65 years). RESULTS Bacterial aetiology was identified in 1522 (35.4%) patients. In seniors, liver disease was independently associated with Gram-negative bacteria (Haemophilus influenzae and Enterobacteriaceae), COPD with Pseudomonas aeruginosa (OR = 2.69 (1.46-4.97)) and Staphylococcus aureus (OR = 2.8 (1.24-6.3)) and neurological diseases with S. aureus. In adults, diabetes mellitus (DM) was a risk factor for Streptococcus pneumoniae and S. aureus, and COPD for H. influenzae (OR = 3.39 (1.06-10.83)). In young adults, DM was associated with S. aureus. Smoking was a risk factor for Legionella pneumophila regardless of age. Alcohol intake was associated with mixed aetiology and Coxiella burnetii in seniors, and with S. pneumoniae in young adults. CONCLUSION It should be considered that the bacterial aetiology may differ according to the patient's age, comorbidities, smoking and alcohol abuse. More extensive microbiological testing is warranted in those with risk factors for infrequent microorganisms.
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Affiliation(s)
| | - Rosario Menéndez
- Pneumology Service, IIS/ University and Politechnic Hospital La Fe, Valencia, Spain. .,CIBERES, Valencia, Spain.
| | - Raúl Méndez
- Pneumology Service, IIS/ University and Politechnic Hospital La Fe, Valencia, Spain.,CIBERES, Valencia, Spain
| | - Isabel Amara-Elori
- Pneumology Service, IIS/ University and Politechnic Hospital La Fe, Valencia, Spain.,CIBERES, Valencia, Spain
| | - Rafael Zalacain
- Pneumology Service, University Hospital Cruces, Bilbao, Spain
| | | | - Javier Aspa
- Pneumology Service, University Hospital of Princesa, Madrid, Spain
| | | | | | - Salvador Bello
- Pneumology Service, University Hospital Miguel Servet, Zaragoza, Spain
| | | | | | - Jordi Rello
- Critical Care Unit, University Hospital Joan XXIII, Tarragona, Spain.,Critical Care Unit, University Hospital Vall Hebron, Autonomous University of Barcelona, Barcelona, Spain
| | - Luis Molinos
- Pneumology Service, University Hospital Central, Oviedo, Spain
| | | | - Antoni Torres
- CIBERES, Valencia, Spain.,Pneumology Service, Clinic Hospital, IDIBAPS, University of Barcelona, Barcelona, Spain
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22
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Wang H, Dai W, Qiu C, Li S, Wang W, Xu J, Li Z, Wang H, Li Y, Yang Z, Feng X, Zhou Q, Han L, Li Y, Zheng Y. Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota. J Thorac Dis 2016; 8:1316-22. [PMID: 27293852 DOI: 10.21037/jtd.2016.04.63] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pneumonia is one of the most serious diseases for children, with which lung microbiota are proved to be associated. We performed 16S rDNA analysis on broncho-alveolar lavage fluid (BALF) for 32 children with tracheomalacia (C group), pneumonia infected with Streptococcus pneumoniae (S. pneumoniae) (D1 group) or Mycoplasma pneumoniae (M. pneumoniae) (D2 group). Children with tracheomalacia held lower microbial diversity and accumulated Lactococcus (mean ± SD, 45.21%±5.07%, P value <0.05), Porphyromonas (0.12%±0.31%, P value <0.05). D1 and D2 group were enriched by Streptococcus (7.57%±11.61%, P value <0.01 when compared with D2 group) and Mycoplasma (0.67%±1.25%, P value <0.01) respectively. Bacterial correlation in C group was mainly intermediated by Pseudomonas and Arthrobacter. Whilst, D1 group harbored simplest microbial correlation in three groups, and D2 group held the most complicated network, involving enriched Staphylococcus (0.26%±0.71%), Massilia (0.81%±2.42%). This will be of significance for understanding pneumonia incidence and progression more comprehensively, and discerning between bacterial infection and carriage.
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Affiliation(s)
- Heping Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Wenkui Dai
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Chuangzhao Qiu
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Shuaicheng Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Wenjian Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Jianqiang Xu
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Zhichuan Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Hongmei Wang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yuzheng Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Zhenyu Yang
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Xin Feng
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Qian Zhou
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Lijuan Han
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yinhu Li
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
| | - Yuejie Zheng
- 1 Department of Respiratory Diseases, Shenzhen Children's Hospital, Shenzhen 518026, China ; 2 WeHealthGene, Shenzhen 518000, China ; 3 Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue Kowloon, Hong Kong, China ; 4 Shenzhen University Medical Center, Shenzhen University, Shenzhen 518052, China
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Murdoch DR. How best to determine causative pathogens of pneumonia. Pneumonia (Nathan) 2016; 8:1. [PMID: 28702281 PMCID: PMC5469189 DOI: 10.1186/s41479-016-0004-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
The biggest recent development in pneumonia diagnostics has been the increased availability and use of nucleic acid detection assays, although this change has brought with it new challenges about the interpretation of positive results. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens.
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Affiliation(s)
- David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, P.O. Box 4345, Christchurch, 8140 New Zealand
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24
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Murdoch DR. How recent advances in molecular tests could impact the diagnosis of pneumonia. Expert Rev Mol Diagn 2016; 16:533-40. [PMID: 26891612 PMCID: PMC7103682 DOI: 10.1586/14737159.2016.1156536] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.
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Affiliation(s)
- David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, and Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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Sircar M, Ranjan P, Gupta R, Jha OK, Gupta A, Kaur R, Chavhan N, Singh M, Singh SK. Authors' commentary: Impact of bronchoalveolar lavage multiplex PCR on microbiological yield and therapeutic decisions in severe pneumonia in ICU. J Crit Care 2016; 33:275-6. [PMID: 27037048 DOI: 10.1016/j.jcrc.2016.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 02/21/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Mrinal Sircar
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Prashant Ranjan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Rajesh Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Onkar Kumar Jha
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Amit Gupta
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Ravneet Kaur
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India; SRL Diagnostics, Fortis Hospital, NOIDA, India.
| | - Neela Chavhan
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Mukta Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
| | - Sujeet Kumar Singh
- Department of Pulmonology and Critical Care Medicine, Fortis Hospital, NOIDA, Uttar Pradesh, India.
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