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Philippot Q, Rammaert B, Dauriat G, Daubin C, Schlemmer F, Costantini A, Tandjaoui-Lambiotte Y, Neuville M, Desrochettes E, Ferré A, Contentin LB, Lescure FX, Megarbane B, Belle A, Dellamonica J, Jaffuel S, Meynard JL, Messika J, Lau N, Terzi N, Runge I, Sanchez O, Zuber B, Guerot E, Rouze A, Pavese P, Bénézit F, Quenot JP, Souloy X, Fanton AL, Boutoille D, Bunel V, Vabret A, Gaillat J, Bergeron A, Lapidus N, Fartoukh M, Voiriot G. Human metapneumovirus infection is associated with a substantial morbidity and mortality burden in adult inpatients. Heliyon 2024; 10:e33231. [PMID: 39035530 PMCID: PMC11259828 DOI: 10.1016/j.heliyon.2024.e33231] [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: 12/05/2023] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/23/2024] Open
Abstract
Background Human metapneumovirus (hMPV) is one of the leading respiratory viruses. This prospective observational study aimed to describe the clinical features and the outcomes of hMPV-associated lower respiratory tract infections in adult inpatients. Methods Consecutive adult patients admitted to one of the 31 participating centers with an acute lower respiratory tract infection and a respiratory multiplex PCR positive for hMPV were included. A primary composite end point of complicated course (hospital death and/or the need for invasive mechanical ventilation) was used. Results Between March 2018 and May 2019, 208 patients were included. The median age was 74 [62-84] years. Ninety-seven (47 %) patients were men, 187 (90 %) had at least one coexisting illness, and 67 (31 %) were immunocompromised. Median time between first symptoms and hospital admission was 3 [2-7] days. The two most frequent symptoms were dyspnea (86 %) and cough (85 %). The three most frequent clinical diagnoses were pneumonia (42 %), acute bronchitis (20 %) and acute exacerbation of chronic obstructive pulmonary disease (16 %). Among the 52 (25 %) patients who had a lung CT-scan, the most frequent abnormality was ground glass opacity (41 %). While over four-fifths of patients (81 %) received empirical antibiotic therapy, a bacterial coinfection was diagnosed in 61 (29 %) patients. Mixed flora (16 %) and enterobacteria (5 %) were the predominant documentations. The composite criterion of complicated course was assessable in 202 (97 %) patients, and present in 37 (18 %) of them. In the subpopulation of pneumonia patients (42 %), we observed a more complicated course in those with a bacterial coinfection (8/24, 33 %) as compared to those without (5/60, 8 %) (p = 0.02). Sixty (29 %) patients were admitted to the intensive care unit. Among them, 23 (38 %) patients required invasive mechanical ventilation. In multivariable analysis, tachycardia and alteration of consciousness were identified as risk factors for complicated course. Conclusion hMPV-associated lower respiratory tract infections in adult inpatients mostly involved elderly people with pre-existing conditions. Bacterial coinfection was present in nearly 30 % of the patients. The need for mechanical ventilation and/or the hospital death were observed in almost 20 % of the patients.
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Affiliation(s)
- Quentin Philippot
- Sorbonne Université, Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, Paris, France
| | | | | | - Cédric Daubin
- CHU de Caen Normandie, médecine intensive réanimation, 14000, CAEN, France
| | - Frédéric Schlemmer
- Université Paris Est Créteil, Faculté de Santé, INSERM, IMRB, Créteil, France
- AP-HP, Hôpitaux Universitaires Henri Mondor, Unité de Pneumologie, Service de Médecine Intensive et Réanimation, Créteil, France
| | | | | | - Mathilde Neuville
- Service de médecine intensive réanimation, AP-HP, Hôpital Bichat Claude-Bernard, France
| | | | - Alexis Ferré
- Service de réanimation médico-chirurgicale, centre hospitalier de Versailles, France
| | - Laetitia Bodet Contentin
- Médecine Intensive Réanimation, INSERM CIC 1415, CRICS-TriGGERSep Network, CHRU de Tours and methodS in Patient-Centered Outcomes and Health ResEarch (SPHERE), INSERM UMR 1246, Université de Tours, Tours, France
| | | | - Bruno Megarbane
- Service de médecine intensive réanimation, AP-HP, Hôpital Lariboisière, France
| | - Antoine Belle
- Service de pneumologie, centre hospitalier intercommunal Compiègne Moyon, France
| | - Jean Dellamonica
- Service de médecine intensive réanimation, UR2CA - Université Cote d’Azur, CHU de Nice, France
| | - Sylvain Jaffuel
- Service de maladies infectieuses et tropicales, CHRU de Brest, France
| | - Jean-Luc Meynard
- Maladies infectieuses et tropicales, AP-HP, Hôpital Saint Antoine, France
| | - Jonathan Messika
- Réanimation médico-chirurgicale, AP-HP, Hôpital Louis Mourier, France
| | - Nicolas Lau
- Réanimation, surveillance continue, Site de Longjumeau Groupe Hospitalier Nord-Essone, France
| | - Nicolas Terzi
- Médecine Intensive Réanimation, CHU Grenoble Alpes, France
| | | | - Olivier Sanchez
- Université Paris Cité, Service de pneumologie et soins Intensifs, HEGP, AP-HP Centre Université Paris Cité, France
| | | | - Emmanuel Guerot
- Service de médecine intensive réanimation, AP-HP, HEGP, France
| | - Anahita Rouze
- Univ. Lille, Inserm U1285, CHU Lille, Service de Médecine Intensive – Réanimation, CNRS, UMR 8576, UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Patricia Pavese
- Service des maladies infectieuses, CHU Grenoble Alpes, France
| | - François Bénézit
- Service de Maladies Infectieuses et Réanimation Médicale, CHU de Rennes, France
| | | | - Xavier Souloy
- Réanimation polyvalente, Centre hospitalier public du Cotentin, France
| | - Anne Lyse Fanton
- Service de pneumologie et soins intensifs respiratoires, CHU Dijon Bourgogne, France
| | - David Boutoille
- Service de maladies infectieuses et tropicales, CHU de Nantes, France
| | - Vincent Bunel
- Service de Pneumologie B, Hôpital Bichat, Paris, France
| | - Astrid Vabret
- FéNoMIH, CHU de Caen et de Rouen, GRAM EA2656, laboratoire de virologie, Normandie université, CHU de Caen, France
| | | | - Anne Bergeron
- Service de pneumologie, Hôpitaux universitaires de Genève, Genève, Switzerland
| | - Nathanaël Lapidus
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Public Health Department, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Muriel Fartoukh
- Sorbonne Université, Groupe de Recherche Clinique CARMAS Université Paris Est Créteil, Assistance Publique - Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, Paris, France
| | - Guillaume Voiriot
- Sorbonne Université, Centre de Recherche Saint-Antoine UMRS_938 INSERM, Assistance Publique – Hôpitaux de Paris, Service de Médecine Intensive Réanimation, Hôpital Tenon, Paris, France
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2
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Bongers KS, Massett A, O'Dwyer DN. The Oral-Lung Microbiome Axis in Connective Tissue Disease-Related Interstitial Lung Disease. Semin Respir Crit Care Med 2024; 45:449-458. [PMID: 38626906 DOI: 10.1055/s-0044-1785673] [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: 05/24/2024]
Abstract
Connective tissue disease-related interstitial lung disease (CTD-ILD) is a frequent and serious complication of CTD, leading to high morbidity and mortality. Unfortunately, its pathogenesis remains poorly understood; however, one intriguing contributing factor may be the microbiome of the mouth and lungs. The oral microbiome, which is a major source of the lung microbiome through recurrent microaspiration, is altered in ILD patients. Moreover, in recent years, several lines of evidence suggest that changes in the oral and lung microbiota modulate the pulmonary immune response and thus may play a role in the pathogenesis of ILDs, including CTD-ILD. Here, we review the existing data demonstrating oral and lung microbiota dysbiosis and possible contributions to the development of CTD-ILD in rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, and systemic lupus erythematosus. We identify several areas of opportunity for future investigations into the role of the oral and lung microbiota in CTD-ILD.
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Affiliation(s)
- Kale S Bongers
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Angeline Massett
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - David N O'Dwyer
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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3
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Hunold KM, Rozycki E, Brummel N. Optimizing Diagnosis and Management of Community-acquired Pneumonia in the Emergency Department. Emerg Med Clin North Am 2024; 42:231-247. [PMID: 38641389 PMCID: PMC11212456 DOI: 10.1016/j.emc.2024.02.001] [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] [Indexed: 04/21/2024]
Abstract
Pneumonia is split into 3 diagnostic categories: community-acquired pneumonia (CAP), health care-associated pneumonia, and ventilator-associated pneumonia. This classification scheme is driven not only by the location of infection onset but also by the predominant associated causal microorganisms. Pneumonia is diagnosed in over 1.5 million US emergency department visits annually (1.2% of all visits), and most pneumonia diagnosed by emergency physicians is CAP.
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Affiliation(s)
- Katherine M Hunold
- Department of Emergency Medicine, The Ohio State University, 376 W 10th Avenue, 760 Prior Hall, Columbus, OH 43220, USA.
| | - Elizabeth Rozycki
- Emergency Medicine, Department of Pharmacy, The Ohio State University, 376 W 10th Avenue, 760 Prior Hall, Columbus, OH 43220, USA
| | - Nathan Brummel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, The Ohio State University, 376 W 10th Avenue, 760 Prior Hall, Columbus, OH 43220, USA
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4
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Noparatvarakorn C, Jakkul W, Seng R, Tandhavanant S, Ottiwet O, Janon R, Saikong W, Chantratita N. Optimization and prospective evaluation of sensitive real-time PCR assays with an internal control for the diagnosis of melioidosis in Thailand. Microbiol Spectr 2023; 11:e0103923. [PMID: 37819125 PMCID: PMC10715024 DOI: 10.1128/spectrum.01039-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/18/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Melioidosis is a serious infectious disease caused by Burkholderia pseudomallei, an environmental Gram-negative bacterium. Early detection of B. pseudomallei infection is crucial for successful antibiotic treatment and reducing mortality rates associated with melioidosis. Bacteria culture is currently used to identify B. pseudomallei in clinical samples, but the method is slow. Therefore, there is a need for more accurate and sensitive molecular-based diagnostic methods that can detect B. pseudomallei in all sample types, including samples from blood. We developed an optimal DNA extraction method for B. pseudomallei from plasma samples and used an internal control for real-time PCR. We evaluated six PCR target genes and identified the most effective target for the early detection of B. pseudomallei infection in patients. To prevent delays in the treatment of melioidosis that can lead to fatal outcomes, we recommend implementing this new approach for routine early detection of B. pseudomallei in clinical settings.
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Affiliation(s)
- Chawitar Noparatvarakorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wallop Jakkul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orawan Ottiwet
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Rachan Janon
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | | | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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5
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Musher DM. Problems with etiologic diagnosis of community-acquired pneumonia using plasma microbial cell-free DNA sequencing. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e206. [PMID: 38028926 PMCID: PMC10654952 DOI: 10.1017/ash.2023.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Daniel M. Musher
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
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6
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Kitsios GD, Nguyen VD, Sayed K, Al-Yousif N, Schaefer C, Shah FA, Bain W, Yang H, Fitch A, Li K, Wang X, Qin S, Gentry H, Zhang Y, Varon J, Arciniegas Rubio A, Englert JA, Baron RM, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ. The upper and lower respiratory tract microbiome in severe aspiration pneumonia. iScience 2023; 26:106832. [PMID: 37250794 PMCID: PMC10212968 DOI: 10.1016/j.isci.2023.106832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/24/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Uncertainty persists whether anaerobic bacteria represent important pathogens in aspiration pneumonia. In a nested case-control study of mechanically ventilated patients classified as macro-aspiration pneumonia (MAsP, n = 56), non-macro-aspiration pneumonia (NonMAsP, n = 91), and uninfected controls (n = 11), we profiled upper (URT) and lower respiratory tract (LRT) microbiota with bacterial 16S rRNA gene sequencing, measured plasma host-response biomarkers, analyzed bacterial communities by diversity and oxygen requirements, and performed unsupervised clustering with Dirichlet Multinomial Models (DMM). MAsP and NonMAsP patients had indistinguishable microbiota profiles by alpha diversity and oxygen requirements with similar host-response profiles and 60-day survival. Unsupervised DMM clusters revealed distinct bacterial clusters in the URT and LRT, with low-diversity clusters enriched for facultative anaerobes and typical pathogens, associated with higher plasma levels of SPD and sCD14 and worse 60-day survival. The predictive inter-patient variability in these bacterial profiles highlights the importance of microbiome study in patient sub-phenotyping and precision medicine approaches for severe pneumonia.
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Affiliation(s)
- Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Vi D. Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- University of California Los Angeles, Department of Medicine, Internal Medicine Residency Program, Los Angeles, CA90095, USA
| | - Khaled Sayed
- University of PittsburghDepartment of Computational & Systems Biology, Pittsburgh, PA15213, USA
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Nameer Al-Yousif
- University of Pittsburgh Medical Center Mercy, Department of Medicine, Pittsburgh, PA15219, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA15240, USA
| | - Haopu Yang
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Heather Gentry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Jack Varon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Antonio Arciniegas Rubio
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Joshua A. Englert
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Columbus, OH43210, USA
| | - Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02115, USA
| | - Janet S. Lee
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO63110, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
| | - Panayiotis V. Benos
- Department of Epidemiology, University of Florida, Gainesville, FL32611, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA15213, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA15213, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA15213, USA
- Acute Lung Injury Center for Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15213, USA
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Gadsby NJ, Dunn JJ, Johnson CL, McQuillan T, McHugh MP, Templeton KE, Rodriguez-Barradas MC, Musher DM. Discordance between semi-quantitative nucleic acid detection of bacteria and quantitative bacteriology in sputum from patients with pneumonia. J Infect 2023; 86:607-609. [PMID: 36863536 DOI: 10.1016/j.jinf.2023.02.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023]
Affiliation(s)
- Naomi J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
| | - James J Dunn
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Coreen L Johnson
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Taylor McQuillan
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Martin P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Maria C Rodriguez-Barradas
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Michael E. DeBakey Veterans Administration Medical Center, and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel M Musher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Michael E. DeBakey Veterans Administration Medical Center, and Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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8
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Mai W, Liu Y, Meng Q, Xu J, Wu J. Bacterial Epidemiology and Antimicrobial Resistance Profiles of Respiratory Specimens of Children with Pneumonia in Hainan, China. Infect Drug Resist 2023; 16:249-261. [PMID: 36660346 PMCID: PMC9842527 DOI: 10.2147/idr.s397513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Purpose To investigate the bacterial species and antimicrobial susceptibility of respiratory specimens of children with pneumonia in Hainan, China. Methods A total of 5017 specimens, including 4986 sputum samples, 19 bronchoalveolar lavage fluid samples and 12 tracheal tube tip samples from hospitalized children with pneumonia from April 1, 2021 to March 31, 2022 were studied. All the bacterial isolates were identified and confirmed with the VITEK 2 system. Antimicrobial susceptibility of all isolates was determined using the Kirby-Bauer method or the VITEK 2 Compact automatic system, following the breakpoints recommended by the Clinical and Laboratory Standards Institute. Results A total of 996 bacterial isolates were collected and classified into 24 species. The top 10 most frequent species were Haemophilus influenzae (356 isolates, 35.7%), Streptococcus pneumoniae (128, 12.9%), Moraxella catarrhalis (114, 11.5%), Escherichia coli (89, 8.9%), Staphylococcus aureus (89, 8.9%), Klebsiella pneumoniae (82, 8.2%), Acinetobacter baumannii (31, 3.1%), Pseudomonas aeruginosa (28, 2.8%), Enterobacter cloacae (18, 1.8%), and Streptococcus agalactiae (13, 1.3%). 70.5% strains had the resistant (R) and/or intermediate (I) phenotypes to at least one of the tested drugs, with a large proportion (54.6%) showing resistance to two or more commonly used antibiotics. In addition, 60.5% (69/114) of M. catarrhalis strains and 42.9% (153/356) of H. influenzae strains produced β-lactamases while 19.1% (17/89) E. coli and 6.1% (5/82) K. pneumoniae strains produced extended-spectrum β-lactamases. Conclusion A diversity of pathogenic bacteria were isolated from the respiratory tract of children with pneumonia in Hainan, China. High-frequency resistance to first-line antimicrobial drugs was observed in Gram-negative and Gram-positive bacteria, including 544 isolates resistant to at least two antibiotics. Rapid identification and susceptibility testing should be implemented for children with bacterial pneumonia in Hainan before drug treatment is recommended.
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Affiliation(s)
- Wenhui Mai
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Laboratory Department, Haikou Maternal and Child Health Hospital, Haikou, Hainan Province, People’s Republic of China
| | - Yiwei Liu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Qiaoyi Meng
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Jianping Xu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jinyan Wu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
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9
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De S, Hakansson AP. Measuring Niche-Associated Metabolic Activity in Planktonic and Biofilm Bacteria. Methods Mol Biol 2023; 2674:3-32. [PMID: 37258957 DOI: 10.1007/978-1-0716-3243-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Most pathobionts of the respiratory tract form biofilms during asymptomatic colonization to survive and persist in this niche. Environmental changes of the host niche, often resulting from infection with respiratory viruses, changes of the microbiota composition, or other host assaults, can result in biofilm dispersion and spread of bacteria to other host niches, resulting in infections, such as otitis media, pneumonia, sepsis, and meningitis. The niches that these bacteria encounter during colonization and infection vary markedly in nutritional availability and contain different carbon sources and levels of other essential nutrients needed for bacterial growth and survival. As these niche-related nutritional variations regulate bacterial behavior and phenotype, a better understanding of bacterial niche-associated metabolic activity is likely to provide a broader understanding of bacterial pathogenesis. In this chapter, we use Streptococcus pneumoniae as a model respiratory pathobiont. We describe methods and models used to grow bacteria planktonically or to form biofilms in vitro by incorporating crucial host environmental factors, including the various carbon sources associated with specific niches, such as the nasopharynx or bloodstream. We then present methods describing how these models can be used to study bacterial phenotypes and their association with metabolic energy production and the generation of fermentation products.
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Affiliation(s)
- Supradipta De
- Department of Translational Medicine, Division of Experimental Infection Medicine, Wallenberg Laboratory, Lund University, Malmö, Sweden
| | - Anders P Hakansson
- Department of Translational Medicine, Division of Experimental Infection Medicine, Wallenberg Laboratory, Lund University, Malmö, Sweden.
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10
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Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev 2022; 35:e0001522. [PMID: 36165783 PMCID: PMC9769922 DOI: 10.1128/cmr.00015-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.
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Affiliation(s)
- Naomi J. Gadsby
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Daniel M. Musher
- Michael E. DeBakey Veterans Administration Medical Center, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
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Lee YW, Huh JW, Hong SB, Jung J, Kim MJ, Chong YP, Kim SH, Sung H, Do KH, Lee SO, Lim CM, Kim YS, Koh Y, Choi SH. Severe Pneumonia Caused by Corynebacterium striatum in Adults, Seoul, South Korea, 2014–2019. Emerg Infect Dis 2022; 28:2147-2154. [PMID: 36287034 PMCID: PMC9622248 DOI: 10.3201/eid2811.220273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Most (70.4%) cases were hospital-acquired, and 51.9% of patients were immunocompromised. We investigated the proportion and characteristics of severe Corynebacterium striatum pneumonia in South Korea during 2014–2019. As part of an ongoing observational study of severe pneumonia among adult patients, we identified 27 severe C. striatum pneumonia cases. Most (70.4%) cases were hospital-acquired, and 51.9% of patients were immunocompromised. C. striatum cases among patients with severe hospital-acquired pneumonia (HAP) increased from 1.0% (2/200) during 2014–2015 to 5.4% (10/185) during 2018–2019, but methicillin-resistant Staphylococcus aureus (MRSA) infections among severe HAP cases decreased from 12.0% to 2.7% during the same timeframe. During 2018–2019, C. striatum was responsible for 13.3% of severe HAP cases from which bacterial pathogens were identified. The 90-day mortality rates were similarly high in the C. striatum and MRSA groups. C. striatum was a major cause of severe HAP and had high mortality rates. This pathogen is emerging as a possible cause for severe pneumonia, especially among immunocompromised patients.
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Zhuo X, Zhao J, Wang L, Sun B, Sun L, Wang C, Li B, Fan Y, Liu Y, Cao B. Development and evaluation of a multiplex quantitative polymerase chain reaction assay for detecting bacteria associated with lower respiratory tract infection. Int J Infect Dis 2022; 122:202-211. [PMID: 35644352 DOI: 10.1016/j.ijid.2022.05.052] [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: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES This study aimed to establish a multiplex quantitative polymerase chain reaction (MQ-PCR) assay for 12 bacterial pathogens found in lower respiratory tract infection (LRTI) and to evaluate its performance in a cohort of 211 patients with LRTI. METHODS The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the pilot study, we established the MQ-PCR and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency. In the clinical validation study, we obtained 211 sputum and/or bronchoalveolar lavage fluid (BALF) samples and detected pathogens by MQ-PCR. The MQ-PCR time was 3 h from sample collection to complete pathogen detection. RESULTS The limit of detection was 1000 copies/ml, and the maximum efficiency was >95%. When cutoffs of ≥105 copies/ml in sputum and ≥104 copies/ml in BALF were applied, the sensitivity, specificity, and positive and negative predictive values of the MQ-PCR were 77% (95% confidence interval [CI] 67-88%), 94% (95% CI 93-95%), 25% (95% CI 19-31%), and 99% (95% CI 99-100%), respectively. CONCLUSIONS This study demonstrates that the new MQ-PCR assay is time-saving, more effective and sensitive, and brings us closer to mainstream adoption of quantitative molecular detection of bacteria.
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Affiliation(s)
- Xianxia Zhuo
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd
| | - Bin Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Lanhua Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yingmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.
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Distribution and Drug Resistance of Bacterial Pathogens Associated with Lower Respiratory Tract Infection in Children and the Effect of COVID-19 on the Distribution of Pathogens. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:1181283. [PMID: 35368516 PMCID: PMC8965734 DOI: 10.1155/2022/1181283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
By studying the distribution and drug resistance of bacterial pathogens associated with lower respiratory tract infection (LRTI) in children in Chengdu and the effect of the COVID-19 on the distribution of pathogens and by analyzing the epidemic trend and drug resistance changes of the main pathogens of LRTI, this research is supposed to provide a useful basis for the prevention of LRTI in children and the rational use of drugs in clinical practice. Hospitalized children clinically diagnosed with LRTI in Chengdu Women and Children's Central Hospital from 2011 to 2020 were selected as the study subjects. The pathogens of LRTI in children and the distribution of pathogens in different ages, genders, seasons, years, and departments and before and after the pandemic situation of COVID-19 were counted. The drug resistance distribution of the top six pathogens with the highest infection rate in the past three years and the trend of drug resistance in the past decade were analyzed. A total of 26,469 pathogens were isolated. Among them, 6240 strains (23.6%) were Gram-positive bacteria, 20152 strains (76.1%) were Gram-negative bacteria, and 73 strains (0.3%) were fungi. Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Staphylococcus aureus were highly isolated in the group of infants aged 0-1 (P < 0.01), Moraxella catarrhalis and Streptococcus pneumoniae were highly isolated in children aged 1–6 (P < 0.01), and Haemophilus influenzae was highly isolated in children over 1 (P < 0.01). The isolation rates of Enterobacteriaceae, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Staphylococcus aureus, and Candida albicans in the lower respiratory tract of 0-1 year-old male infants were higher than those of female infants (p < 0.05). Haemophilus influenzae was highly isolated in spring and summer, and Moraxella catarrhalis was highly isolated in autumn and winter, while the infection of Streptococcus pneumoniae was mainly concentrated in winter. This difference was statistically significant (P < 0.01). Affected by the COVID-19 pandemic, the isolation rates of Haemophilus influenzae and Streptococcus pneumoniae were significantly lower than those before the pandemic, and the isolation rate of Moraxella catarrhalis was significantly higher. The difference was statistically significant (P < 0.01). The proportion of isolated negative bacteria in NICU and PICU was higher than that in positive bacteria, and the infection rates of Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Acinetobacter baumannii were higher than those in other departments. The differences were statistically significant (P < 0.01). The results of drug sensitivity test showed that the drug resistance of Haemophilus influenzae and Moraxella catarrhalis was mainly concentrated in Ampicillin, First- and Second-generation cephalosporins, and Cotrimoxazole, with stable sensitivity to Third-generation cephalosporins, while the drug resistance of Streptococcus pneumoniae was concentrated in Macrolides, Sulfonamides, and Tetracyclines, with stable sensitivity to Penicillin. Staphylococcus aureus is highly resistant to penicillins and macrolides and susceptible to vancomycin. Enterobacteriaceae resistance is concentrated in cephalosporins, with a low rate of carbapenem resistance. From 2018 to 2020, 1557 strains of Staphylococcus aureus were isolated, of which 416 strains were MRSA, accounting for 27% of the isolates; 1064 strains of Escherichia coli were isolated, of which 423 strains were ESBL and 23 strains were CRE, accounting for 40% and 2% of the isolates, respectively; and 1400 strains of Klebsiella pneumoniae were isolated, of which 385 strains were ESBL and 402 strains were CRE, accounting for 28% and 29% of the isolates, respectively. Since 2011, the resistance of Escherichia coli and Klebsiella pneumoniae to Third-generation cephalosporins has increased, peaking in 2017, and has decreased after 2018, years after which carbapenem resistance has increased significantly, corresponding to an increase in the detection rate of Carbapenem-resistant Enterobacteriaceae CRE. Findings from this study revealed that there are significant differences in community-associated infectious pathogens before and after the COVID-19 pandemic, and there are significant age differences, seasonal epidemic trends, and high departmental correlation of pathogens related to lower respiratory tract disease infection in children. There was a significant gender difference in the isolation rate of pathogens associated with LRTI in infants under one year. Vaccination, implementation of isolation measures and social distance, strengthening of personal protective measures, aseptic operation of invasive medical treatment, hand hygiene, and environmental disinfection are beneficial to reducing community-associated pathogen infection, opportunistic pathogen infection, and an increase in resistant bacteria. The strengthening of bacterial culture of lower respiratory tract samples by pediatricians is conducive to the diagnosis of respiratory tract infections caused by different pathogens, contributing to the selection of effective drugs for treatment according to drug susceptibility results, which is important for the rational use of antibiotics and curbing bacterial resistance.
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Suzuki M, Hayakawa K, Asai Y, Matsunaga N, Terada M, Ohtsu H, Toyoda A, Takasaki J, Hojo M, Yanagawa Y, Saito S, Yamamoto K, Ide S, Akiyama Y, Suzuki T, Moriya A, Mezaki K, Ohmagari N. Evaluation of the detection of other pathogens in hospitalized patients with COVID-19 at a tertiary hospital in Japan. Jpn J Infect Dis 2022; 75:419-422. [DOI: 10.7883/yoken.jjid.2021.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Michiyo Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Kayoko Hayakawa
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Yusuke Asai
- AMR Clinical Reference Center, National Center for Global Health and Medicine, Japan
| | - Nobuaki Matsunaga
- AMR Clinical Reference Center, National Center for Global Health and Medicine, Japan
| | - Mari Terada
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Hiroshi Ohtsu
- Center for Clinical Sciences, National Center for Global Health and Medicine, Japan
| | - Ako Toyoda
- Center for Clinical Sciences, National Center for Global Health and Medicine, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Japan
| | - Yasuaki Yanagawa
- AIDS Clinical Center, National Center for Global Health and Medicine, Japan
| | - Sho Saito
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Kei Yamamoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Satoshi Ide
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Yutaro Akiyama
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Tetsuya Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Ataru Moriya
- Microbiology Laboratory, National Center for Global Health and Medicine, Japan
| | - Kazuhisa Mezaki
- Microbiology Laboratory, National Center for Global Health and Medicine, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
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Jensen CS, Dargis R, Shewmaker P, Nielsen XC, Christensen JJ. Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry. Diagn Microbiol Infect Dis 2021; 101:115487. [PMID: 34339919 DOI: 10.1016/j.diagmicrobio.2021.115487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022]
Abstract
This study evaluated the ability of the MALDI-ToF MS from Bruker Daltonics to identify clinical Mitis-Group-Streptococcus isolates with a focus on Streptococcus pseudopneumoniae. The results were analyzed using the standard log(score) and the previously published list(score). Importantly, using the log(score) no misidentifications occurred and 27 of 29 (93%) S. pneumoniae and 27 of 30 (90%) S. oralis strains were identified, but only 1 of 31 (3%) S. pseudopneumoniae and 1 of 13 (8%) S. mitis strains were identified. However, our results show that 30 of 31 S. pseudopneumoniae strains had a S. pseudopneumoniae Main Spectral Profiles within the 3 best matches. Using the list(score) all S. oralis and S. pneumoniae strains were identified correctly, but list(score) misidentified 10 S. pseudopneumoniae and 5 S. mitis. We propose to use the log(score) for identification of S. pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis, but for some strains additional testing may be needed.
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Affiliation(s)
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | | | | | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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Candida species in community-acquired pneumonia in patients with chronic aspiration. Pneumonia (Nathan) 2021; 13:12. [PMID: 34218811 PMCID: PMC8256547 DOI: 10.1186/s41479-021-00090-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/17/2021] [Indexed: 01/26/2023] Open
Abstract
Background When Candida species is found in a sputum culture, clinicians generally dismiss it as a contaminant. We sought to identify cases of community-acquired pneumonia (CAP) in which Candida might play a contributory etiologic role. Methods In a convenience sample of patients hospitalized for CAP, we screened for “high-quality sputum” by Gram stain (> 20 WBC/epithelial cell) and performed quantitative sputum cultures. Criteria for a potential etiologic role for Candida included the observation of large numbers of yeast forms on Gram stain, intracellular organisms and > 106 CFU/ml Candida in sputum. We gathered clinical information on cases that met these criteria for possible Candida infection. Results Sputum from 6 of 154 consecutive CAP patients had large numbers of extra- and intracellular yeast forms on Gram stain, with > 106 CFU/ml Candida albicans, glabrata, or tropicalis on quantitative culture. In all 6 patients, the clinical diagnoses at admission included chronic aspiration. Greater than 105 CFU/ml of a recognized bacterial pathogen (Streptococcus pneumoniae, Staphylococcus aureus, or Pseudomonas) or > 106 CFU/ml of other ‘normal respiratory flora’ (Lactobacillus species) were present together with Candida spp. in every case. Blood cultures yielded Candida in 2 cases, and 1,3-beta-D glucan was > 500 ng/mL in 3 of 3 cases in which it was assayed. Since all patients were treated with anti-bacterial and anti-fungal drugs, no inference about etiology can be derived from therapeutic response. Conclusions Candida spp. together with a recognized bacterial pathogen or normal respiratory flora may contribute to the cause of CAP in patients who chronically aspirate.
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Musher DM. Macrolides as Empiric Therapy for Outpatients With Pneumonia. Open Forum Infect Dis 2021; 8:ofab062. [PMID: 34250182 PMCID: PMC8266641 DOI: 10.1093/ofid/ofab062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel M Musher
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
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Shoar S, Centeno FH, Musher DM. Clinical Features and Outcomes of Community-Acquired Pneumonia Caused by Haemophilus Influenza. Open Forum Infect Dis 2021; 8:ofaa622. [PMID: 33855100 PMCID: PMC8028099 DOI: 10.1093/ofid/ofaa622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background Long regarded as the second most common cause of community-acquired pneumonia (CAP), Haemophilus influenzae has recently been identified with almost equal frequency as pneumococcus in patients hospitalized for CAP. The literature lacks a detailed description of the presentation, clinical features, laboratory and radiologic findings, and outcomes in Haemophilus pneumonia. Methods During 2 prospective studies of patients hospitalized for CAP, we identified 33 patients with Haemophilus pneumonia. In order to provide context, we compared clinical findings in these patients with findings in 36 patients with pneumococcal pneumonia identified during the same period. We included and analyzed separately data from patients with viral coinfection. Patients with coinfection by other bacteria were excluded. Results Haemophilus pneumonia occurred in older adults who had underlying chronic lung disease, cardiac conditions, and alcohol use disorder, the same population at risk for pneumococcal pneumonia. However, in contrast to pneumococcal pneumonia, patients with Haemophilus pneumonia had less severe infection as shown by absence of septic shock on admission, less confusion, fewer cases of leukopenia or extreme leukocytosis, and no deaths at 30 days. Viral coinfection greatly increased the severity of Haemophilus, but not pneumococcal pneumonia. Conclusions We present the first thorough description of Haemophilus pneumonia, show that it is less severe than pneumococcal pneumonia, and document that viral coinfection greatly increases its severity. These distinctions are lost when the label CAP is liberally applied to all patients who come to the hospital from the community for pneumonia.
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Affiliation(s)
- Saeed Shoar
- Baylor College of Medicine, Houston, Texas, USA.,Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Fernando H Centeno
- Baylor College of Medicine, Houston, Texas, USA.,Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Daniel M Musher
- Baylor College of Medicine, Houston, Texas, USA.,Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
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Kitsios GD, Terasawa T. Reply to the author. Clin Infect Dis 2021; 73:e1768-e1769. [PMID: 33388747 DOI: 10.1093/cid/ciaa1914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Teruhiko Terasawa
- Department of Emergency and General Internal Medicine, Fujita Health University, Toyoake, Aichi, Japan
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