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Mori T, Kitano T, Kitagawa D, Murata M, Onishi M, Hachisuka S, Okubo T, Yamamoto N, Nishikawa H, Onaka M, Suzuki R, Sekine M, Suzuki S, Nakamura F, Yoshida S. Risk of admission requirement among children with respiratory infection in the post-COVID-19 pandemic era. J Infect Public Health 2024; 17:102570. [PMID: 39481292 DOI: 10.1016/j.jiph.2024.102570] [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: 07/16/2024] [Revised: 10/17/2024] [Accepted: 10/20/2024] [Indexed: 11/02/2024] Open
Abstract
BACKGROUND To evaluate the effect of the type and codetection of respiratory viruses on admission requirements among children with respiratory infections in the post-COVID-19 pandemic era. METHODS In this retrospective study, we analyzed patients with acute respiratory symptoms using FilmArray® Respiratory Panel between December 2020 and March 2024. The viruses were classified into eight groups: adenovirus, seasonal coronavirus, human metapneumovirus, human rhinovirus/enterovirus, influenza virus, parainfluenza virus, respiratory syncytial virus, and severe acute respiratory virus coronavirus-2. The impact of the detected viral groups and viral codetection on hospitalization rates were examined using multivariable regression analysis in three pediatric age groups (<2 years, 2-4 years, and 5-17 years). RESULTS A total of 4684 tests were performed, of which 3555 (75.9 %) tested positive for at least one respiratory virus and negative for atypical bacteria. Of these, 946 (26.6 %) were hospitalized. Multivariable regression analyses showed that respiratory syncytial virus (RSV) infection was associated with hospitalization requirement among young children (adjusted odds ratios (aOR) 2.46 [1.65-3.67], p < 0.001 in < 2 years, and 1.34 [1.02-2.30], p = 0.042 in 2-4 years). Influenza (aOR 0.23 [0.07-0.83], p = 0.025) and SARS-CoV-2 (aOR 0.39 [0.22-0.69], p = 0.001) were negatively correlated with hospitalization among children younger than 2 years. Viral codetection was not significantly associated with hospitalization in any pediatric age group. CONCLUSION RSV infection was associated with a higher risk of hospitalization in children younger than 5 years than other respiratory viruses. These results highlight the importance of preventive measures against RSV infections, including maternal vaccination and childhood immunization.
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Affiliation(s)
- Takahiro Mori
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Taito Kitano
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan.
| | - Daisuke Kitagawa
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Masayuki Murata
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Mai Onishi
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Soshi Hachisuka
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Tenshin Okubo
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Naohiro Yamamoto
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Hiroki Nishikawa
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Masayuki Onaka
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Rika Suzuki
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Madoka Sekine
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Soma Suzuki
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Fumihiko Nakamura
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Sayaka Yoshida
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
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2
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Risha MA, Reddy KD, Nemani SSP, Jakwerth C, Schmidt-Weber C, Bahmer T, Hansen G, von Mutius E, Rabe KF, Dittrich AM, Grychtol R, Maison N, Schaub B, Kopp MV, Brinkmann F, Meiners S, Jappe U, Weckmann M. Epigenetic training of human bronchial epithelium cells by repeated rhinovirus infections. Allergy 2024; 79:3385-3400. [PMID: 39513674 DOI: 10.1111/all.16388] [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: 06/18/2024] [Revised: 09/20/2024] [Accepted: 10/10/2024] [Indexed: 11/15/2024]
Abstract
BACKGROUND Humans are subjected to various environmental stressors (bacteria, viruses, pollution) throughout life. As such, an inherent relationship exists between the effect of these exposures with age. The impact of these environmental stressors can manifest through DNA methylation (DNAm). However, whether these epigenetic effects selectively target genes, pathways, and biological regulatory mechanisms remains unclear. Due to the frequency of human rhinovirus (HRV) infections throughout life (particularly in early development), we propose the use of HRV under controlled conditions can model the effect of multiple exposures to environmental stressors. METHODS We generated a prediction model by combining transcriptome and DNAm datasets from human epithelial cells after repeated HRV infections. We applied a novel experimental statistical design and method to systematically explore the multifaceted experimental space (number of infections, multiplicity of infections and duration). Our model included 35 samples, each characterized by the three parameters defining their infection status. RESULTS Trainable genes were defined by a consistent linear directionality in DNAm and gene expression changes with successive infections. We identified 77 trainable genes which could be further explored in future studies. The identified methylation sites were tracked within a pediatric cohort to determine the relative changes in candidate-trained sites with disease status and age. CONCLUSIONS Repeated viral infections induce an immune training response in bronchial epithelial cells. Training-sensitive DNAm sites indicate alternate divergent associations in asthma compared to healthy individuals. Our novel model presents a robust tool for identifying trainable genes, providing a foundation for future studies.
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Affiliation(s)
- Marua Abu Risha
- Division of Clinical and Molecular Allergology, PA Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Karosham D Reddy
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Department of Paediatric Pneumology & Allergology, University Clinic Schleswig-Holstein (UKSH), Lübeck, Germany
- Division of Epigenetics of Chronic Lung Diseases, Priority Area Chronic Lung Diseases, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
| | - Sai Sneha Priya Nemani
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Department of Paediatric Pneumology & Allergology, University Clinic Schleswig-Holstein (UKSH), Lübeck, Germany
| | - Constanze Jakwerth
- Centre of Allergy and Environment (ZAUM), Technische Universität and Helmholtz Centre Munich, Munich, Germany
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
| | - Carsten Schmidt-Weber
- Centre of Allergy and Environment (ZAUM), Technische Universität and Helmholtz Centre Munich, Munich, Germany
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
| | - Thomas Bahmer
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Department of Pneumology, LungenClinic Grosshansdorf, Grosshansdorf, Germany
- University Hospital Schleswig-Holstein Campus Kiel, Department for Internal Medicine I, Kiel, Germany
| | - Gesine Hansen
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End stage and Obstructive Lung Disease Hannover (BREATH), Member of the German Centre of Lung Research (DZL), Munich, Germany
| | - Erika von Mutius
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
- Institute for Asthma and Allergy Prevention, Helmholtz Centre Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Department of Pulmonary and Allergy, Dr von Hauner Children's Hospital, University Children's Hospital, Ludwig Maximilian's University, Munich, Germany
| | - Klaus F Rabe
- Centre of Allergy and Environment (ZAUM), Technische Universität and Helmholtz Centre Munich, Munich, Germany
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
| | - Anna-Maria Dittrich
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End stage and Obstructive Lung Disease Hannover (BREATH), Member of the German Centre of Lung Research (DZL), Munich, Germany
| | - Ruth Grychtol
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End stage and Obstructive Lung Disease Hannover (BREATH), Member of the German Centre of Lung Research (DZL), Munich, Germany
| | - Nicole Maison
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
- Institute for Asthma and Allergy Prevention, Helmholtz Centre Munich, German Research Centre for Environmental Health, Neuherberg, Germany
- Department of Pulmonary and Allergy, Dr von Hauner Children's Hospital, University Children's Hospital, Ludwig Maximilian's University, Munich, Germany
| | - Bianca Schaub
- Comprehensive Pneumology Centre Munich (CPC-M), Member of The German Centre for Lung Research (DZL), Munich, Germany
- Department of Pulmonary and Allergy, Dr von Hauner Children's Hospital, University Children's Hospital, Ludwig Maximilian's University, Munich, Germany
- German Center for Child and Adolescent Health (DZKJ), Dr von Hauner Children's Hospital, LMU Munich, Munich, Germany
| | - Matthias V Kopp
- Department of Paediatric Respiratory Medicine, Inselspital, University Children's Hospital of Bern, University of Bern, Bern, Switzerland
| | - Folke Brinkmann
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Department of Paediatric Pneumology & Allergology, University Clinic Schleswig-Holstein (UKSH), Lübeck, Germany
| | - Silke Meiners
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Immunology and Cell Biology, PA Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
| | - Uta Jappe
- Division of Clinical and Molecular Allergology, PA Chronic Lung Diseases, Research Center Borstel, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Interdisciplinary Allergy Outpatient Clinic, Department of Pneumology, University of Lübeck, Lübeck, Germany
| | - Markus Weckmann
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
- Department of Paediatric Pneumology & Allergology, University Clinic Schleswig-Holstein (UKSH), Lübeck, Germany
- Division of Epigenetics of Chronic Lung Diseases, Priority Area Chronic Lung Diseases, Research Center Borstel - Leibniz Lung Center, Borstel, Germany
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3
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Moore AR, Zheng H, Ganesan A, Hasin-Brumshtein Y, Maddali MV, Levitt JE, van der Poll T, Scicluna BP, Giamarellos-Bourboulis EJ, Kotsaki A, Martin-Loeches I, Garduno A, Rothman RE, Sevransky J, Wright DW, Atreya MR, Moldawer LL, Efron PA, Marcela K, Karvunidis T, Giannini HM, Meyer NJ, Sweeney TE, Rogers AJ, Khatri P. International multi-cohort analysis identifies novel framework for quantifying immune dysregulation in critical illness: results of the SUBSPACE consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.12.623298. [PMID: 39605502 PMCID: PMC11601436 DOI: 10.1101/2024.11.12.623298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Progress in the management of critical care syndromes such as sepsis, Acute Respiratory Distress Syndrome (ARDS), and trauma has slowed over the last two decades, limited by the inherent heterogeneity within syndromic illnesses. Numerous immune endotypes have been proposed in sepsis and critical care, however the overlap of the endotypes is unclear, limiting clinical translation. The SUBSPACE consortium is an international consortium that aims to advance precision medicine through the sharing of transcriptomic data. By evaluating the overlap of existing immune endotypes in sepsis across over 6,000 samples, we developed cell-type specific signatures to quantify dysregulation in these immune compartments. Myeloid and lymphoid dysregulation were associated with disease severity and mortality across all cohorts. This dysregulation was not only observed in sepsis but also in ARDS, trauma, and burn patients, indicating a conserved mechanism across various critical illness syndromes. Moreover, analysis of randomized controlled trial data revealed that myeloid and lymphoid dysregulation is linked to differential mortality in patients treated with anakinra or corticosteroids, underscoring its prognostic and therapeutic significance. In conclusion, this novel immunology-based framework for quantifying cellular compartment dysregulation offers a valuable tool for prognosis and therapeutic decision-making in critical illness.
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Affiliation(s)
- Andrew R Moore
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA
| | - Ananthakrishnan Ganesan
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA
| | | | - Manoj V Maddali
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA
| | - Joseph E Levitt
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA
| | - Tom van der Poll
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, the Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, the Netherlands
| | | | | | - Antigone Kotsaki
- 4 Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Greece
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St James’s Hospital, Dublin, Ireland
- Hospital Clinic, Universitat de Barcelona, IDIBAPS, CIBERES, Barcelona, Spain
| | - Alexis Garduno
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St James’s Hospital, Dublin, Ireland
| | - Richard E. Rothman
- Department of Emergency Medicine, The Johns Hopkins University, Baltimore, MD
| | | | - David W Wright
- Department of Emergency Medicine, Emory University, Atlanta, GA
| | - Mihir R. Atreya
- Division of Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, OH
| | - Lyle L. Moldawer
- Sepsis and Critical Illness Research Center and the SPIES Consortium, University of Florida College of Medicine, Gainesville, FL
| | - Philip A Efron
- Sepsis and Critical Illness Research Center and the SPIES Consortium, University of Florida College of Medicine, Gainesville, FL
| | - Kralovcova Marcela
- 1 Department of Internal Medicine, Faculty of Medicine, Teaching Hospital and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Thomas Karvunidis
- 1 Department of Internal Medicine, Faculty of Medicine, Teaching Hospital and Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Heather M. Giannini
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia PA
| | - Nuala J. Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia PA
| | | | - Angela J Rogers
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA
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4
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Rodriguez-Fernandez R, Xu Z, Moreno-Galdó A, Sardón O, Rubi T, Castillo-Corullón S, Torres A, Corcuera P, Callejón Callejón A, Perez G, Cortell I, Rovira-Amigo S, Pastor-Vivero MD, Mondejar-Lopez P, Perez-Frias J, Velasco V, Torres-Borrego J, Figuerola J, de la Serna Blázquez O, Garcia-Hernandez G, Tang L, Mejias A, Ramilo O. Longitudinal transcriptional immune profiles and persistent wheezing in moderate-to-late preterm infants. Pediatr Allergy Immunol 2024; 35:e14261. [PMID: 39445663 DOI: 10.1111/pai.14261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 09/25/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024]
Abstract
BACKGROUND Prematurity is associated with an increased risk of persistent wheezing but the underlying mechanisms are not well defined. The aim of this study was to identify blood transcriptional profiles associated with the development of wheezing in a cohort of moderate to late preterm infants and to define immune gene expression changes associated with wheezing. MATERIALS AND METHODS A convenience sample of a multicenter birth cohort (SAREPREM) of moderate-late preterm children followed during the first 3 years of life was analyzed. Children were enrolled in the first 2 weeks of life (Y0) and longitudinally evaluated at 1 (Y1), 2 (Y2), and 3 years (Y3) of age, for the presence of wheezing and to obtain samples for transcriptional profile analysis. Samples were processed on Illumina HT12 chips and genomic expression analyses performed with R programming, modular analysis for biological function, and QuSAGE for quantitative gene expression. RESULTS Seventy-six children were included in the study; 33 were classified as non-wheezing and 43 (56.6%) in the wheezing group. At Y0, children who developed wheezing had decreased expression of interferon genes and increased expression of B cell genes compared with the non-wheezing group. These changes in IFN and B cell gene expression were especially significant in children with late/persistent wheezing compared with transient wheezers. CONCLUSIONS Changes in IFN and B lymphocyte gene expression identified in early life suggest the existence of specific immunological mechanisms that play an important role in the development of wheezing in late-preterm infants.
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Affiliation(s)
- Rosa Rodriguez-Fernandez
- Department of Pediatrics, Hospital Gregorio Marañon, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IISGM), Madrid, Spain
| | - Zhaohui Xu
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Antonio Moreno-Galdó
- Department of Pediatrics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Olaia Sardón
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Teresa Rubi
- Pediatric Pulmonology Section, Hospital Torrecárdenas, Almería, Spain
| | - Silvia Castillo-Corullón
- Pediatric Pulmonology Unit, Hospital Clínico Universitario, Universidad de Valencia, Valencia, Spain
| | - Antonio Torres
- Department of Pediatrics, Hospital San Juan de la Cruz, Úbeda, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
| | - Alicia Callejón Callejón
- Pediatric Pulmonary Unit, Hospital Universitario Nuestra Señora de la Candelaria, Tenerife, Spain
| | - Guadalupe Perez
- Pediatric Pulmonology Section, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Sevilla, Spain
| | - Isidoro Cortell
- Pediatric Pulmonology Section, Hospital Universitario La Fe, Valencia, Spain
| | - Sandra Rovira-Amigo
- Department of Pediatrics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Maria D Pastor-Vivero
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Universitario Cruces. Health Research Institute Biobizkaia, Barakaldo, Bizkaia, Spain
| | - Pedro Mondejar-Lopez
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Department of Surgery, Paediatrics, Obstetrics and Gynecology, Biomedical Research Institute of Murcia (IMIB), Universidad de Murcia, Murcia, Spain
| | - Javier Perez-Frias
- Departamento de Farmacología y Pediatria, Facultad de Medicina, Universidad de Malaga, Málaga, Spain
| | - Valle Velasco
- Pediatric Pulmonology Unit, Hospital Universitario de Canarias, Tenerife, Spain
| | - Javier Torres-Borrego
- Pediatric Allergy and Pulmonology Unit, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Joan Figuerola
- Pediatric Pulmonology Section and Pediatric Department, Hospital Universitario Son Espases, Palma de Mallorca, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Spain
| | | | | | - Li Tang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Asuncion Mejias
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Octavio Ramilo
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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5
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Li Y, Tao X, Ye S, Tai Q, You YA, Huang X, Liang M, Wang K, Wen H, You C, Zhang Y, Zhou X. A T-Cell-Derived 3-Gene Signature Distinguishes SARS-CoV-2 from Common Respiratory Viruses. Viruses 2024; 16:1029. [PMID: 39066192 PMCID: PMC11281602 DOI: 10.3390/v16071029] [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: 04/28/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Research on the host responses to respiratory viruses could help develop effective interventions and therapies against the current and future pandemics from the host perspective. To explore the pathogenesis that distinguishes SARS-CoV-2 infections from other respiratory viruses, we performed a multi-cohort analysis with integrated bioinformatics and machine learning. We collected 3730 blood samples from both asymptomatic and symptomatic individuals infected with SARS-CoV-2, seasonal human coronavirus (sHCoVs), influenza virus (IFV), respiratory syncytial virus (RSV), or human rhinovirus (HRV) across 15 cohorts. First, we identified an enhanced cellular immune response but limited interferon activities in SARS-CoV-2 infection, especially in asymptomatic cases. Second, we identified a SARS-CoV-2-specific 3-gene signature (CLSPN, RBBP6, CCDC91) that was predominantly expressed by T cells, could distinguish SARS-CoV-2 infection, including Omicron, from other common respiratory viruses regardless of symptoms, and was predictive of SARS-CoV-2 infection before detectable viral RNA on RT-PCR testing in a longitude follow-up study. Thereafter, a user-friendly online tool, based on datasets collected here, was developed for querying a gene of interest across multiple viral infections. Our results not only identify a unique host response to the viral pathogenesis in SARS-CoV-2 but also provide insights into developing effective tools against viral pandemics from the host perspective.
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Affiliation(s)
- Yang Li
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Xinya Tao
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Sheng Ye
- Chongqing Center for Disease Control and Prevention, Chongqing 400707, China;
| | - Qianchen Tai
- Department of Probability and Statistics, School of Mathematical Sciences, Peking University, Beijing 100091, China;
| | - Yu-Ang You
- Institute of Pharmaceutical Science, King’s College London, London WC2R 2LS, UK;
| | - Xinting Huang
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
| | - Mifang Liang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Kai Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China;
| | - Haiyan Wen
- Chongqing International Travel Health Care Center, Chongqing 401120, China;
| | - Chong You
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
- Shanghai Institute for Mathematics and Interdisciplinary Sciences, Fudan University, Shanghai 200433, China
| | - Yan Zhang
- Sports & Medicine Integration Research Center (SMIRC), Capital University of Physical Education and Sports, Beijing 100088, China
| | - Xiaohua Zhou
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
- Chongqing Research Institute of Big Data, Peking University, Chongqing 400041, China; (X.T.); (X.H.)
- Department of Probability and Statistics, School of Mathematical Sciences, Peking University, Beijing 100091, China;
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6
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Casini F, Valentino MS, Lorenzo MG, Caiazzo R, Coppola C, David D, Di Tonno R, Giacomet V. Use of transcriptomics for diagnosis of infections and sepsis in children: A narrative review. Acta Paediatr 2024; 113:670-676. [PMID: 38243675 DOI: 10.1111/apa.17119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
AIM The aim of this review was to summarise the most recent evidence about the use of omics-based techniques as an instrument for a more rapid and accurate characterisation of respiratory tract infections, neurological infections and sepsis in paediatrics. METHODS We performed a narrative review using PubMed and a set of inclusion criteria: English language articles, clinical trials, meta-analysis and reviews including only paediatric population inherited to this topic in the last 15 years. RESULTS The examined studies suggest that host gene expression signatures are an effective method to characterise the different types of infections, to distinguish infection from colonisation and, in some cases, to assess the severity of the disease in children. CONCLUSIONS 'Omics-based techniques' may help to define the aetiology of infections in paediatrics, representing a useful tool to choose the most appropriate therapies and limit antibiotic resistance.
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Affiliation(s)
- Francesca Casini
- Pediatric Department, "Vittore Buzzi" Children's Hospital, Milan, Italy
| | - Maria Sole Valentino
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Marc Garcia Lorenzo
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Roberta Caiazzo
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Crescenzo Coppola
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Daniela David
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Raffaella Di Tonno
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Vania Giacomet
- Pediatric Infectious Disease Unit, Luigi Sacco Hospital, University of Milan, Milan, Italy
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7
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [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: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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8
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Galanti M, Patiño-Galindo JA, Filip I, Morita H, Galianese A, Youssef M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Tagne E, Shittu A, Elliott O, Perea-Chamblee T, Natesan S, Rosenbloom DS, Shaman J, Rabadan R. Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people. PLoS Biol 2024; 22:e3002089. [PMID: 38236818 PMCID: PMC10796020 DOI: 10.1371/journal.pbio.3002089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024] Open
Abstract
Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup, and bacterial coinfections. To understand these interactions within natural infections, we designed a longitudinal cohort study actively surveilling respiratory viruses over the course of 19 months (2016 to 2018) in a diverse cohort in New York City. We integrated the molecular characterization of 800+ nasopharyngeal samples with clinical data from 104 participants. Transcriptomic data enabled the identification of respiratory pathogens in nasopharyngeal samples, the characterization of markers of immune response, the identification of signatures associated with symptom severity, individual viruses, and bacterial coinfections. Specific results include a rapid restoration of baseline conditions after infection, significant transcriptomic differences between symptomatic and asymptomatic infections, and qualitatively similar responses across different viruses. We created an interactive computational resource (Virome Data Explorer) to facilitate access to the data and visualization of analytical results.
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Affiliation(s)
- Marta Galanti
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Juan Angel Patiño-Galindo
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ioan Filip
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Haruka Morita
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Angelica Galianese
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mariam Youssef
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Devon Comito
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Chanel Ligon
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Benjamin Lane
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Nelsa Matienzo
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Sadiat Ibrahim
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Eudosie Tagne
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Atinuke Shittu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Oliver Elliott
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Tomin Perea-Chamblee
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sanjay Natesan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Daniel Scholes Rosenbloom
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, United States of America
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9
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Yang Q, Meyerson NR, Paige CL, Morrison JH, Clark SK, Fattor WT, Decker CJ, Steiner HR, Lian E, Larremore DB, Perera R, Poeschla EM, Parker R, Dowell RD, Sawyer SL. Human mRNA in saliva can correctly identify individuals harboring acute infection. mBio 2023; 14:e0171223. [PMID: 37943059 PMCID: PMC10746177 DOI: 10.1128/mbio.01712-23] [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: 07/03/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE There are a variety of clinical and laboratory criteria available to clinicians in controlled healthcare settings to help them identify whether an infectious disease is present. However, in situations such as a new epidemic caused by an unknown infectious agent, in health screening contexts performed within communities and outside of healthcare facilities or in battlefield or potential biowarfare situations, this gets more difficult. Pathogen-agnostic methods for rapid screening and triage of large numbers of people for infection status are needed, in particular methods that might work on an easily accessible biospecimen like saliva. Here, we identify a small, core set of approximately 70 human genes whose transcripts serve as saliva-based biomarkers of infection in the human body, in a way that is agnostic to the specific pathogen causing infection.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Darwin Biosciences, Inc., Boulder, Colorado, USA
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Darwin Biosciences, Inc., Boulder, Colorado, USA
| | - James H Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Darwin Biosciences, Inc., Boulder, Colorado, USA
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Halley R Steiner
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Elena Lian
- Center for Vector-Borne Infectious Diseases and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel B Larremore
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Rushika Perera
- Center for Vector-Borne Infectious Diseases and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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10
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Mitchell AB, Glanville AR. The role of systemic steroids in lung transplant recipients with community-acquired respiratory viruses: Time for a moratorium, or not? Transpl Infect Dis 2023; 25:e14142. [PMID: 37676748 DOI: 10.1111/tid.14142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Affiliation(s)
- Alicia B Mitchell
- School of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
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11
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Mick E, Tsitsiklis A, Kamm J, Kalantar KL, Caldera S, Lyden A, Tan M, Detweiler AM, Neff N, Osborne CM, Williamson KM, Soesanto V, Leroue M, Maddux AB, Simões EA, Carpenter TC, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children. J Clin Invest 2023; 133:e165904. [PMID: 37009900 PMCID: PMC10065066 DOI: 10.1172/jci165904] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/02/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUNDLower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging because noninfectious respiratory illnesses appear clinically similar and because existing microbiologic tests are often falsely negative or detect incidentally carried microbes, resulting in antimicrobial overuse and adverse outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and treatment remains unclear.METHODSWe used tracheal aspirate RNA-Seq to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n = 117) or of noninfectious respiratory failure (n = 50). We then developed a classifier that integrates the host LRTI probability, abundance of respiratory viruses, and dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.RESULTSThe host classifier achieved a median AUC of 0.967 by cross-validation, driven by activation markers of T cells, alveolar macrophages, and the interferon response. The integrated classifier achieved a median AUC of 0.986 and increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n = 94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those.CONCLUSIONLower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.FUNDINGSupport for this study was provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Heart, Lung, and Blood Institute (UG1HD083171, 1R01HL124103, UG1HD049983, UG01HD049934, UG1HD083170, UG1HD050096, UG1HD63108, UG1HD083116, UG1HD083166, UG1HD049981, K23HL138461, and 5R01HL155418) as well as by the Chan Zuckerberg Biohub.
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Affiliation(s)
- Eran Mick
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, and
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Michelle Tan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Christina M. Osborne
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Victoria Soesanto
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Matthew Leroue
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Aline B. Maddux
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Eric A.F. Simões
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C. Carpenter
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Brandie D. Wagner
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Peter M. Mourani
- Department of Pediatrics, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, Arkansas, USA
| | - Charles R. Langelier
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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12
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Rovira Rubió J, Megremis S, Pasioti M, Lakoumentas J, Constantinides B, Xepapadaki P, Bachert C, Finotto S, Jartti T, Andreakos E, Stanic B, Akdis CA, Akdis M, Papadopoulos NG. Respiratory virome profiles reflect antiviral immune responses. Allergy 2023; 78:1258-1268. [PMID: 36595290 DOI: 10.1111/all.15634] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/01/2022] [Accepted: 12/11/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort. METHODS Peripheral blood mononuclear cells from 51 children (32 asthmatics and 19 healthy controls) participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analysed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high throughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis. RESULTS High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile; however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed among immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations. CONCLUSION Antiviral cytokine responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae, appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not correlated with TLR-induced immune responses.
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Affiliation(s)
- Judit Rovira Rubió
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK
| | - Spyridon Megremis
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK
| | - Maria Pasioti
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - John Lakoumentas
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Bede Constantinides
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paraskevi Xepapadaki
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Claus Bachert
- Upper Airway Research Laboratory, Ghent University Hospital, Ghent, Belgium
| | - Susetta Finotto
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Tuomas Jartti
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Barbara Stanic
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Nikolaos G Papadopoulos
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK.,Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
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13
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Orzołek I, Ambrożej D, Makrinioti H, Zhu Z, Jartti T, Feleszko W. Severe bronchiolitis profiling as the first step towards prevention of asthma. Allergol Immunopathol (Madr) 2023; 51:99-107. [PMID: 37169566 DOI: 10.15586/aei.v51i3.788] [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: 10/27/2022] [Accepted: 02/07/2023] [Indexed: 05/13/2023]
Abstract
Bronchiolitis is the most common respiratory infection leading to hospitalization and constitutes a significant healthcare burden. The two main viral agents causing bronchiolitis, respiratory syncytial virus (RSV) and rhinovirus (RV), have distinct cytopathic, immune response, and clinical characteristics. Different approaches have been suggested for subtyping bronchiolitis based on viral etiology, atopic status, transcriptome profiles in blood, airway metabolome, lipidomic data, and airway microbiota. The highest risk of asthma at school age has been in a subgroup of bronchiolitis characterized by older age, high prevalence of RV infection, previous breathing problems, and/or eczema. Regarding solely viral etiology, RV-bronchiolitis in infancy has been linked to a nearly three times higher risk of developing asthma than RSV-bronchiolitis. Although treatment with betamimetics and systemic corticosteroids has been found ineffective in bronchiolitis overall, it can be beneficial for infants with severe RV bronchiolitis. Thus, there is a need to develop a more individualized therapeutic approach for bronchiolitis and follow-up strategies for infants at higher risk of asthma in the future perspective.
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Affiliation(s)
- Izabela Orzołek
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Ambrożej
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland
- Doctoral School, Medical University of Warsaw, Warsaw, Poland
| | - Heidi Makrinioti
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tuomas Jartti
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Wojciech Feleszko
- Department of Pediatric Pneumonology and Allergy, Medical University of Warsaw, Warsaw, Poland;
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14
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Rao AM, Popper SJ, Gupta S, Davong V, Vaidya K, Chanthongthip A, Dittrich S, Robinson MT, Vongsouvath M, Mayxay M, Nawtaisong P, Karmacharya B, Thair SA, Bogoch I, Sweeney TE, Newton PN, Andrews JR, Relman DA, Khatri P. A robust host-response-based signature distinguishes bacterial and viral infections across diverse global populations. Cell Rep Med 2022; 3:100842. [PMID: 36543117 PMCID: PMC9797950 DOI: 10.1016/j.xcrm.2022.100842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
Limited sensitivity and specificity of current diagnostics lead to the erroneous prescription of antibiotics. Host-response-based diagnostics could address these challenges. However, using 4,200 samples across 69 blood transcriptome datasets from 20 countries from patients with bacterial or viral infections representing a broad spectrum of biological, clinical, and technical heterogeneity, we show current host-response-based gene signatures have lower accuracy to distinguish intracellular bacterial infections from viral infections than extracellular bacterial infections. Using these 69 datasets, we identify an 8-gene signature to distinguish intracellular or extracellular bacterial infections from viral infections with an area under the receiver operating characteristic curve (AUROC) > 0.91 (85.9% specificity and 90.2% sensitivity). In prospective cohorts from Nepal and Laos, the 8-gene classifier distinguished bacterial infections from viral infections with an AUROC of 0.94 (87.9% specificity and 91% sensitivity). The 8-gene signature meets the target product profile proposed by the World Health Organization and others for distinguishing bacterial and viral infections.
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Affiliation(s)
- Aditya M. Rao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Immunology Graduate Program, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen J. Popper
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Sanjana Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew T. Robinson
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Pruksa Nawtaisong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Biraj Karmacharya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Simone A. Thair
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Isaac Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David A. Relman
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, 240 Pasteur Dr., Biomedical Innovation Building, Room 1553, Stanford, CA, USA,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA,Corresponding author
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15
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Yang J, Li D, Wang J, Zhang R, Li J. Design, optimization, and application of multiplex rRT-PCR in the detection of respiratory viruses. Crit Rev Clin Lab Sci 2022:1-18. [PMID: 35559711 DOI: 10.1080/10408363.2022.2072467] [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: 11/03/2022]
Abstract
Viral respiratory infections are common and serious diseases. Because there is no effective treatment method or vaccine for respiratory tract infection, early diagnosis is vital to identify the pathogen so as to determine the infectivity of the patient and to quickly take measures to curb the spread of the virus, if warranted, to avoid serious public health problems. Real-time reverse transcriptase PCR (rRT-PCR), which has high sensitivity and specificity, is the best approach for early diagnosis. Among rRT-PCR methods, multiplex rRT-PCR can resolve issues arising from various types of viruses, high mutation frequency, coinfection, and low concentrations of virus. However, the design, optimization, and validation of multiplex rRT-PCR are more complicated than singleplex rRT-PCR, and comprehensive research on multiplex rRT-PCR methodology is lacking. This review summarizes recent progress in multiplex rRT-PCR methodology, outlines the principles of design, optimization and validation, and describes a scheme to help diagnostic companies to design and optimize their multiplex rRT-PCR detection panel and to assist laboratory staff to solve problems in their daily work. In addition, the analytical validity, clinical validity and clinical utility of multiplex rRT-PCR in viral respiratory tract infection diagnosis are assessed to provide theoretical guidance and useful information for physicians to understand the test results.
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Affiliation(s)
- Jing Yang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jie Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
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16
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Makrinioti H, Maggina P, Lakoumentas J, Xepapadaki P, Taka S, Megremis S, Manioudaki M, Johnston SL, Tsolia M, Papaevangelou V, Papadopoulos NG. Recurrent Wheeze Exacerbations Following Acute Bronchiolitis-A Machine Learning Approach. FRONTIERS IN ALLERGY 2022; 2:728389. [PMID: 35387034 PMCID: PMC8974688 DOI: 10.3389/falgy.2021.728389] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023] Open
Abstract
Introduction: Acute bronchiolitis is one of the most common respiratory infections in infancy. Although most infants with bronchiolitis do not get hospitalized, infants with hospitalized bronchiolitis are more likely to develop wheeze exacerbations during the first years of life. The objective of this prospective cohort study was to develop machine learning models to predict incidence and persistence of wheeze exacerbations following the first hospitalized episode of acute bronchiolitis. Methods: One hundred thirty-one otherwise healthy term infants hospitalized with the first episode of bronchiolitis at a tertiary pediatric hospital in Athens, Greece, and 73 age-matched controls were recruited. All patients/controls were followed up for 3 years with 6-monthly telephone reviews. Through principal component analysis (PCA), a cluster model was used to describe main outcomes. Associations between virus type and the clusters and between virus type and other clinical characteristics and demographic data were identified. Through random forest classification, a prediction model with smallest classification error was identified. Primary outcomes included the incidence and the number of caregiver-reported wheeze exacerbations. Results: PCA identified 2 clusters of the outcome measures (Cluster 1 and Cluster 2) that were significantly associated with the number of recurrent wheeze episodes over 3-years of follow-up (Chi-Squared, p < 0.001). Cluster 1 included infants who presented higher number of wheeze exacerbations over follow-up time. Rhinovirus (RV) detection was more common in Cluster 1 and was more strongly associated with clinical severity on admission (p < 0.01). A prediction model based on virus type and clinical severity could predict Cluster 1 with an overall error 0.1145 (sensitivity 75.56% and specificity 91.86%). Conclusion: A prediction model based on virus type and clinical severity of first hospitalized episode of bronchiolitis could predict sensitively the incidence and persistence of wheeze exacerbations during a 3-year follow-up. Virus type (RV) was the strongest predictor.
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Affiliation(s)
- Heidi Makrinioti
- West Middlesex University Hospital, Chelsea and Westminster Foundation Trust, Isleworth, United Kingdom.,Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
| | - Paraskevi Maggina
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - John Lakoumentas
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Paraskevi Xepapadaki
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Stella Taka
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Spyridon Megremis
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, United Kingdom
| | - Maria Manioudaki
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Sebastian L Johnston
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Maria Tsolia
- Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece
| | - Vassiliki Papaevangelou
- Third Department of Paediatrics, Attikon University General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos G Papadopoulos
- Allergy and Clinical Immunology Laboratory, Second Department of Pediatrics, National and Kapodistrian University of Athens (NKUA), School of Medicine, P. and A. Kyriakou Children's Hospital, Athens, Greece.,Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
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17
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Ramachandran PS, Ramesh A, Creswell FV, Wapniarski A, Narendra R, Quinn CM, Tran EB, Rutakingirwa MK, Bangdiwala AS, Kagimu E, Kandole KT, Zorn KC, Tugume L, Kasibante J, Ssebambulidde K, Okirwoth M, Bahr NC, Musubire A, Skipper CP, Fouassier C, Lyden A, Serpa P, Castaneda G, Caldera S, Ahyong V, DeRisi JL, Langelier C, Crawford ED, Boulware DR, Meya DB, Wilson MR. Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics. Nat Commun 2022; 13:1675. [PMID: 35354815 PMCID: PMC8967864 DOI: 10.1038/s41467-022-29353-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
The epidemiology of infectious causes of meningitis in sub-Saharan Africa is not well understood, and a common cause of meningitis in this region, Mycobacterium tuberculosis (TB), is notoriously hard to diagnose. Here we show that integrating cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) with a host gene expression-based machine learning classifier (MLC) enhances diagnostic accuracy for TB meningitis (TBM) and its mimics. 368 HIV-infected Ugandan adults with subacute meningitis were prospectively enrolled. Total RNA and DNA CSF mNGS libraries were sequenced to identify meningitis pathogens. In parallel, a CSF host transcriptomic MLC to distinguish between TBM and other infections was trained and then evaluated in a blinded fashion on an independent dataset. mNGS identifies an array of infectious TBM mimics (and co-infections), including emerging, treatable, and vaccine-preventable pathogens including Wesselsbron virus, Toxoplasma gondii, Streptococcus pneumoniae, Nocardia brasiliensis, measles virus and cytomegalovirus. By leveraging the specificity of mNGS and the sensitivity of an MLC created from CSF host transcriptomes, the combined assay has high sensitivity (88.9%) and specificity (86.7%) for the detection of TBM and its many mimics. Furthermore, we achieve comparable combined assay performance at sequencing depths more amenable to performing diagnostic mNGS in low resource settings.
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Affiliation(s)
- P S Ramachandran
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- University of Melbourne, Melbourne, VIC, Australia
- UCSF Center for Tuberculosis, San Francisco, CA, USA
- UCSF Center for Encephalitis and Meningitis, San Francisco, CA, USA
| | - A Ramesh
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - F V Creswell
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Medical Research Council-Uganda Virus Research Institute-LSHTM Uganda Research Unit, Entebbe, Uganda
| | - A Wapniarski
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - R Narendra
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - C M Quinn
- University of California School of Medicine, San Francisco, CA, USA
| | - E B Tran
- University of California School of Medicine, San Francisco, CA, USA
| | - M K Rutakingirwa
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | | | - E Kagimu
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - K T Kandole
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - K C Zorn
- UCSF Center for Encephalitis and Meningitis, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - L Tugume
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - J Kasibante
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - K Ssebambulidde
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - M Okirwoth
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - N C Bahr
- Division of Infectious Diseases, Department of Medicine, University of Kansas, Kansas City, KS, USA
| | - A Musubire
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - C P Skipper
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- University of Minnesota, Minneapolis, MN, USA
| | - C Fouassier
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - A Lyden
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - P Serpa
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - G Castaneda
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - S Caldera
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - V Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - J L DeRisi
- UCSF Center for Encephalitis and Meningitis, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - C Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - D B Meya
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- University of Minnesota, Minneapolis, MN, USA
| | - M R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Center for Tuberculosis, San Francisco, CA, USA.
- UCSF Center for Encephalitis and Meningitis, San Francisco, CA, USA.
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18
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Myxovirus Resistance Protein A as a Marker of Viral Cause of Illness in Children Hospitalized with an Acute Infection. Microbiol Spectr 2022; 10:e0203121. [PMID: 35080443 PMCID: PMC8791186 DOI: 10.1128/spectrum.02031-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A biomarker for viral infection could improve the differentiation between viral and bacterial infections and reduce antibiotic overuse. We examined blood myxovirus resistance protein A (MxA) as a biomarker for viral infections in children with an acute infection. We recruited 251 children presenting with a clinical suspicion of serious bacterial infection, determined by need for a blood bacterial culture collection, and 14 children with suspected viral infection at two pediatric emergency departments. All children were aged between 4 weeks and 16 years. We classified cases according to the viral, bacterial, or other etiology of the final diagnosis. The ability of MxA to differentiate between viral and bacterial infections was assessed. The median blood MxA levels were 467 (interquartile range, 235 to 812) μg/L in 39 children with a viral infection, 469 (178 to 827) μg/L in 103 children with viral-bacterial coinfection, 119 (68 to 227) μg/L in 75 children with bacterial infection, and 150 (101 to 212) μg/L in 26 children with bacterial infection and coincidental virus finding (P < 0.001). In a receiver operating characteristics analysis, MxA cutoff level of 256 μg/L differentiated between children with viral and bacterial infections with an area under the curve of 0.81 (95% confidence interval [CI] = 0.73 to 0.90), a sensitivity of 74.4%, and a specificity of 80.0%. In conclusion, MxA protein showed moderate accuracy as a biomarker for symptomatic viral infections in children hospitalized with an acute infection. High prevalence of viral-bacterial coinfections supports the use of MxA in combination with biomarkers of bacterial infection. IMPORTANCE Due to the diagnostic uncertainty concerning the differentiation between viral and bacterial infections, children with viral infections are often treated with antibiotics, predisposing them to adverse effects and contributing to the emerging antibiotic resistance. Since currently available biomarkers only estimate the risk of bacterial infection, a biomarker for viral infection is needed in attempts of reducing antibiotic overuse. Blood MxA protein, which has broad antiviral activity and is rapidly induced in acute, symptomatic viral infections, is a potential biomarker for viral infection. In this diagnostic study of 265 children hospitalized because of an acute infection, blood MxA cutoff level of 256 μg/L discriminated between viral and bacterial infections with a sensitivity of 74% and specificity of 80%. MxA could improve the differential diagnostics of febrile children at the emergency department but, because of frequently detected viral-bacterial coinfections, a combination with biomarkers of bacterial infection may be needed.
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19
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Zhang Z, Ma P, Ahmed R, Wang J, Akin D, Soto F, Liu BF, Li P, Demirci U. Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103646. [PMID: 34623709 DOI: 10.1002/adma.202103646] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/25/2021] [Indexed: 04/14/2023]
Abstract
The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.
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Affiliation(s)
- Zhaowei Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Peng Ma
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rajib Ahmed
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Jie Wang
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Demir Akin
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Fernando Soto
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Peiwu Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
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20
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Ivaska L, Niemelä J, Gröndahl-Yli-Hannuksela K, Putkuri N, Vuopio J, Vuorinen T, Waris M, Rantakokko-Jalava K, Peltola V. Detection of group A streptococcus in children with confirmed viral pharyngitis and antiviral host response. Eur J Pediatr 2022; 181:4059-4065. [PMID: 36163516 PMCID: PMC9512968 DOI: 10.1007/s00431-022-04633-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 08/05/2022] [Accepted: 09/18/2022] [Indexed: 11/03/2022]
Abstract
UNLABELLED Our aim was to study the detection of group A streptococcus (GAS) with different diagnostic methods in paediatric pharyngitis patients with and without a confirmed viral infection. In this prospective observational study, throat swabs and blood samples were collected from children (age 1-16 years) presenting to the emergency department with febrile pharyngitis. A confirmed viral infection was defined as a positive virus diagnostic test (nucleic acid amplification test [NAAT] and/or serology) together with an antiviral immune response of the host demonstrated by elevated (≥ 175 µg/L) myxovirus resistance protein A (MxA) blood concentration. Testing for GAS was performed by a throat culture, by 2 rapid antigen detection tests (StrepTop and mariPOC) and by 2 NAATs (Simplexa and Illumigene). Altogether, 83 children were recruited of whom 48 had samples available for GAS testing. Confirmed viral infection was diagnosed in 30/48 (63%) children with febrile pharyngitis. Enteroviruses 11/30 (37%), adenoviruses 9/30 (30%) and rhinoviruses 9/30 (30%) were the most common viruses detected. GAS was detected by throat culture in 5/30 (17%) with and in 6/18 (33%) patients without a confirmed viral infection. Respectively, GAS was detected in 4/30 (13%) and 6/18 (33%) by StrepTop, 13/30 (43%) and 10/18 (56%) by mariPOC, 6/30 (20%) and 9/18 (50%) by Simplexa, and 5/30 (17%) and 6/18 (30%) patients by Illumigene. CONCLUSION GAS was frequently detected also in paediatric pharyngitis patients with a confirmed viral infection. The presence of antiviral host response and increased GAS detection by sensitive methods suggest incidental throat carriage of GAS in viral pharyngitis. WHAT IS KNOWN •The frequency and significance of GAS-virus co-detection are poorly characterised in children with pharyngitis. •Detection of a virus and the antiviral host response likely indicates symptomatic infection. WHAT IS NEW •Group A streptococcus (GAS) was detected in 17-43% of the children with confirmed viral pharyngitis depending on the GAS diagnostic method. •Our results emphasize the risk of detecting and treating incidental pharyngeal carriage of GAS in children with viral pharyngitis.
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Affiliation(s)
- Lauri Ivaska
- Departments of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland. .,Emergency Services, Turku University Hospital and University of Turku, Turku, Finland.
| | - Jussi Niemelä
- grid.410552.70000 0004 0628 215XDepartments of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XEmergency Services, Turku University Hospital and University of Turku, Turku, Finland
| | - Kirsi Gröndahl-Yli-Hannuksela
- grid.1374.10000 0001 2097 1371Medical Microbiology and Immunology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Niina Putkuri
- grid.410552.70000 0004 0628 215XDivision of Clinical Microbiology, Turku University Hospital, Turku, Finland ,grid.452433.70000 0000 9387 9501Finnish Red Cross, Blood Service, Helsinki, Finland
| | - Jaana Vuopio
- grid.1374.10000 0001 2097 1371Medical Microbiology and Immunology, Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XDivision of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Tytti Vuorinen
- grid.1374.10000 0001 2097 1371Medical Microbiology and Immunology, Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XDivision of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Matti Waris
- grid.1374.10000 0001 2097 1371Medical Microbiology and Immunology, Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XDivision of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Kaisu Rantakokko-Jalava
- grid.410552.70000 0004 0628 215XDivision of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Ville Peltola
- grid.410552.70000 0004 0628 215XDepartments of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
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21
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Costa-Martins AG, Mane K, Lindsey BB, Ogava RL, Castro Í, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B, Ellis-Watson R, Tregoning JS, Bingle CD, Bogaert D, Clarke E, Ordovas-Montanes J, Jeffries D, Kampmann B, Nakaya HI, de Silva TI. Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Rep Med 2021; 2:100465. [PMID: 35028607 PMCID: PMC8714852 DOI: 10.1016/j.xcrm.2021.100465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/28/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023]
Abstract
In children lacking influenza-specific adaptive immunity, upper respiratory tract innate immune responses may influence viral replication and disease outcome. We use trivalent live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children aged 24-59 months to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. Upregulation of interferon signaling pathways prior to LAIV is significantly associated with lower strain-specific viral loads (VLs) at days 2 and 7. Several interferon-stimulated genes are differentially expressed in children with pre-LAIV asymptomatic respiratory viral infections and negatively correlated with LAIV VLs. Upregulation of genes enriched in macrophages, neutrophils, and eosinophils is associated with lower VLs and found more commonly in children with asymptomatic viral infections. Variability in pre-infection mucosal interferon gene expression in children may impact the course of subsequent influenza infections. This variability may be due to frequent respiratory viral infections, demonstrating the potential importance of mucosal virus-virus interactions in children.
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Affiliation(s)
- André G. Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
| | - Karim Mane
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Rodrigo L.T. Ogava
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ícaro Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ya Jankey Jagne
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Hadijatou J. Sallah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Edwin P. Armitage
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Bankole Ahadzie
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Rebecca Ellis-Watson
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - John S. Tregoning
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Colin D. Bingle
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Debby Bogaert
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Vaccine Centre, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
- Corresponding author
| | - Thushan I. de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
- Corresponding author
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22
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Ross M, Henao R, Burke TW, Ko ER, McClain MT, Ginsburg GS, Woods CW, Tsalik EL. A comparison of host response strategies to distinguish bacterial and viral infection. PLoS One 2021; 16:e0261385. [PMID: 34905580 PMCID: PMC8670660 DOI: 10.1371/journal.pone.0261385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Compare three host response strategies to distinguish bacterial and viral etiologies of acute respiratory illness (ARI). METHODS In this observational cohort study, procalcitonin, a 3-protein panel (CRP, IP-10, TRAIL), and a host gene expression mRNA panel were measured in 286 subjects with ARI from four emergency departments. Multinomial logistic regression and leave-one-out cross validation were used to evaluate the protein and mRNA tests. RESULTS The mRNA panel performed better than alternative strategies to identify bacterial infection: AUC 0.93 vs. 0.83 for the protein panel and 0.84 for procalcitonin (P<0.02 for each comparison). This corresponded to a sensitivity and specificity of 92% and 83% for the mRNA panel, 81% and 73% for the protein panel, and 68% and 87% for procalcitonin, respectively. A model utilizing all three strategies was the same as mRNA alone. For the diagnosis of viral infection, the AUC was 0.93 for mRNA and 0.84 for the protein panel (p<0.05). This corresponded to a sensitivity and specificity of 89% and 82% for the mRNA panel, and 85% and 62% for the protein panel, respectively. CONCLUSIONS A gene expression signature was the most accurate host response strategy for classifying subjects with bacterial, viral, or non-infectious ARI.
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Affiliation(s)
- Melissa Ross
- Duke University School of Medicine, Durham, NC, United States of America
| | - Ricardo Henao
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States of America
| | - Thomas W. Burke
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Emily R. Ko
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Duke Regional Hospital, Durham, NC, United States of America
| | - Micah T. McClain
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC, United States of America
| | - Geoffrey S. Ginsburg
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Christopher W. Woods
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC, United States of America
| | - Ephraim L. Tsalik
- Duke Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, United States of America
- Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, NC, United States of America
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23
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Novel Biomarkers Differentiating Viral from Bacterial Infection in Febrile Children: Future Perspectives for Management in Clinical Praxis. CHILDREN (BASEL, SWITZERLAND) 2021; 8:children8111070. [PMID: 34828783 PMCID: PMC8623137 DOI: 10.3390/children8111070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/31/2021] [Accepted: 11/18/2021] [Indexed: 01/12/2023]
Abstract
Differentiating viral from bacterial infections in febrile children is challenging and often leads to an unnecessary use of antibiotics. There is a great need for more accurate diagnostic tools. New molecular methods have improved the particular diagnostics of viral respiratory tract infections, but defining etiology can still be challenging, as certain viruses are frequently detected in asymptomatic children. For the detection of bacterial infections, time consuming cultures with limited sensitivity are still the gold standard. As a response to infection, the immune system elicits a cascade of events, which aims to eliminate the invading pathogen. Recent studies have focused on these host–pathogen interactions to identify pathogen-specific biomarkers (gene expression profiles), or “pathogen signatures”, as potential future diagnostic tools. Other studies have assessed combinations of traditional bacterial and viral biomarkers (C-reactive protein, interleukins, myxovirus resistance protein A, procalcitonin, tumor necrosis factor-related apoptosis-inducing ligand) to establish etiology. In this review we discuss the performance of such novel diagnostics and their potential role in clinical praxis. In conclusion, there are several promising novel biomarkers in the pipeline, but well-designed randomized controlled trials are needed to evaluate the safety of using these novel biomarkers to guide clinical decisions.
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24
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Tsalik EL, Henao R, Montgomery JL, Nawrocki JW, Aydin M, Lydon EC, Ko ER, Petzold E, Nicholson BP, Cairns CB, Glickman SW, Quackenbush E, Kingsmore SF, Jaehne AK, Rivers EP, Langley RJ, Fowler VG, McClain MT, Crisp RJ, Ginsburg GS, Burke TW, Hemmert AC, Woods CW. Discriminating Bacterial and Viral Infection Using a Rapid Host Gene Expression Test. Crit Care Med 2021; 49:1651-1663. [PMID: 33938716 PMCID: PMC8448917 DOI: 10.1097/ccm.0000000000005085] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Host gene expression signatures discriminate bacterial and viral infection but have not been translated to a clinical test platform. This study enrolled an independent cohort of patients to describe and validate a first-in-class host response bacterial/viral test. DESIGN Subjects were recruited from 2006 to 2016. Enrollment blood samples were collected in an RNA preservative and banked for later testing. The reference standard was an expert panel clinical adjudication, which was blinded to gene expression and procalcitonin results. SETTING Four U.S. emergency departments. PATIENTS Six-hundred twenty-three subjects with acute respiratory illness or suspected sepsis. INTERVENTIONS Forty-five-transcript signature measured on the BioFire FilmArray System (BioFire Diagnostics, Salt Lake City, UT) in ~45 minutes. MEASUREMENTS AND MAIN RESULTS Host response bacterial/viral test performance characteristics were evaluated in 623 participants (mean age 46 yr; 45% male) with bacterial infection, viral infection, coinfection, or noninfectious illness. Performance of the host response bacterial/viral test was compared with procalcitonin. The test provided independent probabilities of bacterial and viral infection in ~45 minutes. In the 213-subject training cohort, the host response bacterial/viral test had an area under the curve for bacterial infection of 0.90 (95% CI, 0.84-0.94) and 0.92 (95% CI, 0.87-0.95) for viral infection. Independent validation in 209 subjects revealed similar performance with an area under the curve of 0.85 (95% CI, 0.78-0.90) for bacterial infection and 0.91 (95% CI, 0.85-0.94) for viral infection. The test had 80.1% (95% CI, 73.7-85.4%) average weighted accuracy for bacterial infection and 86.8% (95% CI, 81.8-90.8%) for viral infection in this validation cohort. This was significantly better than 68.7% (95% CI, 62.4-75.4%) observed for procalcitonin (p < 0.001). An additional cohort of 201 subjects with indeterminate phenotypes (coinfection or microbiology-negative infections) revealed similar performance. CONCLUSIONS The host response bacterial/viral measured using the BioFire System rapidly and accurately discriminated bacterial and viral infection better than procalcitonin, which can help support more appropriate antibiotic use.
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Affiliation(s)
- Ephraim L. Tsalik
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Informatics, Duke University, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | | | | | - Mert Aydin
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Emily C. Lydon
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Regional Hospital, Durham, NC, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Charles B. Cairns
- University of North Carolina Medical Center, Chapel Hill, NC, USA
- Drexel University, Philadelphia, PA, USA
| | - Seth W. Glickman
- University of North Carolina Medical Center, Chapel Hill, NC, USA
| | | | | | | | | | | | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | - Micah T. McClain
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Christopher W. Woods
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
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25
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Mthembu N, Ikwegbue P, Brombacher F, Hadebe S. Respiratory Viral and Bacterial Factors That Influence Early Childhood Asthma. FRONTIERS IN ALLERGY 2021; 2:692841. [PMID: 35387053 PMCID: PMC8974778 DOI: 10.3389/falgy.2021.692841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a chronic respiratory condition characterised by episodes of shortness of breath due to reduced airway flow. The disease is triggered by a hyperreactive immune response to innocuous allergens, leading to hyper inflammation, mucus production, changes in structural cells lining the airways, and airway hyperresponsiveness. Asthma, although present in adults, is considered as a childhood condition, with a total of about 6.2 million children aged 18 and below affected globally. There has been progress in understanding asthma heterogeneity in adults, which has led to better patient stratification and characterisation of multiple asthma endotypes with distinct, but overlapping inflammatory features. The asthma inflammatory profile in children is not well-defined and heterogeneity of the disease is less described. Although many factors such as genetics, food allergies, antibiotic usage, type of birth, and cigarette smoke exposure can influence asthma development particularly in children, respiratory infections are thought to be the major contributing factor in poor lung function and onset of the disease. In this review, we focus on viral and bacterial respiratory infections in the first 10 years of life that could influence development of asthma in children. We also review literature on inflammatory immune heterogeneity in asthmatic children and how this overlaps with early lung development, poor lung function and respiratory infections. Finally, we review animal studies that model early development of asthma and how these studies could inform future therapies and better understanding of this complex disease.
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Affiliation(s)
- Nontobeko Mthembu
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Paul Ikwegbue
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Frank Brombacher
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Health Science Faculty, International Centre for Genetic Engineering and Biotechnology (ICGEB) and Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Sabelo Hadebe
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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26
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Heinonen S, Velazquez VM, Ye F, Mertz S, Acero-Bedoya S, Smith B, Bunsow E, Garcia-Mauriño C, Oliva S, Cohen DM, Moore-Clingenpeel M, Peeples ME, Ramilo O, Mejias A. Immune profiles provide insights into respiratory syncytial virus disease severity in young children. Sci Transl Med 2021; 12:12/540/eaaw0268. [PMID: 32321862 DOI: 10.1126/scitranslmed.aaw0268] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 11/21/2019] [Accepted: 03/05/2020] [Indexed: 12/29/2022]
Abstract
Respiratory syncytial virus (RSV) is associated with major morbidity in infants, although most cases result in mild disease. The pathogenesis of the disease is incompletely understood, especially the determining factors of disease severity. A better characterization of these factors may help with development of RSV vaccines and antivirals. Hence, identification of a "safe and protective" immunoprofile induced by natural RSV infection could be used as a as a surrogate of ideal vaccine-elicited responses in future clinical trials. In this study, we integrated blood transcriptional and cell immune profiling, RSV loads, and clinical data to identify factors associated with a mild disease phenotype in a cohort of 190 children <2 years of age. Children with mild disease (outpatients) showed higher RSV loads, greater induction of interferon (IFN) and plasma cell genes, and decreased expression of inflammation and neutrophil genes versus children with severe disease (inpatients). Additionally, only infants with severe disease had increased numbers of HLA-DRlow monocytes, not present in outpatients. Multivariable analyses confirmed that IFN overexpression was associated with decreased odds of hospitalization, whereas increased numbers of HLA-DRlow monocytes were associated with increased risk of hospitalization. These findings suggest that robust innate immune responses are associated with mild RSV infection in infants.
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Affiliation(s)
- Santtu Heinonen
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Victoria M Velazquez
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Fang Ye
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sara Mertz
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Santiago Acero-Bedoya
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Eleonora Bunsow
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Cristina Garcia-Mauriño
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Silvia Oliva
- Division of Pediatric Emergency Medicine and Critical Care, Hospital Regional Universitario de Málaga, Málaga 29001, Spain.,Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, Málaga 29071, Spain
| | - Daniel M Cohen
- Division of Emergency Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Melissa Moore-Clingenpeel
- Biostatistics Core, The Research Institute at Nationwide Children's Hospital Columbus, OH 43205, USA
| | - Mark E Peeples
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA. .,Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA. .,Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, Málaga 29071, Spain.,Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
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27
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Zandstra J, Jongerius I, Kuijpers TW. Future Biomarkers for Infection and Inflammation in Febrile Children. Front Immunol 2021; 12:631308. [PMID: 34079538 PMCID: PMC8165271 DOI: 10.3389/fimmu.2021.631308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/12/2021] [Indexed: 01/08/2023] Open
Abstract
Febrile patients, suffering from an infection, inflammatory disease or autoimmunity may present with similar or overlapping clinical symptoms, which makes early diagnosis difficult. Therefore, biomarkers are needed to help physicians form a correct diagnosis and initiate the right treatment to improve patient outcomes following first presentation or admittance to hospital. Here, we review the landscape of novel biomarkers and approaches of biomarker discovery. We first discuss the use of current plasma parameters and whole blood biomarkers, including results obtained by RNA profiling and mass spectrometry, to discriminate between bacterial and viral infections. Next we expand upon the use of biomarkers to distinguish between infectious and non-infectious disease. Finally, we discuss the strengths as well as the potential pitfalls of current developments. We conclude that the use of combination tests, using either protein markers or transcriptomic analysis, have advanced considerably and should be further explored to improve current diagnostics regarding febrile infections and inflammation. If proven effective when combined, these biomarker signatures will greatly accelerate early and tailored treatment decisions.
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Affiliation(s)
- Judith Zandstra
- Division Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
| | - Ilse Jongerius
- Division Research and Landsteiner Laboratory, Department of Immunopathology, Sanquin Blood Supply, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
| | - Taco W. Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Amsterdam, Netherlands
- Division Research and Landsteiner Laboratory, Department of Blood Cell Research, Sanquin Blood Supply, Amsterdam UMC, Amsterdam, Netherlands
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28
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Khan T, Das RS, Chaudhary A, Chatterjee J, Bhattacharya SD. Association of nasopharyngeal viruses and pathogenic bacteria in children and their parents with and without HIV. Pneumonia (Nathan) 2021; 13:8. [PMID: 33947476 PMCID: PMC8096464 DOI: 10.1186/s41479-021-00088-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Bacteria and respiratory viruses co-occur in the nasopharynx, and their interactions may impact pathogenesis of invasive disease. Associations of viruses and bacteria in the nasopharynx may be affected by HIV. METHODS We conducted a nested case-control study from a larger cohort study of banked nasopharyngeal swabs from families with and without HIV in West Bengal India, to look at the association of viruses and bacteria in the nasopharynx of parents and children when they are asymptomatic. Quantitative polymerase chain reaction for 4 bacteria and 21 respiratory viruses was run on 92 random nasopharyngeal swabs from children--49 from children living with HIV (CLH) and 43 from HIV uninfected children (HUC)-- and 77 swabs from their parents (44 parents of CLH and 33 parents of HUC). RESULTS Bacteria was found in 67% of children, viruses in 45%, and both in 27% of child samples. Staphylococcus aureus (53%) was the most common bacteria, followed by Streptococcus pneumoniae (pneumococcus) (37%) in children and parents (53, 20%). Regardless of HIV status, viruses were detected in higher numbers (44%) in children than their parents (30%) (p = 0.049), particularly rhinovirus (p = 0.02). Human rhinovirus was the most frequently found virus in both CLH and HUC. Children with adenovirus were at six times increased risk of also having pneumococcus (Odds ratio OR 6, 95% CI 1.12-31.9) regardless of HIV status. In addition, the presence of rhinovirus in children was associated with increased pneumococcal density (Regression coeff 4.5, 1.14-7.9). In CLH the presence of rhinovirus increased the risk of pneumococcal colonization by nearly sixteen times (OR 15.6, 1.66-146.4), and, pneumococcus and S. aureus dual colonization by nearly nine times (OR 8.7). CONCLUSIONS Children more frequently carried viruses regardless of HIV status. In CLH the presence of rhinovirus, the most frequently detected virus, significantly increased co-colonization with pneumococcus and S. aureus.
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Affiliation(s)
- Tila Khan
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Ranjan Saurav Das
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Amrita Chaudhary
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Jyotirmoy Chatterjee
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Sangeeta Das Bhattacharya
- School of Medical Science & Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
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29
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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Presence of microorganisms in children with pharyngotonsillitis and healthy controls: a prospective study in primary healthcare. Infection 2021; 49:715-724. [PMID: 33686635 PMCID: PMC7938884 DOI: 10.1007/s15010-021-01595-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/23/2021] [Indexed: 11/29/2022]
Abstract
Purpose Most studies on paediatric pharyngotonsillitis focus on group A streptococci. This study, however, analyses a broad spectrum of bacteria and viruses related to paediatric pharyngotonsillitis and evaluates their associated clinical symptoms and courses. Methods This observational prospective study in primary healthcare includes 77 children aged < 15 with a sore throat and 34 asymptomatic children, all of whom were sampled from the tonsils with an E-swab® for analysis with culture and PCR for 14 bacteria and 15 viruses. Patients were evaluated clinically, and their symptoms recorded in diaries for 10 days. Participants were followed up for 3 months by reviewing medical records. Results A pathogen was detected in 86% of patients and in 71% of controls (P = 0.06). Bacteria were found in 69% of patients and 59% of controls (P = 0.3), and viruses in 36% and 26%, respectively (P = 0.3). Group A streptococci was the most common finding, with a prevalence of 49% and 32%, respectively (P = 0.1). Clinical signs were not useful for distinguishing pathogens. None of the controls and 16% of the patients reconsulted for a sore throat within 3 months. Conclusion Bacteria were more common than viruses in both study groups. The high rate of pathogens in asymptomatic children interferes with diagnoses based on aetiology. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-021-01595-9.
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Lei H, Xu X, Wang C, Xue D, Wang C, Chen J. A host-based two-gene model for the identification of bacterial infection in general clinical settings. Int J Infect Dis 2021; 105:662-667. [PMID: 33667695 DOI: 10.1016/j.ijid.2021.02.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES In this study, we aimed to develop a simple gene model to identify bacterial infection, which can be implemented in general clinical settings. METHODS We used a clinically availablereal-time quantitative polymerase chain reaction platform to conduct focused gene expression assays on clinical blood samples. Samples were collected from 2 tertiary hospitals. RESULTS We found that the 8 candidate genes for bacterial infection were significantly dysregulated in bacterial infection and displayed good performance in group classification, whereas the 2 genes for viral infection displayed poor performance. A two-gene model (S100A12 and CD177) displayed 93.0% sensitivity and 93.7% specificity in the modeling stage. In the independent validation stage, 87.8% sensitivity and 96.6% specificity were achieved in one set of case-control groups, and 93.6% sensitivity and 97.1% specificity in another set. CONCLUSIONS We have validated the signature genes for bacterial infection and developed a two-gene model to identify bacterial infection in general clinical settings.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China; Cunji Medical School, University of Chinese Academy of Sciences, Beijing, China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China.
| | - Xiaoyue Xu
- Department of Clinical Laboratory, 307th Hospital of Chinese People's Liberation Army, Beijing, China
| | - Chi Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA general hospital & Medical School of Chinese PLA, Beijing, China
| | - Dandan Xue
- Department of Clinical Laboratory of Medicine, Chinese PLA general hospital & Medical School of Chinese PLA, Beijing, China
| | - Chengbin Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA general hospital & Medical School of Chinese PLA, Beijing, China.
| | - Jiankui Chen
- Department of Clinical Laboratory, 307th Hospital of Chinese People's Liberation Army, Beijing, China.
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Viral Loads and Disease Severity in Children with Rhinovirus-Associated Illnesses. Viruses 2021; 13:v13020295. [PMID: 33668603 PMCID: PMC7918889 DOI: 10.3390/v13020295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/23/2022] Open
Abstract
The role of rhinoviruses (RVs) in children with clinical syndromes not classically associated with RV infections is not well understood. We analyzed a cohort of children ≤21 years old who were PCR+ for RV at a large Pediatric Hospital from 2011 to 2013. Using univariate and multivariable logistic regression, we analyzed the associations between demographic, clinical characteristics, microbiology data, and clinical outcomes in children with compatible symptoms and incidental RV detection. Of the 2473 children (inpatients and outpatients) with an RV+ PCR, 2382 (96%) had compatible symptoms, and 91 (4%) did not. The overall median age was 14 months and 78% had underlying comorbidities. No differences in RV viral loads were found according to the presence of compatible symptoms, while in children with classic RV symptoms, RV viral loads were higher in single RV infections versus RV viral co-infections. Bacterial co-infections were more common in RV incidental detection (7.6%) than in children with compatible symptoms (1.9%, p < 0.001). The presence of compatible symptoms independently increased the odds ratio (OR, 95% CI) of hospitalization 4.8 (3.1-7.4), prolonged hospital stays 1.9 (1.1-3.1), need for oxygen 12 (5.8-25.0) and pediatric intensive care unit (PICU) admission 4.13 (2.0-8.2). Thus, despite comparable RV loads, disease severity was significantly worse in children with compatible symptoms.
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Mahle RE, Suchindran S, Henao R, Steinbrink JM, Burke TW, McClain MT, Ginsburg GS, Woods CW, Tsalik EL. Validation of a host gene expression test for bacterial/viral discrimination in immunocompromised hosts. Clin Infect Dis 2021; 73:605-613. [PMID: 33462581 DOI: 10.1093/cid/ciab043] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host gene expression has emerged as a complementary strategy to pathogen detection tests for the discrimination of bacterial and viral infection. The impact of immunocompromise on host response tests remains unknown. We evaluated a host response test discriminating bacterial, viral, and non-infectious conditions in immunocompromised subjects. METHODS An 81-gene signature was measured using RT-PCR in subjects with immunocompromise (chemotherapy, solid organ transplant, immunomodulatory agents, AIDS) with bacterial infection, viral infection, or noninfectious illness. A regularized logistic regression model trained in immunocompetent subjects was used to estimate the likelihood of each class in immunocompromised subjects. RESULTS Accuracy in the 136-subject immunocompetent training cohort was 84.6% for bacterial vs. non-bacterial discrimination and 80.8% for viral vs. non-viral discrimination. Model validation in 134 immunocompromised subjects showed overall accuracy of 73.9% for bacterial infection (p=0.04 relative to immunocompetent subjects) and 75.4% for viral infection (p=0.30). A scheme reporting results by quartile improved test utility. The highest probability quartile ruled-in bacterial and viral infection with 91.4% and 84.0% specificity, respectively. The lowest probability quartile ruled-out infection with 90.1% and 96.4% sensitivity for bacterial and viral infection, respectively. Performance was independent of the type or number of immunocompromising conditions. CONCLUSION A host gene expression test discriminated bacterial, viral, and non-infectious etiologies at a lower overall accuracy in immunocompromised patients compared to immunocompetent patients, though this difference was only significant for bacterial infection classification. With modified interpretive criteria, a host response strategy may offer clinically useful diagnostic information for patients with immunocompromise.
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Affiliation(s)
- Rachael E Mahle
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Sunil Suchindran
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University, Durham, North Carolina, USA
| | - Julie M Steinbrink
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas W Burke
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah T McClain
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham VA Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham VA Health Care System, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Emergency Medicine Service, Durham VA Health Care System, Durham, North Carolina, USA
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Lei H, Wang C, Wang Y, Wang C. Single-cell RNA-Seq revealed profound immune alteration in the peripheral blood of patients with bacterial infection. Int J Infect Dis 2020; 103:527-535. [PMID: 33278616 DOI: 10.1016/j.ijid.2020.11.205] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Bacterial infection remains one of the greatest threats to human health. However, how human hosts respond to bacterial infection has not been thoroughly understood. Better understanding of this response will improve human health. METHODS Here, we conducted an investigation on host response to bacterial infection using unperturbed clinical samples and single-cell RNA-Seq (scRNA-Seq) technology. To evaluate immune alteration upon bacterial infection in scRNA-Seq data of peripheral blood mononuclear cells (PBMCs), we developed a barcode analytical framework named PBMCode. RESULTS Using this PBMCode framework, we revealed profound immune alteration in peripheral blood under bacterial infection, including the emergence of natural killer T (NKT) cell cluster, reduction of B cell population, and considerable changes in T cells and monocytes. In addition, we also observed a large quantity of low-density neutrophils. CONCLUSIONS Our investigation on single cells provided unprecedented details in the alteration of both cell population and cell state under bacterial infection. These findings may be relevant to clinical decisions. The complexity of host response to bacterial infection revealed by scRNA-Seq deserves further attention in future studies.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China; Cunji Medical School, University of Chinese Academy of Sciences, Beijing, China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China.
| | - Chi Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA General Hospital & Medical School of Chinese PLA, Beijing, China
| | - Yunlai Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Chengbin Wang
- Department of Clinical Laboratory of Medicine, Chinese PLA General Hospital & Medical School of Chinese PLA, Beijing, China.
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35
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Ortega H, Nickle D, Carter L. Rhinovirus and asthma: Challenges and opportunities. Rev Med Virol 2020; 31:e2193. [PMID: 33217098 PMCID: PMC8365703 DOI: 10.1002/rmv.2193] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
Human rhinoviruses (RVs) are the primary aetiological agent of the common cold. Generally, the associated infection is mild and self‐limiting, but may also be associated with bronchiolitis in infants, pneumonia in the immunocompromised and exacerbation in patients with pulmonary conditions such as asthma or chronic obstructive pulmonary disease. Viral infection accounts for as many as two thirds of asthma exacerbations in children and more than half in adults. Allergy and asthma are major risk factors for more frequent and severe RV‐related illnesses. The prevalence of RV‐induced wheezing will likely continue to increase given that asthma affects a significant proportion of the population, with allergic asthma accounting for the majority. Several new respiratory viruses and their subgroups have been discovered, with various degrees of relevance. This review will focus on RV infection in the context of the epidemiologic evidence, genetic variability, pathobiology, clinical studies in the context of asthma, differences with other viruses including COVID‐19 and current treatment interventions.
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36
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Sundararaman A, Ray M, Ravindra PV, Halami PM. Role of probiotics to combat viral infections with emphasis on COVID-19. Appl Microbiol Biotechnol 2020; 104:8089-8104. [PMID: 32813065 PMCID: PMC7434852 DOI: 10.1007/s00253-020-10832-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Interspecies transmissions of viruses between animals and humans may result in unpredictable pathogenic potential and new transmissible diseases. This mechanism has recently been exemplified by the discovery of new pathogenic viruses, such as the novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic, Middle-East respiratory syndrome-coronavirus epidemic in Saudi Arabia, and the deadly outbreak of Ebola in West Africa. The. SARS-CoV-2 causes coronavirus disease-19 (COVID-19), which is having a massive global impact in terms of economic disruption, and, above all, human health. The disease is characterized by dry cough, fever, fatigue, myalgia, and dyspnea. Other symptoms include headache, sore throat, rhinorrhea, and gastrointestinal disorders. Pneumonia appears to be the most common and severe manifestation of the infection. Currently, there is no vaccine or specific drug for COVID-19. Further, the development of new antiviral requires a considerable length of time and effort for drug design and validation. Therefore, repurposing the use of natural compounds can provide alternatives and can support therapy against COVID-19. In this review, we comprehensively discuss the prophylactic and supportive therapeutic role of probiotics for the management of COVID-19. In addition, the unique role of probiotics to modulate the gut microbe and assert gut homeostasis and production of interferon as an antiviral mechanism is described. Further, the regulatory role of probiotics on gut-lung axis and mucosal immune system for the potential antiviral mechanisms is reviewed and discussed.Key points• Gut microbiota role in antiviral diseases• Factors influencing the antiviral mechanism• Probiotics and Covid-19.
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Affiliation(s)
- Aravind Sundararaman
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - Mousumi Ray
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - P V Ravindra
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India
| | - Prakash M Halami
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India.
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Wahlund M, Sinha I, Broliden K, Saghafian-Hedengren S, Nilsson A, Berggren A. The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia. Int J Mol Sci 2020; 21:ijms21155305. [PMID: 32722616 PMCID: PMC7432212 DOI: 10.3390/ijms21155305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 12/23/2022] Open
Abstract
Infection is a common and serious complication of cancer treatment in children that often presents as febrile neutropenia (FN). Gene-expression profiling techniques can reveal transcriptional signatures that discriminate between viral, bacterial and asymptomatic infections in otherwise healthy children. Here, we examined whether gene-expression profiling was feasible in children with FN who were undergoing cancer treatment. The blood transcriptome of the children (n = 63) was investigated at time of FN diagnosed as viral, bacterial, co-infection or unknown etiology, respectively, and compared to control samples derived from 12 of the patients following the FN episode. RNA sequencing was successful in 43 (68%) of the FN episodes. Only two genes were significantly differentially expressed in the bacterial versus the control group. Significantly up-regulated genes in patients with the other three etiologies versus the control group were enriched with cellular processes related to proliferation and cellular stress response, with no clear enrichment with innate responses to pathogens. Among the significantly down-regulated genes, a few clustered into pathways connected to responses to infection. In the present study of children during cancer treatment, the blood transcriptome was not suitable for determining the etiology of FN because of too few circulating immune cells for reliable gene expression analysis.
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Affiliation(s)
- Martina Wahlund
- Department of Medicine Solna, Infectious Disease Unit, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, 171 76 Stockholm, Sweden; (M.W.); (K.B.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Indranil Sinha
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 171 76 Stockholm, Sweden; (I.S.); (S.S.-H.); (A.N.)
| | - Kristina Broliden
- Department of Medicine Solna, Infectious Disease Unit, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, 171 76 Stockholm, Sweden; (M.W.); (K.B.)
| | - Shanie Saghafian-Hedengren
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 171 76 Stockholm, Sweden; (I.S.); (S.S.-H.); (A.N.)
| | - Anna Nilsson
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, 171 76 Stockholm, Sweden; (I.S.); (S.S.-H.); (A.N.)
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Berggren
- Department of Medicine Solna, Infectious Disease Unit, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, 171 76 Stockholm, Sweden; (M.W.); (K.B.)
- Correspondence:
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Ouellette CP, Sánchez PJ, Xu Z, Blankenship D, Zeray F, Ronchi A, Shimamura M, Chaussabel D, Lee L, Owen KE, Shoup AG, Ramilo O, Mejias A. Blood genome expression profiles in infants with congenital cytomegalovirus infection. Nat Commun 2020; 11:3548. [PMID: 32669541 PMCID: PMC7363904 DOI: 10.1038/s41467-020-17178-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 06/10/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital CMV infection (cCMVi) affects 0.5–1% of all live births worldwide, making it the leading cause of sensorineural hearing loss (SNHL) in childhood. The majority of infants with cCMVi have normal hearing at birth, but are at risk of developing late-onset SNHL. Currently, we lack reliable biomarkers to predict the development of SNHL in these infants. Here, we evaluate blood transcriptional profiles in 80 infants with cCMVi (49 symptomatic, 31 asymptomatic), enrolled in the first 3 weeks of life, and followed for 3 years to assess emergence of late-onset SNHL. The biosignatures of symptomatic and asymptomatic cCMVi are indistinguishable, suggesting that immune responses of infants with asymptomatic and symptomatic cCMVi are not different. Random forest analyses of initial samples in infants with cCMVi, irrespective of their clinical classification, identify a 16-gene classifier signature associated with the development of SNHL with 92% accuracy, suggesting its potential value as a biomarker. Congenital CMV infection can result in sensorineural hearing loss, but predicting this outcome is not yet possible. Here, the authors show that while blood gene expression profiles are not substantially different between symptomatic and asymptomatic infants with congenital CMV infection, a 16-gene signature is identified and able to predict late-onset hearing loss in these children.
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Affiliation(s)
- Christopher P Ouellette
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA
| | - Pablo J Sánchez
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Division of Neonatology, Nationwide Children's Hospital-The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhaohui Xu
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Fiker Zeray
- Children's Medical Center Dallas, Dallas, TX, USA
| | - Andrea Ronchi
- Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Neonatal intensive care unit, Fondazione IRCCS, Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Masako Shimamura
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Lizette Lee
- Department of Pediatrics, Divisions of Neonatal-Perinatal Medicine and Pediatric Infectious Diseases, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Children's Medical Center Dallas, Dallas, TX, USA
| | - Kris E Owen
- Children's Medical Center Dallas, Dallas, TX, USA.,Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Angela G Shoup
- Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Parkland Health and Hospital System, Dallas, TX, USA
| | - Octavio Ramilo
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Asuncion Mejias
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital -The Ohio State University College of Medicine, Columbus, OH, USA. .,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
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Mansbach JM, Geller RJ, Hasegawa K, Piedra PA, Avadhanula V, Gern JE, Bochkov YA, Espinola JA, Sullivan AF, Camargo CA. Detection of Respiratory Syncytial Virus or Rhinovirus Weeks After Hospitalization for Bronchiolitis and the Risk of Recurrent Wheezing. J Infect Dis 2020; 223:268-277. [PMID: 32564083 DOI: 10.1093/infdis/jiaa348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/12/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In severe bronchiolitis, it is unclear if delayed clearance or sequential infection of respiratory syncytial virus (RSV) or rhinovirus (RV) is associated with recurrent wheezing. METHODS In a 17-center severe bronchiolitis cohort, we tested nasopharyngeal aspirates (NPA) upon hospitalization and 3 weeks later (clearance swab) for respiratory viruses using PCR. The same RSV subtype or RV genotype in NPA and clearance swab defined delayed clearance (DC); a new RSV subtype or RV genotype at clearance defined sequential infection (SI). Recurrent wheezing by age 3 years was defined per national asthma guidelines. RESULTS Among 673 infants, RSV DC and RV DC were not associated with recurrent wheezing, and RSV SI was rare. The 128 infants with RV SI (19%) had nonsignificantly higher risk of recurrent wheezing (hazard ratio [HR], 1.31; 95% confidence interval [CI], .95-1.80; P = .10) versus infants without RV SI. Among infants with RV at hospitalization, those with RV SI had a higher risk of recurrent wheezing compared to children without RV SI (HR, 2.49; 95% CI, 1.22-5.06; P = .01). CONCLUSIONS Among infants with severe bronchiolitis, those with RV at hospitalization followed by a new RV infection had the highest risk of recurrent wheezing.
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Affiliation(s)
- Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruth J Geller
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Cheemarla NR, Brito AF, Fauver JR, Alpert T, Vogels CB, Omer SB, Ko A, Grubaugh ND, Landry ML, Foxman EF. Host response-based screening to identify undiagnosed cases of COVID-19 and expand testing capacity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.06.04.20109306. [PMID: 32577694 PMCID: PMC7302303 DOI: 10.1101/2020.06.04.20109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has created unprecedented challenges in diagnostic testing. At the beginning of the epidemic, a confluence of factors resulted in delayed deployment of PCR-based diagnostic tests, resulting in lack of testing of individuals with symptoms of the disease. Although these tests are now more widely available, it is estimated that a three- to ten-fold increase in testing capacity will be required to ensure adequate surveillance as communities reopen(1). In response to these challenges, we evaluated potential roles of host-response based screening in the diagnosis of COVID-19. Previous work from our group showed that the nasopharyngeal (NP) level of CXCL10, a protein produced as part of the host response to viral infection, is a sensitive predictor of respiratory virus infection across a wide spectrum of viruses(2). Here, we show that NP CXCL10 is elevated during SARS-CoV-2 infection and use a CXCL10-based screening strategy to identify four undiagnosed cases of COVID-19 in Connecticut in early March. In a second set of samples tested at the Yale New Haven Hospital, we show that NP CXCL10 had excellent performance as a rule-out test (NPV 0.99, 95% C.I. 0.985-0.997). Our results demonstrate how biomarker-based screening could be used to leverage existing PCR testing capacity to rapidly enable widespread testing for COVID-19.
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Creary S, Shrestha CL, Kotha K, Minta A, Fitch J, Jaramillo L, Zhang S, Pinto S, Thompson R, Ramilo O, White P, Mejias A, Kopp BT. Baseline and Disease-Induced Transcriptional Profiles in Children with Sickle Cell Disease. Sci Rep 2020; 10:9013. [PMID: 32487996 PMCID: PMC7265336 DOI: 10.1038/s41598-020-65822-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/22/2020] [Indexed: 12/24/2022] Open
Abstract
Acute chest syndrome (ACS) is a significant cause of morbidity and mortality in sickle cell disease (SCD), but preventive, diagnostic, and therapeutic options are limited. Further, ACS and acute vasoccclusive pain crises (VOC) have overlapping features, which causes diagnostic dilemmas. We explored changes in gene expression profiles among patients with SCD hospitalized for VOC and ACS episodes to better understand ACS disease pathogenesis. Whole blood RNA-Seq was performed for 20 samples from children with SCD at baseline and during a hospitalization for either an ACS (n = 10) or a VOC episode (n = 10). Respiratory viruses were identified from nasopharyngeal swabs. Functional gene analyses were performed using modular repertoires, IPA, Gene Ontology, and NetworkAnalyst 3.0. The VOC group had a numerically higher percentage of female, older, and hemoglobin SS participants compared to the ACS group. Viruses were detected in 50% of ACS cases and 20% of VOC cases. We identified 3004 transcripts that were differentially expressed during ACS episodes, and 1802 transcripts during VOC episodes. Top canonical pathways during ACS episodes were related to interferon signaling, neuro-inflammation, pattern recognition receptors, and macrophages. Top canonical pathways in patients with VOC included IL-10 signaling, iNOS signaling, IL-6 signaling, and B cell signaling. Several genes related to antimicrobial function were down-regulated during ACS compared to VOC. Gene enrichment nodal interactions demonstrated significantly altered pathways during ACS and VOC. A complex network of changes in innate and adaptive immune gene expression were identified during both ACS and VOC episodes. These results provide unique insights into changes during acute events in children with SCD.
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Affiliation(s)
- Susan Creary
- Center for Innovation in Pediatric Practice, The Abigail Wexner Research Institute, Columbus, OH, USA
- Division of Hematology and Oncology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Chandra L Shrestha
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - Kavitha Kotha
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Abena Minta
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - James Fitch
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - Lisa Jaramillo
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - Shuzhong Zhang
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - Swaroop Pinto
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Rohan Thompson
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Columbus, OH, USA
- Division of Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- The Institute for Genomic Medicine, The Abigail Wexner Research Institute, Columbus, OH, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Columbus, OH, USA
- Division of Infectious Diseases, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin T Kopp
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute, Columbus, OH, USA.
- Division of Pulmonary Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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Yu J, Peterson DR, Baran AM, Bhattacharya S, Wylie TN, Falsey AR, Mariani TJ, Storch GA. Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection. J Infect Dis 2020; 219:1151-1161. [PMID: 30339221 DOI: 10.1093/infdis/jiy608] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Recently there has been a growing interest in the potential for host transcriptomic analysis to augment the diagnosis of infectious diseases. METHODS We compared nasal and blood samples for evaluation of the host transcriptomic response in children with acute respiratory syncytial virus (RSV) infection, symptomatic non-RSV respiratory virus infection, asymptomatic rhinovirus infection, and virus-negative asymptomatic controls. We used nested leave-one-pair-out cross-validation and supervised principal components analysis to define small sets of genes whose expression patterns accurately classified subjects. We validated gene classification scores using an external data set. RESULTS Despite lower quality of nasal RNA, the number of genes detected by microarray in each sample type was equivalent. Nasal gene expression signal derived mainly from epithelial cells but also included a variable leukocyte contribution. The number of genes with increased expression in virus-infected children was comparable in nasal and blood samples, while nasal samples also had decreased expression of many genes associated with ciliary function and assembly. Nasal gene expression signatures were as good or better for discriminating between symptomatic, asymptomatic, and uninfected children. CONCLSUSIONS Our results support the use of nasal samples to augment pathogen-based tests to diagnose viral respiratory infection.
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Affiliation(s)
- Jinsheng Yu
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine, New York
| | - Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Ann R Falsey
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School of Medicine, New York
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
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Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Am J Respir Crit Care Med 2019; 197:524-528. [PMID: 28686513 DOI: 10.1164/rccm.201706-1097le] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Matt S Zinter
- 1 University of California, San Francisco San Francisco, California
| | - Katrina Kalantar
- 1 University of California, San Francisco San Francisco, California
| | | | | | - Brian O'Donovan
- 1 University of California, San Francisco San Francisco, California
| | - Corin White
- 1 University of California, San Francisco San Francisco, California
| | - Michael Wilson
- 1 University of California, San Francisco San Francisco, California
| | - Anil Sapru
- 1 University of California, San Francisco San Francisco, California
| | | | - Steve Miller
- 1 University of California, San Francisco San Francisco, California
| | - Charles Y Chiu
- 1 University of California, San Francisco San Francisco, California
| | - Joseph L DeRisi
- 1 University of California, San Francisco San Francisco, California.,3 Chan Zuckerberg Biohub San Francisco, California
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Landry ML, Foxman EF. Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection. J Infect Dis 2019; 217:897-905. [PMID: 29281100 PMCID: PMC5853594 DOI: 10.1093/infdis/jix648] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022] Open
Abstract
Background Despite the high burden of respiratory infection and the importance of early and accurate diagnosis, there is no simple diagnostic test to rule in viral infection as a cause of respiratory symptoms. Methods We performed RNA sequencing on human nasal epithelial cells following stimulation of the intracellular viral recognition receptor RIG-I. Next, we evaluated whether measuring identified host mRNAs and proteins from patient nasopharyngeal swabs could predict the presence of a respiratory virus in the sample. Results Our first study showed that a signature of 3 mRNAs, CXCL10, IFIT2, and OASL, predicted respiratory virus detection with an accuracy of 97% (95% confidence interval [CI], 0.9–1.0), and identified proteins correlating with virus detection. In a second study, elevated CXCL11 or CXCL10 protein levels identified samples containing respiratory viruses, including viruses not on the initial test panel. Overall area under the curve (AUC) values were: CXCL11 AUC = 0.901 (95% CI, 0.86–0.94); CXCL10 AUC = 0.85 (95% CI, 0.80–0.91). Conclusions Host antiviral mRNAs and single host proteins detectable using nasopharyngeal swabs accurately predict the presence of viral infection. This approach holds promise for developing rapid, cost-effective tests to improve management of patients with respiratory illnesses.
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Affiliation(s)
- Marie L Landry
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut.,Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Ellen F Foxman
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut
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Abstract
Respiratory viral infections are associated with significant morbidity and mortality in children < 5 years of age worldwide. Among all respiratory viruses, respiratory syncytial virus (RSV) is the world's leading cause of bronchiolitis and pneumonia in young children. There are known populations at risk for severe disease but the majority of children who require hospitalization for RSV infection are previously healthy. Viral and host factors have been associated with the pathogenesis of RSV disease; however, the mechanisms that explain the wide variability in the clinical presentation are not completely understood. Recent studies suggest that the complex interaction between the respiratory microbiome, the host's immune response and the virus may have an impact on the pathogenesis and severity of RSV infection. In this review, we summarize the current evidence regarding the epidemiologic link, the mechanisms of viral-bacterial interactions, and the associations between the upper respiratory tract microbiome and RSV disease severity.
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47
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Dubourg G, Edouard S, Raoult D. Relationship between nasopharyngeal microbiota and patient's susceptibility to viral infection. Expert Rev Anti Infect Ther 2019; 17:437-447. [PMID: 31106653 DOI: 10.1080/14787210.2019.1621168] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: The burden of respiratory viral infections is a global public health concern with significant mortality, morbidity, and economic impact. While Koch's postulate led to considering only the etiological agent, numerous works have demonstrated that commensal microbes could contribute to both the susceptibility and the severity of these infections, in particular those of the nasopharynx. Areas covered: Herein, we first propose to briefly recall the historical background that led to considering microbes inhabiting the nasopharyngeal microbiota as a potential contributor to human viral infections. We describe the evolution of the normal nasopharyngeal microbiota composition over time, especially during the first year of life. We aimed to resume the changes of the nasopharyngeal microbiota during viral respiratory infections. We also develop how nasopharyngeal microbiota could contribute to the acquisition of respiratory viral infections. We finally provide the potential therapeutic perspectives deriving from these findings. Expert opinion: Prospective studies focusing on children have identified that nasopharyngeal microbiota composition is associated with predisposition to acute respiratory illness and bronchiolitis, while data are scarce regarding adults. For the latter, further works are needed, in particular as a part of the multi-OMICS approach that should probably be performed in conjunction with gut microbiota studies.
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Affiliation(s)
- Grégory Dubourg
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Sophie Edouard
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
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48
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Heinonen S, Rodriguez-Fernandez R, Diaz A, Oliva Rodriguez-Pastor S, Ramilo O, Mejias A. Infant Immune Response to Respiratory Viral Infections. Immunol Allergy Clin North Am 2019; 39:361-376. [PMID: 31284926 DOI: 10.1016/j.iac.2019.03.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Of all respiratory viruses that affect infants, respiratory syncytial virus (RSV) and rhinovirus (RV) represent the leading pathogens causing acute disease (bronchiolitis) and are associated with the development of recurrent wheezing and asthma. The immune system in infants is still developing, and several factors contribute to their increased susceptibility to viral infections. These factors include differences in pathogen detection, weaker interferon responses, lack of immunologic memory toward the invading pathogen, and T-cell responses that are balanced to promote tolerance and restrain inflammation. These aspects are reviewed here with a focus on RSV and RV infections.
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Affiliation(s)
- Santtu Heinonen
- New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, PO Box 347, Helsinki 00029 HUS, Finland
| | - Rosa Rodriguez-Fernandez
- Department of Pediatrics, Instituto de Investigación Sanitaria Gregorio Marañón (IISGM), Hospital Materno-Infantil Gregorio Marañón, Madrid 28009, Spain; Section of General Pediatrics, Hospital Gregorio Marañón, Madrid, Spain
| | - Alejandro Diaz
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA; Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA
| | - Silvia Oliva Rodriguez-Pastor
- Division of Pediatric Emergency Medicine and Critical Care, Hospital Regional Universitario de Malaga, Malaga 29001, Spain; Department of Pharmacology and Pediatrics, Malaga Medical Shool, Malaga University (UMA), Malaga, Spain
| | - Octavio Ramilo
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA; Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA; Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State Collage of Medicine, 700 Children's Drive, Columbus, OH 43205, USA; Department of Pharmacology and Pediatrics, Malaga Medical Shool, Malaga University (UMA), Malaga, Spain.
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49
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Mitchell AB, Glanville AR. Introduction to Techniques and Methodologies for Characterizing the Human Respiratory Virome. Methods Mol Biol 2019; 1838:111-123. [PMID: 30128993 DOI: 10.1007/978-1-4939-8682-8_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.
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Affiliation(s)
- Alicia B Mitchell
- The Woolcock Institute of Medical Research, Sydney, NSW, Australia. .,University of Technology Sydney, Sydney, NSW, Australia. .,The Lung Transplant Unit, St. Vincent's Hospital, Sydney, NSW, Australia.
| | - Allan R Glanville
- The Lung Transplant Unit, St. Vincent's Hospital, Sydney, NSW, Australia
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50
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Bhuiyan MU, Snelling TL, West R, Lang J, Rahman T, Granland C, de Gier C, Borland ML, Thornton RB, Kirkham LAS, Sikazwe C, Martin AC, Richmond PC, Smith DW, Jaffe A, Blyth CC. The contribution of viruses and bacteria to community-acquired pneumonia in vaccinated children: a case -control study. Thorax 2019; 74:261-269. [PMID: 30337417 PMCID: PMC6467248 DOI: 10.1136/thoraxjnl-2018-212096] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 10/31/2022]
Abstract
INTRODUCTION Respiratory pathogens associated with childhood pneumonia are often detected in the upper respiratory tract of healthy children, making their contribution to pneumonia difficult to determine. We aimed to determine the contribution of common pathogens to pneumonia adjusting for rates of asymptomatic detection to inform future diagnosis, treatment and preventive strategies. METHODS A case-control study was conducted among children <18 years in Perth, Western Australia. Cases were children hospitalised with radiologically confirmed pneumonia; controls were healthy children identified from outpatient and local immunisation clinics. Nasopharyngeal swabs were collected and tested for 14 respiratory viruses and 6 bacterial species by Polymerase chain reaction (PCR). For each pathogen, adjusted odds ratio (aOR; 95% CI) was calculated using multivariate logistic regression and population-attributable fraction (95% CI) for pneumonia was estimated. RESULTS From May 2015 to October 2017, 230 cases and 230 controls were enrolled. At least one respiratory virus was identified in 57% of cases and 29% of controls (aOR: 4.7; 95% CI: 2.8 to 7.8). At least one bacterial species was detected in 72% of cases and 80% of controls (aOR: 0.7; 95% CI: 0.4 to 1.2). Respiratory syncytial virus (RSV) detection was most strongly associated with pneumonia (aOR: 58.4; 95% CI: 15.6 to 217.5). Mycoplasma pneumoniae was the only bacteria associated with pneumonia (aOR: 14.5; 95% CI: 2.2 to 94.8). We estimated that RSV, human metapneumovirus (HMPV), influenza, adenovirus and Mycoplasma pneumoniae were responsible for 20.2% (95% CI: 14.6 to 25.5), 9.8% (5.6% to 13.7%), 6.2% (2.5% to 9.7%), 4% (1.1% to 7.1%) and 7.2% (3.5% to 10.8%) of hospitalisations for childhood pneumonia, respectively. CONCLUSIONS Respiratory viruses, particularly RSV and HMPV, are major contributors to pneumonia in Australian children.
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Affiliation(s)
- Mejbah Uddin Bhuiyan
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Thomas L Snelling
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Rachel West
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Jurissa Lang
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
| | - Tasmina Rahman
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Caitlyn Granland
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Camilla de Gier
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Meredith L Borland
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Emergency Department, Perth Children's Hospital, Perth, Western Australia, Australia
- Division of Emergency Medicine, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ruth B Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Lea-Ann S Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Chisha Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Peter C Richmond
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher C Blyth
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
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