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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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2
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Kohns Vasconcelos M, Meyer Sauteur PM, Keitel K, Santoro R, Egli A, Coslovsky M, Seiler M, Lurà M, Köhler H, Loevy N, Kahlert CR, Heininger U, Van den Anker J, Bielicki JA. Detection of mostly viral pathogens and high proportion of antibiotic treatment initiation in hospitalised children with community-acquired pneumonia in Switzerland - baseline findings from the first two years of the KIDS-STEP trial. Swiss Med Wkly 2023; 153:40040. [PMID: 36800889 DOI: 10.57187/smw.2023.40040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
AIMS OF THE STUDY Globally, since the introduction of conjugate-vaccines against encapsulated bacteria, respiratory viruses have caused most hospitalisations for community-acquired pneumonia. The aim of this study was to describe pathogens detected and their association with clinical findings in Switzerland. METHODS Baseline data were analysed for all trial participants enrolled between September 2018 and September 2020 into the KIDS-STEP Trial, a randomised controlled superiority trial on the effect of betamethasone on clinical stabilisation of children admitted with community-acquired pneumonia. Data included clinical presentation, antibiotic use and results of pathogen detection. In addition to routine sampling, nasopharyngeal specimens were analysed for respiratory pathogens using a panel polymerase chain reaction test covering 18 viral and 4 bacterial pathogens. RESULTS 138 children with a median age of 3 years were enrolled at the eight trial sites. Fever (obligatory for enrolment) had been present for median 5 days before admission. Most common symptoms were reduced activity (129, 93.5%) and reduced oral intake (108, 78.3%). Oxygen saturation <92% was found in 43 (31.2%). Forty-three participants (29.0%) were already on antibiotic treatment prior to admission and 104 participants (75.4%) received antibiotic treatment on admission. Pathogen testing results were available from 132 children: 31 (23.5%) had respiratory syncytial virus detected, 21 (15.9%) human metapneumovirus. The pathogens detected showed expected seasonal and age preponderance and were not associated with chest X-ray findings. CONCLUSIONS In the context of the predominantly viral pathogens detected, the majority of antibiotic treatment is probably unnecessary. The ongoing trial, as well as other studies, will be able to provide comparative pathogen detection data to compare pre- and post-COVID-19-pandemic settings.
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Affiliation(s)
- Malte Kohns Vasconcelos
- Department of Infectious Diseases and Vaccinology, University of Basel Children's Hospital (UKBB), SwitzerlandX.,Department of Paediatric Pharmacology, University of Basel Children's Hospital (UKBB), Basel, Switzerland.,Institute for Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Germany
| | - Patrick M Meyer Sauteur
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Switzerland
| | - Kristina Keitel
- Department of Paediatric Emergency Medicine, Department of Paediatrics, University Children's Hospital, Inselspital, University of Bern, Switzerland.,Swiss Tropical and Public Health Institute, University of Basel, Switzerland
| | - Regina Santoro
- Paediatric Research Centre, University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, and Applied Microbiology Research, University of Basel, Switzerland
| | | | - Michelle Seiler
- Paediatric Emergency Department, University Children's Hospital Zurich, Switzerland
| | - Marco Lurà
- Division of Paediatric Pulmonology, Children's Hospital Lucerne, Switzerland
| | - Henrik Köhler
- Paediatric Emergency Unit, Children's Hospital Aarau (KSA), Switzerland
| | - Natasha Loevy
- Paediatric Platform for Clinical Research, Department of Woman, Child and Adolescent Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Christian R Kahlert
- Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St Gallen, Switzerland
| | - Ulrich Heininger
- Department of Infectious Diseases and Vaccinology, University of Basel Children's Hospital (UKBB), SwitzerlandX
| | - Johannes Van den Anker
- Department of Paediatric Pharmacology, University of Basel Children's Hospital (UKBB), Basel, Switzerland
| | - Julia A Bielicki
- Department of Infectious Diseases and Vaccinology, University of Basel Children's Hospital (UKBB), SwitzerlandX.,Department of Paediatric Pharmacology, University of Basel Children's Hospital (UKBB), Basel, Switzerland
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A Multicenter Study of Viral Aetiology of Community-Acquired Pneumonia in Hospitalized Children in Chinese Mainland. Virol Sin 2021; 36:1543-1553. [PMID: 34523109 PMCID: PMC8440149 DOI: 10.1007/s12250-021-00437-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
Community-acquired pneumonia (CAP) is one of the leading causes of morbidity and mortality in children worldwide. In this study, we aimed to describe the aetiology of viral infection of pediatric CAP in Chinese mainland. During November 2014 to June 2016, the prospective study was conducted in 13 hospitals. The hospitalized children under 18 years old who met the criteria for CAP were enrolled. The throat swabs or nasopharyngeal aspirates (NPAs) were collected which were then screened 18 respiratory viruses using multiplex PCR assay. Viral pathogens were present in 56.6% (1539/2721) of the enrolled cases, with the detection rate of single virus in 39.8% of the cases and multiple viruses in 16.8% of the cases. The most frequently detected virus was respiratory syncytial virus (RSV) (15.2%, 414/2721). The highest detection rate of virus was in < 6-month-age group (70.7%, 292/413). RSV, human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs) and influenza B virus (Flu B) showed the similar prevalence patterns both in north and south China, but HPIVs, Flu A, human bocavirus (HBoV), human adenovirus (HAdV) and human coronaviruses (HCoVs) showed the distinct circulating patterns in north and south China. Human enterovirus/human rhinovirus (HEV/HRV) (27.6%, 27/98), HBoV (18.4%, 18/98), RSV (16.3%, 16/98) and HMPV (14.3%, 14/98) were the most commonly detected viruses in severe pneumonia cases with single virus infection. In conclusion, viral pathogens are frequently detected in pediatric CAP cases and may therefore play a vital role in the aetiology of CAP. RSV was the most important virus in hospitalized children with CAP in Chinese mainland.
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Moore DP, Baillie VL, Mudau A, Wadula J, Adams T, Mangera S, Verwey C, Prosperi C, Higdon MM, Haddix M, Hammitt LL, Feikin DR, O’Brien KL, Deloria Knoll M, Murdoch DR, Simões EA, Madhi SA. The Etiology of Pneumonia in HIV-uninfected South African Children: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study. Pediatr Infect Dis J 2021; 40:S59-S68. [PMID: 34448745 PMCID: PMC8448398 DOI: 10.1097/inf.0000000000002650] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Pneumonia is the major contributor to under 5 childhood mortality globally. We evaluated the etiology of pneumonia amongst HIV-uninfected South African children enrolled into the Pneumonia Etiology Research for Child Health case-control study. METHODS Cases, 1-59 months of age hospitalized with World Health Organization clinically defined severe/very severe pneumonia, were frequency-matched by age and season to community controls. Nasopharyngeal-oropharyngeal swabs were analyzed using polymerase chain reaction for 33 respiratory pathogens, and whole blood was tested for pneumococcal autolysin. Cases were also tested for Mycobacterium tuberculosis. Population etiologic fractions (EF) of pneumonia with radiologic evidence of consolidation/infiltrate were derived for each pathogen through Bayesian analysis. RESULTS Of the 805 HIV-uninfected cases enrolled based on clinical criteria, radiologically confirmed pneumonia was evident in 165 HIV-exposed, -uninfected, and 246 HIV-unexposed children. In HIV-exposed and HIV-unexposed children, respiratory syncytial virus was the most important pathogen with EFs of 31.6% [95% credible interval (CrI), 24.8%-38.8%] and 36.4% (95% CrI, 30.5%-43.1%), respectively. M. tuberculosis contributed EFs of 11.6% (95% CrI, 6.1%-18.8%) in HIV-exposed and 8.3% (95% CrI, 4.5%-13.8%) in HIV-unexposed children, including an EF of 16.3% (95% CrI, 6.1%-33.3%) in HIV-exposed children ≥12 months of age. Bacteremia (3.0% vs. 1.6%) and case fatality risk (3.6% vs. 3.7%) were similar in HIV-exposed and HIV-unexposed children. CONCLUSIONS Vaccination strategies targeting respiratory syncytial virus should be prioritized for prevention of pneumonia in children. Furthermore, interventions are required to address the high burden of tuberculosis in the pathogenesis of acute community-acquired pneumonia in settings such as ours.
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Affiliation(s)
- David P. Moore
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Vicky L. Baillie
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Azwifarwi Mudau
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology and Infectious Diseases, Chris Hani Baragwanath Academic Hospital, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Tanja Adams
- Department of Clinical Microbiology and Infectious Diseases, Chris Hani Baragwanath Academic Hospital, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Shafeeka Mangera
- Department of Clinical Microbiology and Infectious Diseases, Chris Hani Baragwanath Academic Hospital, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Charl Verwey
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paediatrics & Child Health, Chris Hani Baragwanath Academic Hospital and University of the Witwatersrand, South Africa
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Melissa M. Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Meredith Haddix
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Laura L. Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Daniel R. Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Katherine L. O’Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Eric A.F. Simões
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Pediatrics, University of Colorado School of Medicine and Center for Global Health, Colorado School of Public Health, Aurora, CO
| | - Shabir A. Madhi
- From the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Kim YK, Lee JH, Kim SY, Ahn JY, Choi KH, Lee YH, Jang KM, Hau YS, Lee JM. Rapid Molecular Tests for Detecting Respiratory Pathogens Reduced the Use of Antibiotics in Children. Antibiotics (Basel) 2021; 10:283. [PMID: 33801828 PMCID: PMC8001485 DOI: 10.3390/antibiotics10030283] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/06/2021] [Accepted: 03/07/2021] [Indexed: 12/25/2022] Open
Abstract
Multiplex polymerase chain reaction (mPCR) is increasingly being used to diagnose infections caused by respiratory pathogens in pediatric inpatient facilities. mPCR assays detect a broader array of viruses, with higher specificity and sensitivity and faster turnaround than previous assays. We adapted the FilmArray Respiratory Panel (FA-RP) for diagnosing respiratory infections. FA-RP is an in vitro mPCR assay that simultaneously and rapidly (in about 1 h) detects 20 pathogens directly from respiratory specimens. Here, we studied the clinical efficacy of FA-RP in children who underwent testing for respiratory pathogens at Yeungnam University Hospital from November 2015 to August 2018. From November 2015 to June 2016, routine mPCR testing was performed on nasopharyngeal swabs using the routine mPCR kit. From November 2016 to July 2018, mPCR testing was performed using FA-RP. A total of 321 tests by routine mPCR and 594 tests by FA-RP were included. The positive detection rates for routine mPCR and FA-RP were 71.3% and 83.3%, respectively. FA-RP reduced the lead time, waiting time, turnaround time, intravenous (IV) antibiotic use, and length of hospital stay for pediatric patients. The decreased use of antibiotics is expected to reduce antibiotic resistance in children.
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Affiliation(s)
- Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Jong Ho Lee
- Department of Laboratory Medicine, Yeungnam University College of Medicine, Daegu 42415, Korea;
| | - Sae Yoon Kim
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Ji Young Ahn
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Kwang Hae Choi
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Young Hwan Lee
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Kyung Mi Jang
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
| | - Yong Sauk Hau
- Department of Business Administration, School of Business, Yeungnam University, Gyeongsan 38541, Korea;
| | - Jae Min Lee
- Department of Pediatrics, College of Medicine, Yeungnam University, Daegu 42415, Korea; (S.Y.K.); (J.Y.A.); (K.H.C.); (Y.H.L.); (K.M.J.)
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Zar HJ, Moore DP, Andronikou S, Argent AC, Avenant T, Cohen C, Green RJ, Itzikowitz G, Jeena P, Masekela R, Nicol MP, Pillay A, Reubenson G, Madhi SA. Diagnosis and management of community-acquired pneumonia in children: South African Thoracic Society guidelines. Afr J Thorac Crit Care Med 2020; 26:10.7196/AJTCCM.2020.v26i3.104. [PMID: 34471872 PMCID: PMC7433705 DOI: 10.7196/ajtccm.2020.v26i3.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pneumonia remains a major cause of morbidity and mortality amongst South African children. More comprehensive immunisation regimens, strengthening of HIV programmes, improvement in socioeconomic conditions and new preventive strategies have impacted on the epidemiology of pneumonia. Furthermore, sensitive diagnostic tests and better sampling methods in young children improve aetiological diagnosis. OBJECTIVES To produce revised guidelines for pneumonia in South African children under 5 years of age. METHODS The Paediatric Assembly of the South African Thoracic Society and the National Institute for Communicable Diseases established seven expert subgroups to revise existing South African guidelines focusing on: (i) epidemiology; (ii) aetiology; (iii) diagnosis; (iv) antibiotic management and supportive therapy; (v) management in intensive care; (vi) prevention; and (vii) considerations in HIV-infected or HIVexposed, uninfected (HEU) children. Each subgroup reviewed the published evidence in their area; in the absence of evidence, expert opinion was accepted. Evidence was graded using the British Thoracic Society (BTS) grading system. Sections were synthesized into an overall guideline which underwent peer review and revision. RECOMMENDATIONS Recommendations include a diagnostic approach, investigations, management and preventive strategies. Specific recommendations for HIV infected and HEU children are provided. VALIDATION The guideline is based on available published evidence supplemented by the consensus opinion of SA paediatric experts. Recommendations are consistent with those in published international guidelines.
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Affiliation(s)
- H J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
- South African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, South Africa
| | - D P Moore
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Academic Hospital, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - S Andronikou
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
- Department of Pediatric Radiology, Perelman School of Medicine, University of Philadephia, USA
| | - A C Argent
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
| | - T Avenant
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - C Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - R J Green
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - G Itzikowitz
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and Faculty of Health Sciences, University of Cape Town, South Africa
| | - P Jeena
- Department of Paediatrics and Child Health, Nelson R Mandela School of Medicine, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - R Masekela
- Department of Paediatrics and Child Health, Nelson R Mandela School of Medicine, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - M P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa; and Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - A Pillay
- Department of Paediatrics and Child Health, Nelson R Mandela School of Medicine, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - G Reubenson
- Department of Paediatrics and Child Health, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - S A Madhi
- South African Medical Research Council Vaccine and Infectious Diseases Analytics Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: South African Research Chair in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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7
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Wetzke M, Kopp MV, Seidenberg J, Vogelberg C, Ankermann T, Happle C, Voigt G, Köster H, Illig T, Lex C, Schuster A, Panning M, Barten G, Rohde G, Welte T, Hansen G. PedCAPNETZ - prospective observational study on community acquired pneumonia in children and adolescents. BMC Pulm Med 2019; 19:238. [PMID: 31818288 PMCID: PMC6902429 DOI: 10.1186/s12890-019-1013-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Background Pediatric community acquired pneumonia (pedCAP) is one of the leading causes for childhood morbidity accounting for up to 20% of pediatric hospital admissions in high income countries. In spite of its high morbidity, updated epidemiological and pathogen data after introduction of preventive vaccination and novel pathogen screening strategies are limited. Moreover, there is a need for validated recommendations on diagnostic and treatment regimens in pedCAP. Through collection of patient data and analysis of pathogen and host factors in a large sample of unselected pedCAP patients in Germany, we aim to address and substantially improve this situation. Methods pedCAPNETZ is an observational, multi-center study on pedCAP. Thus far, nine study centers in hospitals, outpatient clinics and practices have been initiated and more than 400 patients with radiologically confirmed pneumonia have been enrolled, aiming at a total of 1000 study participants. Employing an online data base, information on disease course, treatment as well as demographical and socioeconomical data is recorded. Patients are followed up until day 90 after enrollment; Comprehensive biosample collection and a central pedCAPNETZ biobank allow for in-depth analyses of pathogen and host factors. Standardized workflows to assure sample logistics and data management in more than fifteen future study centers have been established. Discussion Through comprehensive epidemiological, clinical and biological analyses, pedCAPNETZ fills an important gap in pediatric and infection research. To secure dissemination of the registry, we will raise clinical and scientific awareness at all levels. We aim at participating in decision making processes for guidelines and prevention strategies. Ultimately, we hope the results of the pedCAPNETZ registry will help to improve care and quality of life in pedCAP patients in the future.
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Affiliation(s)
- Martin Wetzke
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, D -, 30625, Hannover, Germany.,German Center for Infection Research (DZIF), Site Hannover-, Braunschweig, Germany.,German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Matthias Volkmar Kopp
- German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,Department of Pediatric Allergy and Pulmonology, Clinic of Pediatrics UKSH, University of Luebeck, Luebeck, Germany
| | - Jürgen Seidenberg
- Department of Pediatric Pneumology and Allergology, Universitätsklinik für Kinder- und Jugendmedizin Oldenburg, Oldenburg, Germany
| | - Christian Vogelberg
- University Children's Hospital, Technical University Dresden, Dresden, Germany
| | - Tobias Ankermann
- Department of Pediatric Pulmonology, Clinic of Pediatrics UKSH, University of Kiel, Kiel, Germany
| | - Christine Happle
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, D -, 30625, Hannover, Germany.,German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Gesche Voigt
- German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,Department of Pediatric Allergy and Pulmonology, Clinic of Pediatrics UKSH, University of Luebeck, Luebeck, Germany
| | - Holger Köster
- Department of Pediatric Pneumology and Allergology, Universitätsklinik für Kinder- und Jugendmedizin Oldenburg, Oldenburg, Germany
| | - Thomas Illig
- German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Christiane Lex
- Department of Pediatric Pulmonology, University of Göttingen, Göttingen, Germany
| | - Antje Schuster
- Department of Pediatric Pulmonology, University of Düsseldorf, Düsseldorf, Germany
| | - Marcus Panning
- Institute of Virology, University of Freiburg, Freiburg, Germany
| | - Grit Barten
- German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,CAPNETZ Foundation, Hannover, Germany
| | - Gernot Rohde
- CAPNETZ Foundation, Hannover, Germany.,Department of Respiratory Medicine, University Hospital Frankfurt, Frankfurt, Germany
| | - Tobias Welte
- German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.,CAPNETZ Foundation, Hannover, Germany.,Department of Pulmonary Medicine, German Centre for Lung Research, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, D -, 30625, Hannover, Germany. .,German Center for Lung Research DZL, Airway Center North (ARCN) Lübeck and Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany. .,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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8
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Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A 2018; 115:E12353-E12362. [PMID: 30482864 PMCID: PMC6310811 DOI: 10.1073/pnas.1809700115] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In critically ill patients, noninfectious respiratory syndromes that resemble LRTIs further complicate diagnosis and confound targeted treatment. To address this, we developed a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response. We studied this approach in a prospective cohort of critically ill patients with acute respiratory failure and found that combining pathogen, microbiome, and host gene expression metrics achieved accurate LRTI diagnosis and identified etiologic pathogens in patients with clinically identified infections but otherwise negative testing. Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86–1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63–0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75–1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.
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9
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Bozio CH, Flanders WD, Finelli L, Bramley AM, Reed C, Gandhi NR, Vidal JE, Erdman D, Levine MZ, Lindstrom S, Ampofo K, Arnold SR, Self WH, Williams DJ, Grijalva CG, Anderson EJ, McCullers JA, Edwards KM, Pavia AT, Wunderink RG, Jain S. Use of Multiple Imputation to Estimate the Proportion of Respiratory Virus Detections Among Patients Hospitalized With Community-Acquired Pneumonia. Open Forum Infect Dis 2018; 5:ofy061. [PMID: 29946553 DOI: 10.1093/ofid/ofy061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/14/2018] [Indexed: 11/14/2022] Open
Abstract
Background Real-time polymerase chain reaction (PCR) on respiratory specimens and serology on paired blood specimens are used to determine the etiology of respiratory illnesses for research studies. However, convalescent serology is often not collected. We used multiple imputation to assign values for missing serology results to estimate virus-specific prevalence among pediatric and adult community-acquired pneumonia hospitalizations using data from an active population-based surveillance study. Methods Presence of adenoviruses, human metapneumovirus, influenza viruses, parainfluenza virus types 1-3, and respiratory syncytial virus was defined by positive PCR on nasopharyngeal/oropharyngeal specimens or a 4-fold rise in paired serology. We performed multiple imputation by developing a multivariable regression model for each virus using data from patients with available serology results. We calculated absolute and relative differences in the proportion of each virus detected comparing the imputed to observed (nonimputed) results. Results Among 2222 children and 2259 adults, 98.8% and 99.5% had nasopharyngeal/oropharyngeal specimens and 43.2% and 37.5% had paired serum specimens, respectively. Imputed results increased viral etiology assignments by an absolute difference of 1.6%-4.4% and 0.8%-2.8% in children and adults, respectively; relative differences were 1.1-3.0 times higher. Conclusions Multiple imputation can be used when serology results are missing, to refine virus-specific prevalence estimates, and these will likely increase estimates.
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Affiliation(s)
- Catherine H Bozio
- Department of Epidemiology, Emory University, Atlanta, Georgia.,Department of Global Health, Emory University, Atlanta, Georgia
| | - W Dana Flanders
- Department of Epidemiology, Emory University, Atlanta, Georgia
| | - Lyn Finelli
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Neel R Gandhi
- Department of Epidemiology, Emory University, Atlanta, Georgia.,Graduate Program in Molecules to Mankind, Emory University, Atlanta, Georgia.,Emory University School of Medicine, Atlanta, Georgia
| | - Jorge E Vidal
- Graduate Program in Molecules to Mankind, Emory University, Atlanta, Georgia
| | - Dean Erdman
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Min Z Levine
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Sandra R Arnold
- Le Bonheur Children's Hospital, Memphis, Tennessee.,University of Tennessee Health Science Center, Memphis, Tennessee
| | - Wesley H Self
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Derek J Williams
- Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | | | | | - Jonathan A McCullers
- Le Bonheur Children's Hospital, Memphis, Tennessee.,University of Tennessee Health Science Center, Memphis, Tennessee.,St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn M Edwards
- Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City, Utah
| | | | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
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10
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Connors TJ, Baird JS, Yopes MC, Zens KD, Pethe K, Ravindranath TM, Ho SH, Farber DL. Developmental Regulation of Effector and Resident Memory T Cell Generation during Pediatric Viral Respiratory Tract Infection. THE JOURNAL OF IMMUNOLOGY 2018; 201:432-439. [PMID: 29848753 DOI: 10.4049/jimmunol.1800396] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/08/2018] [Indexed: 01/07/2023]
Abstract
Viral respiratory tract infections (VRTI) remain a leading cause of morbidity and mortality among infants and young children. In mice, optimal protection to VRTI is mediated by recruitment of effector T cells to the lungs and respiratory tract, and subsequent establishment of tissue resident memory T cells (Trm), which provide long-term protection. These critical processes of T cell recruitment to the respiratory tract, their role in disease pathogenesis, and establishment of local protective immunity remain undefined in pediatric VRTI. In this study, we investigated T cell responses in the upper respiratory tract (URT) and lower respiratory tract (LRT) of infants and young children with VRTI, revealing developmental regulation of T cell differentiation and Trm generation in situ. We show a direct concurrence between T cell responses in the URT and LRT, including a preponderance of effector CD8+ T cells that was associated with disease severity. During infant VRTI, there was an accumulation of terminally differentiated effector cells (effector memory RA+ T cells) in the URT and LRT with reduced Trm in the early neonatal period, and decreased effector memory RA+ T cell and increased Trm formation with age during the early years of childhood. Moreover, human infant T cells exhibit increased expression of the transcription factor T-bet compared with adult T cells, suggesting a mechanism for preferential generation of effector over Trm. The developmental regulation of respiratory T cell responses as revealed in the present study is important for diagnosing, monitoring, and treating VRTI in the critical early life stages.
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Affiliation(s)
- Thomas J Connors
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032.,Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032
| | - J Scott Baird
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032
| | - Margot C Yopes
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032
| | - Kyra D Zens
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032
| | - Kalpana Pethe
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032
| | | | - Siu-Hong Ho
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032; .,Department of Surgery, Columbia University Medical Center, New York, NY 10032; and.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032
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11
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Kim L, Rha B, Abramson JS, Anderson LJ, Byington CL, Chen GL, DeVincenzo J, Edwards KM, Englund JA, Falsey AR, Griffin MR, Karron RA, Martin KG, Meissner HC, Munoz FM, Pavia AT, Piedra PA, Schaffner W, Simões EAF, Singleton R, Talbot HK, Walsh EE, Zucker JR, Gerber SI. Identifying Gaps in Respiratory Syncytial Virus Disease Epidemiology in the United States Prior to the Introduction of Vaccines. Clin Infect Dis 2018; 65:1020-1025. [PMID: 28903503 DOI: 10.1093/cid/cix432] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
Abstract
Respiratory syncytial virus (RSV) causes lower respiratory tract illness frequently. No effective antivirals or vaccines for RSV are approved for use in the United States; however, there are at least 50 vaccines and monoclonal antibody products in development, with those targeting older adults and pregnant women (to protect young infants) in phase 2 and 3 clinical trials. Unanswered questions regarding RSV epidemiology need to be identified and addressed prior to RSV vaccine introduction to guide the measurement of impact and future recommendations. The Centers for Disease Control and Prevention (CDC) convened a technical consultation to gather input from external subject matter experts on their individual perspectives regarding evidence gaps in current RSV epidemiology in the United States, potential studies and surveillance platforms needed to fill these gaps, and prioritizing efforts. Participants articulated their individual views, and CDC staff synthesized individuals' input into this report.
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Affiliation(s)
- Lindsay Kim
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon S Abramson
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | | | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - John DeVincenzo
- Pediatrics.,Microbiology, Immunology, and Biochemistry, University of Tennessee Center for Health Sciences.,Children's Foundation Research Institute, Lebonheur Children's Hospital, Memphis
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Ann R Falsey
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Marie R Griffin
- Health Policy.,Medicine, Vanderbilt University Medical Center.,Mid-South Geriatric Research Education and Clinical Center, VA Tennessee Valley Health Care System, Nashville
| | - Ruth A Karron
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Karen G Martin
- Council of State and Territorial Epidemiologists, Atlanta, Georgia.,Minnesota Department of Health, St Paul
| | - H Cody Meissner
- Department of Pediatrics, Tufts University School of Medicine, Boston, Massachusetts
| | - Flor M Munoz
- Departments of Pediatrics, Molecular Virology, and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Andrew T Pavia
- Departments of Pediatrics and Medicine, University of Utah School of Medicine, Salt Lake City
| | - Pedro A Piedra
- Departments of Pediatrics, Molecular Virology, and Microbiology, Baylor College of Medicine, Houston, Texas
| | - William Schaffner
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Eric A F Simões
- Department of Pediatrics, University of Colorado School of Medicine.,Department of Epidemiology, Center for Global Health, Colorado School of Public Health, Aurora
| | - Rosalyn Singleton
- Alaska Native Tribal Health Consortium.,Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Edward E Walsh
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Jane R Zucker
- New York City Department of Health and Mental Hygiene, Bureau of Immunization.,Immunization Services Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susan I Gerber
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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12
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13
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Zens KD, Connors T, Farber DL. Tissue compartmentalization of T cell responses during early life. Semin Immunopathol 2017; 39:593-604. [PMID: 28894935 PMCID: PMC5743209 DOI: 10.1007/s00281-017-0648-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/07/2017] [Indexed: 12/21/2022]
Abstract
The immune system in early life is tasked with transitioning from a relatively protected environment to one in which it encounters a wide variety of innocuous antigens and dangerous pathogens. The immaturity of the developing immune system, and particularly the distinct functionality of T lymphocytes in early life, has been implicated in increased susceptibility to infection. Previous work has demonstrated that immune responses in early life are skewed toward limited inflammation and atopy; however, there is mounting evidence that such responses are context- and tissue-dependent. The regulation, differentiation, and maintenance of infant T cell responses, particularly as it relates to tissue compartmentalization, remains poorly understood. How the tissue environment impacts early-life immune responses and whether the development of localized protective immune memory cell subsets are established is an emerging area of research. As infectious diseases affecting the respiratory and digestive tracts are a leading cause of morbidity and mortality worldwide in infants and young children, a deeper understanding of site-specific immunity is essential to addressing these challenges. Here, we review the current paradigms of T cell responses during infancy as they relate to tissue localization and discuss implications for the development of vaccines and therapeutics.
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Affiliation(s)
- Kyra D Zens
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Thomas Connors
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY, 10032, USA.
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA.
- Department of Surgery, Columbia University Medical Center, New York, NY, 10032, USA.
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14
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Abstract
Pulmonary infections remain a major cause of infant and child mortality worldwide and are responsible for a substantial burden of morbidity. During the 2015 European Respiratory Society International Congress in Amsterdam, some of the main findings from peer-reviewed articles addressing this topic that were published in the preceding 12 months were reviewed in a Paediatric Clinical Year in Review session. The following article highlights some of the insights provided by these articles into the complex interactions of the human host with the extensive and dynamic populations of microorganisms that call an individual "home".
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Affiliation(s)
- Mark L Everard
- School of Paediatrics and Child Health, University of Western Australia, Princess Margaret Hospital, Subiaco, Australia
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15
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16
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Abstract
Human parainfluenza viruses (HPIVs) are single-stranded, enveloped RNA viruses of the Paramyoviridaie family. There are four serotypes which cause respiratory illnesses in children and adults. HPIVs bind and replicate in the ciliated epithelial cells of the upper and lower respiratory tract and the extent of the infection correlates with the location involved. Seasonal HPIV epidemics result in a significant burden of disease in children and account for 40% of pediatric hospitalizations for lower respiratory tract illnesses (LRTIs) and 75% of croup cases. Parainfluenza viruses are associated with a wide spectrum of illnesses which include otitis media, pharyngitis, conjunctivitis, croup, tracheobronchitis, and pneumonia. Uncommon respiratory manifestations include apnea, bradycardia, parotitis, and respiratory distress syndrome and rarely disseminated infection. Immunity resulting from disease in childhood is incomplete and reinfection with HPIV accounts for 15% of respiratory illnesses in adults. Severe disease and fatal pneumonia may occur in elderly and immunocompromised adults. HPIV pneumonia in recipients of hematopoietic stem cell transplant (HSCT) is associated with 50% acute mortality and 75% mortality at 6 months. Though sensitive molecular diagnostics are available to rapidly diagnose HPIV infection, effective antiviral therapies are not available. Currently, treatment for HPIV infection is supportive with the exception of croup where the use of corticosteroids has been found to be beneficial. Several novel drugs including DAS181 appear promising in efforts to treat severe disease in immunocompromised patients, and vaccines to decrease the burden of disease in young children are in development.
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Affiliation(s)
- Angela R Branche
- Department of Medicine, University of Rochester, Rochester, New York
| | - Ann R Falsey
- Department of Medicine, University of Rochester, Rochester, New York
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17
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Cohen AL, Sahr PK, Treurnicht F, Walaza S, Groome MJ, Kahn K, Dawood H, Variava E, Tempia S, Pretorius M, Moyes J, Olorunju SAS, Malope-Kgokong B, Kuonza L, Wolter N, von Gottberg A, Madhi SA, Venter M, Cohen C. Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009-2014. Open Forum Infect Dis 2015; 2:ofv139. [PMID: 26566534 PMCID: PMC4630450 DOI: 10.1093/ofid/ofv139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/16/2015] [Indexed: 11/13/2022] Open
Abstract
Parainfluenza is associated with a significant amount of severe respiratory disease in South Africa, especially among children <5 years of age and individuals that are HIV-infected. Background. Parainfluenza virus (PIV) is a common cause of acute respiratory tract infections, but little is known about PIV infection in children and adults in Africa, especially in settings where human immunodeficiency virus (HIV) prevalence is high. Methods. We conducted active, prospective sentinel surveillance for children and adults hospitalized with severe acute respiratory illness (SARI) from 2009 to 2014 in South Africa. We enrolled controls (outpatients without febrile or respiratory illness) to calculate the attributable fraction for PIV infection. Respiratory specimens were tested by multiplex real-time reverse-transcription polymerase chain reaction assay for parainfluenza types 1, 2, and 3. Results. Of 18 282 SARI cases enrolled, 1188 (6.5%) tested positive for any PIV type: 230 (19.4%) were type 1; 168 (14.1%) were type 2; 762 (64.1%) were type 3; and 28 (2.4%) had coinfection with 2 PIV types. After adjusting for age, HIV serostatus, and respiratory viral coinfection, the attributable fraction for PIV was 65.6% (95% CI [confidence interval], 47.1–77.7); PIV contributed to SARI among HIV-infected and -uninfected children <5 years of age and among individuals infected with PIV types 1 and 3. The observed overall incidence of PIV-associated SARI was 38 (95% CI, 36–39) cases per 100 000 population and was highest in children <1 year of age (925 [95% CI, 864–989] cases per 100 000 population). Compared with persons without HIV, persons with HIV had an increased relative risk of PIV hospitalization (9.4; 95% CI, 8.5–10.3). Conclusions. Parainfluenza virus causes substantial severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV.
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Affiliation(s)
- Adam L Cohen
- Centers for Disease Control and Prevention , Pretoria , South Africa ; Centers for Disease Control and Prevention , Atlanta, Georgia ; US Public Health Service, Rockville, Maryland
| | - Philip K Sahr
- South African Field Epidemiology Training Program, Johannesburg ; School of Health Systems and Public Health, Faculty of Health Sciences , University of Pretoria
| | - Florette Treurnicht
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg
| | - Sibongile Walaza
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; School of Public Health
| | - Michelle J Groome
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences ; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health ; Centre for Global Health Research , Umeå University , Sweden ; INDEPTH Network, Accra , Ghana
| | - Halima Dawood
- Pietermaritzburg Metropolitan Hospital Complex ; University of KwaZulu-Natal , Durban
| | - Ebrahim Variava
- Department of Internal Medicine ; Department of Internal Medicine , Klerksdorp-Tshepong Hospital Complex
| | - Stefano Tempia
- Centers for Disease Control and Prevention , Pretoria , South Africa ; Centers for Disease Control and Prevention , Atlanta, Georgia ; Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg
| | - Marthi Pretorius
- Department of Medical Virology, Zoonoses Research Unit , University of Pretoria ; National Health Laboratory Service, Tshwane Academic Division
| | - Jocelyn Moyes
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; School of Public Health
| | | | - Babatyi Malope-Kgokong
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg
| | - Lazarus Kuonza
- South African Field Epidemiology Training Program, Johannesburg
| | - Nicole Wolter
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; School of Pathology, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa
| | - Anne von Gottberg
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; School of Pathology, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa
| | - Shabir A Madhi
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences ; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases
| | - Marietjie Venter
- Centers for Disease Control and Prevention , Pretoria , South Africa ; Department of Medical Virology, Zoonoses Research Unit , University of Pretoria
| | - Cheryl Cohen
- Center for Respiratory Diseases and Meningitis , National Institute for Communicable Diseases , Johannesburg ; School of Public Health
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