1
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Medrano PG, Weerasinghe N, Nagahawatte A, Vanderburg S, Park LP, Wijayaratne GB, Devasiri V, Dilshan B, Sheng T, Kurukulasooriya R, Anderson J, Nicholson BP, Woods CW, Bodinayake CK, Tillekeratne LG. Prevalence and predictors of antibiotic prescription among patients hospitalized with viral lower respiratory tract infections in Southern Province, Sri Lanka. PLoS One 2024; 19:e0304690. [PMID: 38861513 PMCID: PMC11166322 DOI: 10.1371/journal.pone.0304690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Antimicrobial overprescription is common for lower respiratory tract infections (LRTI), as viral and bacterial infections generally present with similar clinical features. Overprescription is associated with downstream antimicrobial resistance. This study aims to identify the prevalence and predictors of antibiotic prescription among patients hospitalized with viral LRTI. METHODS A prospective cohort study was conducted among patients aged ≥1 year hospitalized with viral LRTI in a tertiary care hospital in Southern Province, Sri Lanka from 2018-2021. Demographic, clinical, and laboratory data were recorded. Nasopharyngeal and blood samples were collected for multiplex polymerase chain reaction testing for 21 respiratory pathogens and procalcitonin (PCT) detection, respectively. Demographic and clinical features associated with antibiotic prescription were identified using Chi Square and t-tests; significant variables (p<0.05) were further included in multivariable logistic regression models. The potential impact of biomarker testing on antibiotic prescription was simulated using standard c-reactive protein (CRP) and PCT cut-offs. RESULTS Of 1217 patients enrolled, 438 (36.0%) had ≥1 respiratory virus detected, with 48.4% of these patients being male and 30.8% children. Influenza A (39.3%) and human rhinovirus/ enterovirus (28.3%) were most commonly detected. A total of 114 (84.4%) children and 266 (87.8%) adults with respiratory viruses were treated with antibiotics. Among children, neutrophil percentage (median 63.6% vs 47.6%, p = 0.04) was positively associated with antibiotic prescription. Among adults, headache (60.6% vs 35.1%, p = 0.003), crepitations/crackles (55.3% vs 21.6%, p<0.001), rhonchi/wheezing (42.9% vs 18.9%, p = 0.005), and chest x-ray opacities (27.4% vs 8.1%, p = 0.01) were associated with antibiotic prescription. Access to CRP and procalcitonin test results could have potentially decreased inappropriate antibiotic prescription in this study by 89.5% and 83.3%, respectively. CONCLUSIONS High proportions of viral detection and antibiotic prescription were observed among a large inpatient cohort with LRTI. Increased access to point-of-care biomarker testing may improve antimicrobial prescription.
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Affiliation(s)
- Perla G. Medrano
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | - Ajith Nagahawatte
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Sky Vanderburg
- University of California, San Francisco, California, United States of America
| | - Lawrence P. Park
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | | | | | - Tianchen Sheng
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | | | - Jack Anderson
- Duke University, Durham, North Carolina, United States of America
| | - Bradly P. Nicholson
- Institute for Medical Research, Durham, North Carolina, United States of America
| | - Christopher W. Woods
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Champica K. Bodinayake
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - L. Gayani Tillekeratne
- Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
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Bell C, Goss M, Norton D, Barlow S, Temte E, He C, Hamer C, Walters S, Sabry A, Johnson K, Chen G, Uzicanin A, Temte J. Descriptive Epidemiology of Pathogens Associated with Acute Respiratory Infection in a Community-Based Study of K-12 School Children (2015-2023). Pathogens 2024; 13:340. [PMID: 38668295 PMCID: PMC11053468 DOI: 10.3390/pathogens13040340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
School-based outbreaks often precede increased incidence of acute respiratory infections in the greater community. We conducted acute respiratory infection surveillance among children to elucidate commonly detected pathogens in school settings and their unique characteristics and epidemiological patterns. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a longitudinal, laboratory-supported, school-based, acute respiratory illness (ARI) surveillance study designed to evaluate the utility of cause-specific student absenteeism monitoring for early detection of increased activity of influenza and other respiratory viruses in schools from kindergarten through 12th grade. Eligible participants with ARIs provided demographic, epidemiologic, and symptom data, along with a nasal swab or oropharyngeal specimen. Multipathogen testing using reverse-transcription polymerase chain reaction (RT-PCR) was performed on all specimens for 18 respiratory viruses and 2 atypical bacterial pathogens (Chlamydia pneumoniae and Mycoplasma pneumoniae). Between 5 January 2015 and 9 June 2023, 3498 children participated. Pathogens were detected in 2455 of 3498 (70%) specimens. Rhinovirus/enteroviruses (36%) and influenza viruses A/B (35%) were most commonly identified in positive specimens. Rhinovirus/enteroviruses and parainfluenza viruses occurred early in the academic year, followed by seasonal coronaviruses, RSV, influenza viruses A/B, and human metapneumovirus. Since its emergence in 2020, SARS-CoV-2 was detected year-round and had a higher median age than the other pathogens. A better understanding of the etiologies, presentations, and patterns of pediatric acute respiratory infections can help inform medical and public health system responses.
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Affiliation(s)
- Cristalyne Bell
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Maureen Goss
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Derek Norton
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (D.N.); (G.C.)
| | - Shari Barlow
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Emily Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Cecilia He
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Caroline Hamer
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Sarah Walters
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Alea Sabry
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Kelly Johnson
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (D.N.); (G.C.)
| | - Amra Uzicanin
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
| | - Jonathan Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
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3
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Gu T, Zhong J, Ge M, Shi R, He L, Bai P. Water-stable perovskite-silica nanocomposites for encoded microbeads construction and multiplexed detection. J Colloid Interface Sci 2024; 657:580-589. [PMID: 38071807 DOI: 10.1016/j.jcis.2023.11.185] [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: 10/01/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 01/02/2024]
Abstract
All-inorganic lead halide perovskite nanocrystals exhibiting bright luminescence have great potential as fluorescence elements for optical encoding. However, their limited stability in water hinders the application in biosensing. In this study, novel optical encoded microbeads based on CsPbX3 (X = Cl, Br) nanocrystals are developed and applied in bead-based suspension arrays for the first time. Through the in-situ crystallization of CsPbX3 nanocrystals within mesoporous silica nano-templates (MSNs), accompanied by mesopores collapse after sintering, CsPbX3@MSNs (X3M) nanocomposites with uniform morphology and stable fluorescence intensity in aqueous solutions for up to 50 days are obtained. By assembling X3M with microspheres to form a host-guest structure, an optical encoding microbead (MX3M) library is established by varying the X3M ratio, halide composition, and the size of host microspheres, which can be easily decoded under multi-channel flow cytometer. As a result, MX3M exhibits outstanding capacity for specific target capture and negligible nonspecific absorption performance in the multiplex nucleic acid detection of respiratory viruses, with a low limit of detection (10 copies/rxn). This result highlights the tremendous potential of MX3M encoded microbeads constructed based on CsPbX3 nanocrystals for multiplexed bioassays.
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Affiliation(s)
- Tongxu Gu
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China.
| | - Jiajun Zhong
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China
| | - Minghao Ge
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China
| | - Ruiju Shi
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China
| | - Liang He
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China; CAS Key Lab of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, People's Republic of China
| | - Pengli Bai
- Jihua Laboratory, No.28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong 528200, People's Republic of China; CAS Key Lab of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, People's Republic of China.
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4
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Dunbar SA. Nucleic acid sample preparation techniques for bead-based suspension arrays. Methods 2023; 219:22-29. [PMID: 37716477 DOI: 10.1016/j.ymeth.2023.09.003] [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: 05/31/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023] Open
Abstract
Multiplexing in biological assays allows the simultaneous detection of multiple analytes in a single reaction, which reduces time, labor, and cost as compared to single reaction-based detection methods. Microsphere- or bead-based suspension array technologies, such as the Luminex® xMAP® system, offer high-throughput detection of nucleic acids through a variety of different assay chemistries. Common with most nucleic acid chemistries, for bead-based or other microarray technologies, is the need for efficient extraction and purification of the nucleic acids from the specimen of interest. Often, the optimal method will be dictated by the requirements of the up-front enzymatic chemistry, such as PCR, primer extension, branched DNA (bDNA), etc. For bead-based microarray platforms, the user must also be cognizant of proteins and other contaminants present in reactions that require heat denaturation, as that can lead to bead aggregation or agglutination, preventing the reading of assay results. This review describes and highlights some of the nucleic acid extraction and purification methods that have been used successfully for bead-based nucleic acid analysis, for both prokaryotic and eucaryotic nucleic acids, from a variety of sample types.
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Affiliation(s)
- Sherry A Dunbar
- Scientific Affairs, Luminex, A DiaSorin Company, 12212 Technology Blvd., Austin, TX 78727, USA.
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5
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff LE, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Nguyen TT, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell 2023; 186:4632-4651.e23. [PMID: 37776858 PMCID: PMC10724861 DOI: 10.1016/j.cell.2023.08.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/18/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
The dynamics of immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infants and young children by analyzing blood samples and weekly nasal swabs collected before, during, and after infection with Omicron and non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, showed no sign of decay for up to 300 days. Infants mounted a robust mucosal immune response characterized by inflammatory cytokines, interferon (IFN) α, and T helper (Th) 17 and neutrophil markers (interleukin [IL]-17, IL-8, and CXCL1). The immune response in blood was characterized by upregulation of activation markers on innate cells, no inflammatory cytokines, but several chemokines and IFNα. The latter correlated with viral load and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell multi-omics. Together, these data provide a snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; DFG Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy" (iFIT), University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Baden-Wuerttemberg, Germany
| | - Allison R Burrell
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lindsay E Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katherine C Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - R Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Tran T Nguyen
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B Haslam
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA; Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taia T Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mary A Staat
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
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6
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Sahni LC, Naioti EA, Olson SM, Campbell AP, Michaels MG, Williams JV, Staat MA, Schlaudecker EP, McNeal MM, Halasa NB, Stewart LS, Chappell JD, Englund JA, Klein EJ, Szilagyi PG, Weinberg GA, Harrison CJ, Selvarangan R, Schuster JE, Azimi PH, Singer MN, Avadhanula V, Piedra PA, Munoz FM, Patel MM, Boom JA. Sustained Within-season Vaccine Effectiveness Against Influenza-associated Hospitalization in Children: Evidence From the New Vaccine Surveillance Network, 2015-2016 Through 2019-2020. Clin Infect Dis 2023; 76:e1031-e1039. [PMID: 35867698 DOI: 10.1093/cid/ciac577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Adult studies have demonstrated within-season declines in influenza vaccine effectiveness (VE); data in children are limited. METHODS We conducted a prospective, test-negative study of children 6 months through 17 years hospitalized with acute respiratory illness at 7 pediatric medical centers during the 2015-2016 through 2019-2020 influenza seasons. Case-patients were children with an influenza-positive molecular test matched by illness onset to influenza-negative control-patients. We estimated VE [100% × (1 - odds ratio)] by comparing the odds of receipt of ≥1 dose of influenza vaccine ≥14 days before illness onset among influenza-positive children to influenza-negative children. Changes in VE over time between vaccination date and illness onset date were estimated using multivariable logistic regression. RESULTS Of 8430 children, 4653 (55%) received ≥1 dose of influenza vaccine. On average, 48% were vaccinated through October and 85% through December each season. Influenza vaccine receipt was lower in case-patients than control-patients (39% vs 57%, P < .001); overall VE against hospitalization was 53% (95% confidence interval [CI]: 46, 60%). Pooling data across 5 seasons, the odds of influenza-associated hospitalization increased 4.2% (-3.2%, 12.2%) per month since vaccination, with an average VE decrease of 1.9% per month (n = 4000, P = .275). Odds of hospitalization increased 2.9% (95% CI: -5.4%, 11.8%) and 9.6% (95% CI: -7.0%, 29.1%) per month in children ≤8 years (n = 3084) and 9-17 years (n = 916), respectively. These findings were not statistically significant. CONCLUSIONS We observed minimal, not statistically significant within-season declines in VE. Vaccination following current Advisory Committee on Immunization Practices (ACIP) guidelines for timing of vaccine receipt remains the best strategy for preventing influenza-associated hospitalizations in children.
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Affiliation(s)
- Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Eric A Naioti
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Samantha M Olson
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela P Campbell
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marian G Michaels
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John V Williams
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary Allen Staat
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Elizabeth P Schlaudecker
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Monica M McNeal
- Department of Pediatrics, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Cincinnati, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Natasha B Halasa
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | - James D Chappell
- Vanderbilit University Medical Center, Nashville, Tennessee, USA
| | | | | | - Peter G Szilagyi
- University of California Los Angeles (UCLA) Mattel Children's Hospital, Los Angeles, California, USA
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Christopher J Harrison
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Rangaraj Selvarangan
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Jennifer E Schuster
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri, USA
| | - Parvin H Azimi
- University of California San Francisco (UCSF) Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Monica N Singer
- University of California San Francisco (UCSF) Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Vasanthi Avadhanula
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Flor M Munoz
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Manish M Patel
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff L, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.28.23285133. [PMID: 36778389 PMCID: PMC9915811 DOI: 10.1101/2023.01.28.23285133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, Tuebingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functional Instructed Tumor Therapy’ (iFIT), University of Tuebingen, Tuebingen, Germany
- German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Allison R. Burrell
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lindsay Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Katherine C. Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - R. Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C. Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B. Haslam
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Steven E. Bosinger
- Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Mary A. Staat
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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Distribution of Viral Respiratory Infections during the COVID-19 Pandemic Using the FilmArray Respiratory Panel. Biomedicines 2022; 10:biomedicines10112734. [DOI: 10.3390/biomedicines10112734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
This study was conducted to evaluate the distribution of respiratory viral pathogens in the emergency department during the coronavirus disease 2019 (COVID-19) pandemic. Between May 2020 and September 2022, patients aged between 0.1 and 98 years arrived at the emergency department of Asia University Hospital, and samples from nasopharyngeal swabs were tested by the FilmArrayTM Respiratory Panel (RP). SARS-CoV-2 positivity was subsequently retested by the cobas Liat system. There were 804 patients for whom the FilmArrayTM RP was tested, and 225 (27.9%) of them had positive results for respiratory viruses. Rhinovirus/enterovirus was the most commonly detected pathogen, with 170 (61.8%) cases, followed by adenovirus with 38 (13.8%), SARS-CoV-2 with 16 (5.8%) cases, and coronavirus 229E, with 16 (5.8%) cases. SARS-CoV-2 PCR results were positive in 16 (5.8%) cases, and there were two coinfections of SARS-CoV-2 with adenovirus and rhinovirus/enterovirus. A total of 43 (5.3%) patients were coinfected; the most coinfection was adenovirus plus rhinovirus/enterovirus, which was detectable in 18 (41.9%) cases. No atypical pathogens were found in this study. Intriguingly, our results showed that there was prefect agreement between the detection of SARS-CoV-2 conducted with the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test and the FilmArrayTM RP. Therefore, the FilmArrayTM RP assay is a reliable and feasible method for the detection of SARS-CoV-2. In summary, FilmArrayTM RP significantly broadens our capability to detect multiple respiratory infections due to viruses and atypical bacteria. It provides a prompt evaluation of pathogens to enhance patient care and clinical selection strategies in emergency departments during the COVID-19 pandemic.
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Comparative Performance of the Luminex NxTAG Respiratory Pathogen Panel, GenMark eSensor Respiratory Viral Panel, and BioFire FilmArray Respiratory Panel. Microbiol Spectr 2022; 10:e0124822. [PMID: 35766513 PMCID: PMC9431521 DOI: 10.1128/spectrum.01248-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This study compares three of the most inclusive and widely used panels for respiratory syndromic testing in the United States, namely, Luminex NxTAG Respiratory Pathogen Panel (RPP), BioFire FilmArray Respiratory Panel (RP), and GenMark eSensor Respiratory Viral Panel (RVP). We compared the three assays using nasopharyngeal swab samples (n = 350) collected from symptomatic patients (n = 329) in the pre-coronavirus disease 2019 (COVID-19) era. There was no significant difference in the overall accuracies of BioFire and Luminex assays (P = 0.6171); however, significant differences were found between BioFire and GenMark (P = 0.0003) and between GenMark and Luminex (P = 0.0009). The positive percent agreement of the BioFire RP assay was 94.1%, compared to 97.3% for GenMark RVP and 96.5% for Luminex RPP. Overall negative percent agreement values were high for all three assays, i.e., 99.9% for BioFire and Luminex and 99.5% for GenMark. The three assays were equivalent for adenovirus, human metapneumovirus, influenza A, and respiratory syncytial virus. Increased false-positive results were seen with BioFire for the endemic coronaviruses and with GenMark for influenza B and the parainfluenza viruses. IMPORTANCE Clinical laboratories have multiple choices when it is comes to syndromic respiratory testing. Here, the Luminex NxTAG RPP is compared to the BioFire FilmArray RP and GenMark eSensor RVP for overall and per-target accuracy. As new tests come to market, it is important to ascertain their performance characteristics, compared to other widely used in vitro diagnostic products.
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10
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Sanz I, Perez D, Rojo S, Domínguez-Gil M, de Lejarazu RO, Eiros JM. Coinfections of influenza and other respiratory viruses are associated to children. An Pediatr (Barc) 2022; 96:334-341. [DOI: 10.1016/j.anpede.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/11/2020] [Indexed: 11/29/2022] Open
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11
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Campbell AP, Ogokeh C, Weinberg GA, Boom JA, Englund JA, Williams JV, Halasa NB, Selvarangan R, Staat MA, Klein EJ, McNeal M, Michaels MG, Sahni LC, Stewart LS, Szilagyi PG, Harrison CJ, Lively JY, Rha B, Patel M. Effect of Vaccination on Preventing Influenza-Associated Hospitalizations Among Children During a Severe Season Associated With B/Victoria Viruses, 2019-2020. Clin Infect Dis 2021; 73:e947-e954. [PMID: 33502489 DOI: 10.1093/cid/ciab060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The 2019-2020 influenza season was characterized by early onset with B/Victoria followed by A(H1N1)pdm09 viruses. Emergence of new B/Victoria viruses raised concerns about possible vaccine mismatch. We estimated vaccine effectiveness (VE) against influenza-associated hospitalizations and emergency department (ED) visits among children in the United States. METHODS We assessed VE among children aged 6 months-17 years with acute respiratory illness and ≤10 days of symptoms enrolled at 7 pediatric medical centers in the New Vaccine Surveillance Network. Combined midturbinate/throat swabs were tested for influenza virus using molecular assays. Vaccination history was collected from parental report, state immunization information systems, and/or provider records. We estimated VE from a test-negative design using logistic regression to compare odds of vaccination among children testing positive vs negative for influenza. RESULTS Among 2029 inpatients, 335 (17%) were influenza positive: 37% with influenza B/Victoria alone and 44% with influenza A(H1N1)pdm09 alone. VE was 62% (95% confidence interval [CI], 52%-71%) for influenza-related hospitalizations, 54% (95% CI, 33%-69%) for B/Victoria viruses, and 64% (95% CI, 49%-75%) for A(H1N1)pdm09. Among 2102 ED patients, 671 (32%) were influenza positive: 47% with influenza B/Victoria alone and 42% with influenza A(H1N1)pdm09 alone. VE was 56% (95% CI, 46%-65%) for an influenza-related ED visit, 55% (95% CI, 40%-66%) for B/Victoria viruses, and 53% (95% CI, 37%-65%) for A(H1N1)pdm09. CONCLUSIONS Influenza vaccination provided significant protection against laboratory-confirmed influenza-associated hospitalizations and ED visits associated with the 2 predominantly circulating influenza viruses among children, including against the emerging B/Victoria virus subclade.
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Affiliation(s)
- Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Constance Ogokeh
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Julie A Boom
- Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | | | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Rangaraj Selvarangan
- Children's Mercy Hospital, Kansas City, Missouri, USA
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Mary A Staat
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Monica McNeal
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Marian G Michaels
- Department of Pediatrics, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leila C Sahni
- Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Laura S Stewart
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peter G Szilagyi
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- University of California at Los Angeles, Los Angeles, California, USA
| | | | - Joana Y Lively
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Atlanta, Georgia, USA
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Lee N, Smith S, Zelyas N, Klarenbach S, Zapernick L, Bekking C, So H, Yip L, Tipples G, Taylor G, Mubareka S. Burden of noninfluenza respiratory viral infections in adults admitted to hospital: analysis of a multiyear Canadian surveillance cohort from 2 centres. CMAJ 2021; 193:E439-E446. [PMID: 33782171 PMCID: PMC8099164 DOI: 10.1503/cmaj.201748] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND: Data on the outcomes of noninfluenza respiratory virus (NIRV) infections among hospitalized adults are lacking. We aimed to study the burden, severity and outcomes of NIRV infections in this population. METHODS: We analyzed pooled patient data from 2 hospital-based respiratory virus surveillance cohorts in 2 regions of Canada during 3 consecutive seasons (2015/16, 2016/17, 2017/18; n = 2119). We included patients aged ≥ 18 years who developed influenza-like illness or pneumonia and were hospitalized for management. We included patients confirmed positive for ≥ 1 virus by multiplex polymerase chain reaction assays (respiratory syncytial virus [RSV], human rhinovirus/enterovirus (hRV), human coronavirus (hCoV), metapneumovirus, parainfluenza virus, adenovirus, influenza viruses). We compared patient characteristics, clinical severity conventional outcomes (e.g., hospital length-of stay, 30-day mortality) and ordinal outcomes (5 levels: discharged, receiving convalescent care, acute ward or intensive care unit [ICU] care and death) for patients with NIRV infections and those with influenza. RESULTS: Among 2119 adults who were admitted to hospital, 1156 patients (54.6%) had NIRV infections (hRV 14.9%, RSV 12.9%, hCoV 8.2%) and 963 patients (45.4%) had influenza (n = 963). Patients with NIRVs were younger (mean 66.4 [standard deviation 20.4] yr), and more commonly had immunocompromising conditions (30.3%) and delay in diagnosis (median 4.0 [interquartile range (IQR) 2.0–7.0] days). Overall, 14.6% (12.4%–19.5%) of NIRV infections were acquired in hospital. Admission to ICU (18.2%, median 6.0 [IQR 3.0–13.0] d), hospital length-of-stay (median 5.0 [IQR 2.0–10.0] d) and 30-day mortality (8.4%; RSV 9.5%, hRV 6.6%, hCoV 9.2%) and the ordinal outcomes were similar for patients with NIRV infection and those with influenza. Age > 60 years, immunocompromised state and hospital-acquired viral infection were associated with worse outcomes. The estimated median cost per acute care admission was $6000 (IQR $2000–$16 000). INTERPRETATION: The burden of NIRV infection is substantial in adults admitted to hospital and associated outcomes may be as severe as for influenza, suggesting a need to prioritize therapeutics and vaccines for at-risk people.
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Affiliation(s)
- Nelson Lee
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont.
| | - Stephanie Smith
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Nathan Zelyas
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Scott Klarenbach
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Lori Zapernick
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Christian Bekking
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Helen So
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Lily Yip
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Graham Tipples
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Geoff Taylor
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont
| | - Samira Mubareka
- Division of Infectious Disease (Lee, Smith, Zapernick, Taylor), Department of Medicine, and Department of Laboratory Medicine and Pathology (Zelyas, Tipples), and Division of Nephrology (Klarenbach, So), Department of Medicine, University of Alberta, Edmonton, Alta.; Sunnybrook Research Institute (Bekking, Yip, Mubareka); Department of Laboratory Medicine and Pathobiology (Mubareka), University of Toronto, Toronto, Ont.
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13
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Feldstein LR, Ogokeh C, Rha B, Weinberg GA, Staat MA, Selvarangan R, Halasa NB, Englund JA, Boom JA, Azimi PH, Szilagyi PG, McNeal M, Harrison CJ, Williams JV, Klein EJ, Sahni LC, Singer MN, Lively JY, Payne DC, Fry AM, Patel M, Campbell AP. Vaccine Effectiveness Against Influenza Hospitalization Among Children in the United States, 2015-2016. J Pediatric Infect Dis Soc 2021; 10:75-82. [PMID: 32108879 DOI: 10.1093/jpids/piaa017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/06/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Annual United States (US) estimates of influenza vaccine effectiveness (VE) in children typically measure protection against outpatient medically attended influenza illness, with limited data evaluating VE against influenza hospitalizations. We estimated VE for preventing laboratory-confirmed influenza hospitalization among US children. METHODS We included children aged 6 months-17 years with acute respiratory illness enrolled in the New Vaccine Surveillance Network during the 2015-2016 influenza season. Documented influenza vaccination status was obtained from state immunization information systems, the electronic medical record, and/or provider records. Midturbinate nasal and throat swabs were tested for influenza using molecular assays. We estimated VE as 100% × (1 - odds ratio), comparing the odds of vaccination among subjects testing influenza positive with subjects testing negative, using multivariable logistic regression. RESULTS Of 1653 participants, 36 of 707 (5%) of those fully vaccinated, 18 of 226 (8%) of those partially vaccinated, and 85 of 720 (12%) of unvaccinated children tested positive for influenza. Of those vaccinated, almost 90% were documented to have received inactivated vaccine. The majority (81%) of influenza cases were in children ≤ 8 years of age. Of the 139 influenza-positive cases, 42% were A(H1N1)pdm09, 42% were B viruses, and 14% were A(H3N2). Overall, adjusted VE for fully vaccinated children was 56% (95% confidence interval [CI], 34%-71%) against any influenza-associated hospitalization, 68% (95% CI, 36%-84%) for A(H1N1)pdm09, and 44% (95% CI, -1% to 69%) for B viruses. CONCLUSIONS These findings demonstrate the importance of annual influenza vaccination in prevention of severe influenza disease and of reducing the number of children who remain unvaccinated or partially vaccinated against influenza.
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Affiliation(s)
- Leora R Feldstein
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Constance Ogokeh
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education Fellowship Program, Oak Ridge, Tennessee, USA
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary A Staat
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Janet A Englund
- Department of Pediatrics, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Parvin H Azimi
- Department of Infectious Diseases, University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Peter G Szilagyi
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Pediatrics, Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, California, USA
| | - Monica McNeal
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Christopher J Harrison
- Department of Infectious Diseases, University of Missouri-Kansas City, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Eileen J Klein
- Department of Pediatrics, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Monica N Singer
- Department of Infectious Diseases, University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Joana Y Lively
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Atlanta, Georgia, USA
| | - Daniel C Payne
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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14
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Sanz I, Perez D, Rojo S, Domínguez-Gil M, Lejarazu ROD, Eiros JM. [Coinfections of influenza and other respiratory viruses are associated to children]. An Pediatr (Barc) 2021; 96:S1695-4033(21)00143-0. [PMID: 33745837 DOI: 10.1016/j.anpedi.2020.12.024] [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: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Coinfections of influenza and other respiratory viruses (ORVs) are frequent in the epidemic season. The aim of this study was to examine the demographic and virological variables associated with coinfections by influenza and ORVs. MATERIALS AND METHODS We analysed respiratory samples of patients with laboratory-confirmed influenza using molecular diagnostic methods obtained in 8 consecutive influenza seasons (2011-2012 to 2018-2019). We analysed data focusing on different variables: age, sex, type of patient (hospitalized/sentinel) and detected type/subtype of influenza. RESULTS Coinfections of influenza and ORVs were detected in 17.8% of influenza-positive samples. The probability of detecting coinfection was significantly higher in young children (0-4 years; OR: 2.7; 95% CI: 2.2-3.4), children (5-14 years; OR: 1.6; 95% CI: 1.2-2.1) and patients infected with the A(H3N2) subtype (OR: 1.4; 95% CI: 1.14-1.79). Also, we found a significantly higher frequency of coinfections involving influenza and 2 or more other respiratory viruses in young children (0-4 years; OR: 0.5; 95% CI: 0.32-0.8), adults (40-64 years; OR: 0.5; 95% CI: 0.3-0.9) and women (OR: 0.7; 95% CI: 0.5-0.9). DISCUSSION These results show that coinfections of influenza and ORVs are more frequent in young children and children, and in cases involving the A(H3N2) influenza subtype. Our findings can be useful to guide the use of multiplex diagnostic methods in laboratories with limited resources.
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Affiliation(s)
- Ivan Sanz
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España.
| | - Diana Perez
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - Silvia Rojo
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Unidad de Virología, Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - Marta Domínguez-Gil
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, España
| | - Raúl Ortiz de Lejarazu
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - José María Eiros
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Unidad de Virología, Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Valladolid, España; Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, España
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15
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Jacky L, Yurk D, Alvarado J, Belitz P, Fathe K, MacDonald C, Fraser S, Rajagopal A. Robust Multichannel Encoding for Highly Multiplexed Quantitative PCR. Anal Chem 2021; 93:4208-4216. [PMID: 33631072 DOI: 10.1021/acs.analchem.0c04626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gold standard of molecular pathogen detection is the quantitative polymerase chain reaction (qPCR). Modern qPCR instruments are capable of detecting 4-6 analytes in a single sample: one per optical detection channel. However, many clinical applications require multiplexing beyond this traditional single-well capacity, including the task of simultaneously testing for SARS-CoV-2 and other respiratory pathogens. This can be addressed by dividing a sample across multiple wells, or using technologies such as genomic sequencing and spatial arrays, but at the expense of significantly higher cost and lower throughput compared with single-well qPCR. These trade-offs represent unacceptable compromises in high-throughput screening scenarios such as SARS-CoV-2 testing. We demonstrate a novel method of detecting up to 20 targets per well with standard qPCR instrumentation: high-definition PCR (HDPCR). HDPCR combines TaqMan chemistry and familiar workflows with robust encoding to enable far higher levels of multiplexing on a traditional qPCR system without an increase in cost or reduction in throughput. We utilize HDPCR with a custom 20-Plex assay, an 8-Plex assay using unmodified predesigned single-plex assays from Integrated DNA Technologies and a 9-Plex pathogen panel inclusive of SARS-CoV-2 and other common respiratory viruses. All three assays were successful when tested on a variety of samples, with overall sample accuracies of 98.8, 98.3, and 100%, respectively. The HDPCR technology enables the large install base of qPCR instrumentation to perform mid-density multiplex diagnostics without modification to instrumentation or workflow, meeting the urgent need for increased diagnostic yield at an affordable price without sacrificing assay performance.
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Affiliation(s)
- Lucien Jacky
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Dominic Yurk
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - John Alvarado
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Paul Belitz
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Kristin Fathe
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Chris MacDonald
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Scott Fraser
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, United States
| | - Aditya Rajagopal
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
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16
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Rha B, Curns AT, Lively JY, Campbell AP, Englund JA, Boom JA, Azimi PH, Weinberg GA, Staat MA, Selvarangan R, Halasa NB, McNeal MM, Klein EJ, Harrison CJ, Williams JV, Szilagyi PG, Singer MN, Sahni LC, Figueroa-Downing D, McDaniel D, Prill MM, Whitaker BL, Stewart LS, Schuster JE, Pahud BA, Weddle G, Avadhanula V, Munoz FM, Piedra PA, Payne DC, Langley G, Gerber SI. Respiratory Syncytial Virus-Associated Hospitalizations Among Young Children: 2015-2016. Pediatrics 2020; 146:peds.2019-3611. [PMID: 32546583 DOI: 10.1542/peds.2019-3611] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of hospitalized acute respiratory illness (ARI) among young children. With RSV vaccines and immunoprophylaxis agents in clinical development, we sought to update estimates of US pediatric RSV hospitalization burden. METHODS Children <5 years old hospitalized for ARI were enrolled through active, prospective, population-based surveillance from November 1, 2015, to June 30, 2016, at 7 US pediatric hospital sites. Clinical information was obtained from parent interviews and medical records. Midturbinate nasal and throat flocked swabs were collected and tested for RSV by using molecular diagnostic assays at each site. We conducted descriptive analyses and calculated population-based rates of RSV-associated hospitalizations. RESULTS Among 2969 hospitalized children included in analyses, 1043 (35%) tested RSV-positive; 903 (87%) children who were RSV-positive were <2 years old, and 526 (50%) were <6 months old. RSV-associated hospitalization rates were 2.9 per 1000 children <5 years old and 14.7 per 1000 children <6 months old; the highest age-specific rate was observed in 1-month-old infants (25.1 per 1000). Most children who were infected with RSV (67%) had no underlying comorbid conditions and no history of preterm birth. CONCLUSIONS During the 2015-2016 season, RSV infection was associated with one-third of ARI hospitalizations in our study population of young children. Hospitalization rates were highest in infants <6 months. Most children who were RSV-positive had no history of prematurity or underlying medical conditions, suggesting that all young children could benefit from targeted interventions against RSV.
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Affiliation(s)
| | | | - Joana Y Lively
- Division of Viral Diseases and.,IHRC, Inc, Atlanta, Georgia
| | - Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Julie A Boom
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and
| | - Parvin H Azimi
- University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California
| | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Mary A Staat
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rangaraj Selvarangan
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | | | - Monica M McNeal
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Christopher J Harrison
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - John V Williams
- University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter G Szilagyi
- Department of Pediatrics, UCLA Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, California
| | - Monica N Singer
- University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California
| | | | | | - Darius McDaniel
- Division of Viral Diseases and.,Maximus Federal, Atlanta, Georgia
| | | | | | | | - Jennifer E Schuster
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Barbara A Pahud
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Gina Weddle
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Vasanthi Avadhanula
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Flor M Munoz
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Pedro A Piedra
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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17
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Ma ZY, Deng H, Hua LD, Lei W, Zhang CB, Dai QQ, Tao WJ, Zhang L. Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection. BMC Infect Dis 2020; 20:168. [PMID: 32087697 PMCID: PMC7036252 DOI: 10.1186/s12879-020-4900-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.
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Affiliation(s)
- Zhan-Ying Ma
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Li-Dong Hua
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Chang-Bin Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Qi-Qiang Dai
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Wei-Jing Tao
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
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18
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Esposito S, Mencacci A, Cenci E, Camilloni B, Silvestri E, Principi N. Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? Front Cell Infect Microbiol 2019; 9:196. [PMID: 31275863 PMCID: PMC6593267 DOI: 10.3389/fcimb.2019.00196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/21/2019] [Indexed: 01/31/2023] Open
Abstract
Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Antonella Mencacci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Elio Cenci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Barbara Camilloni
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Ettore Silvestri
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
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19
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McFarlin BK, Curtis JH. Advances in Bead-Based Biomarker Detection. Methods 2019; 158:1. [DOI: 10.1016/j.ymeth.2019.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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