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Galli C, Mazzola G, Arosio M, Pellegrinelli L, Boldrini A, Guarneri D, Lombarda E, Farina C, Cereda D, Pariani E. Real-time investigation of an influenza A(H3N2) virus outbreak in a refugee community, November 2022. Public Health 2024; 230:157-162. [PMID: 38554473 DOI: 10.1016/j.puhe.2024.02.027] [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: 09/09/2023] [Revised: 02/02/2024] [Accepted: 02/27/2024] [Indexed: 04/01/2024]
Abstract
OBJECTIVES To report epidemiological and virological results of an outbreak investigation of influenza-like illness (ILI) among refugees in Northern Italy. STUDY DESIGN Outbreak investigation of ILI cases observed among nearly 100 refugees in Northern Italy unvaccinated for influenza. METHODS An epidemiological investigation matched with a differential diagnosis was carried out for each sample collected from ILI cases to identify 10 viral pathogens (SARS-CoV-2, influenza virus type A and B, respiratory syncytial virus, metapneumovirus, parainfluenza viruses, rhinovirus, enterovirus, parechovirus, and adenovirus) by using specific real-time PCR assays according to the Centers for Disease Control and Prevention (CDC) protocols. In cases where the influenza virus type was identified, complete hemagglutinin (HA) gene sequencing and the related phylogenetic analysis were conducted. RESULTS The outbreak was caused by influenza A(H3N2): the attack rate was 83.3% in children aged 9-14 years, 84.6% in those aged 15-24 years, and 28.6% in adults ≥25 years. Phylogenetic analyses uncovered that A(H3N2) strains were closely related since they segregated in the same cluster, showing both a high mean nucleotide identity (100%), all belonging to the genetic sub-group 3C.2a1b.2a.2, as those mainly circulating into the general population in the same period. CONCLUSIONS The fact that influenza outbreak strains as well as the community strains were genetically related to the seasonal vaccine strain suggests that if an influenza prevention by vaccination strategy had been implemented, a lower attack rate of A(H3N2) and ILI cases might have been achieved.
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Affiliation(s)
- C Galli
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | - G Mazzola
- Department of Hygiene and Health Prevention (HPA of Bergamo/ATS of Bergamo), Italy
| | - M Arosio
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy; Biobank, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - L Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | - A Boldrini
- Department of Hygiene and Health Prevention (HPA of Bergamo/ATS of Bergamo), Italy
| | - D Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - E Lombarda
- Department of Hygiene and Health Prevention (HPA of Bergamo/ATS of Bergamo), Italy
| | - C Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - D Cereda
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - E Pariani
- Department of Biomedical Sciences for Health, University of Milan, Italy.
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Hassan MZ, Islam MA, Haider S, Shirin T, Chowdhury F. Respiratory Syncytial Virus-Associated Deaths among Children under Five before and during the COVID-19 Pandemic in Bangladesh. Viruses 2024; 16:111. [PMID: 38257812 PMCID: PMC10818674 DOI: 10.3390/v16010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory infections in young children worldwide. RSV-associated deaths in children are underreported in Bangladesh. We analyzed hospital-based surveillance data on severe acute respiratory infections (SARIs) in under-five children before (August 2009-February 2020) and during the COVID-19 pandemic (March 2020-March 2022). Using the World Health Organization definition, we identified SARI cases in 14 tertiary-level hospitals. Nasopharyngeal and oropharyngeal swabs were collected for real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) testing of six respiratory viruses, including RSV. SARI deaths during the pandemic (2.6%, 66) were higher than pre-pandemic (1.8%, 159; p < 0.001). Nearly half of pandemic deaths (47%) had underlying respiratory viruses, similar to the pre-pandemic rate (45%). RSV detection in deaths was consistent pre-pandemic (13%, 20/159) and during the pandemic (12%, 8/66). Children aged < 6 months constituted 57% (16) of RSV-related deaths. Evaluating interventions like maternal vaccination and infant monoclonal antibody prophylaxis is crucial to address RSV, a major contributor to under-five SARI deaths.
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Affiliation(s)
- Md Zakiul Hassan
- International Centre for Diarrhoeal Disease Bangladesh (icddr,b), Dhaka 1213, Bangladesh; (M.A.I.); (S.H.); (F.C.)
| | - Md. Ariful Islam
- International Centre for Diarrhoeal Disease Bangladesh (icddr,b), Dhaka 1213, Bangladesh; (M.A.I.); (S.H.); (F.C.)
| | - Saleh Haider
- International Centre for Diarrhoeal Disease Bangladesh (icddr,b), Dhaka 1213, Bangladesh; (M.A.I.); (S.H.); (F.C.)
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Fahmida Chowdhury
- International Centre for Diarrhoeal Disease Bangladesh (icddr,b), Dhaka 1213, Bangladesh; (M.A.I.); (S.H.); (F.C.)
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3
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Rao G, Capone D, Zhu K, Knoble A, Linden Y, Clark R, Lai A, Kim J, Huang CH, Bivins A, Brown J. Simultaneous detection and quantification of multiple pathogen targets in wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.23.23291792. [PMID: 37425908 PMCID: PMC10327253 DOI: 10.1101/2023.06.23.23291792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
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Affiliation(s)
- Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Kevin Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abigail Knoble
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ryan Clark
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ching-Hua Huang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Bastos-Moreira Y, Ouédraogo L, De Boevre M, Argaw A, de Kok B, Hanley-Cook GT, Deng L, Ouédraogo M, Compaoré A, Tesfamariam K, Ganaba R, Huybregts L, Toe LC, Lachat C, Kolsteren P, De Saeger S, Dailey-Chwalibóg T. A Multi-Omics and Human Biomonitoring Approach to Assessing the Effectiveness of Fortified Balanced Energy-Protein Supplementation on Maternal and Newborn Health in Burkina Faso: A Study Protocol. Nutrients 2023; 15:4056. [PMID: 37764838 PMCID: PMC10535470 DOI: 10.3390/nu15184056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Fortified balanced energy-protein (BEP) supplementation is a promising intervention for improving maternal health, birth outcomes and infant growth in low- and middle-income countries. This nested biospecimen sub-study aimed to evaluate the physiological effect of multi-micronutrient-fortified BEP supplementation on pregnant and lactating women and their infants. Pregnant women (15-40 years) received either fortified BEP and iron-folic acid (IFA) (intervention) or IFA only (control) throughout pregnancy. The same women were concurrently randomized to receive either a fortified BEP supplement during the first 6 months postpartum in combination with IFA for the first 6 weeks (i.e., intervention) or the postnatal standard of care, which comprised IFA alone for 6 weeks postpartum (i.e., control). Biological specimens were collected at different timepoints. Multi-omics profiles will be characterized to assess the mediating effect of BEP supplementation on the different trial arms and its effect on maternal health, as well as birth and infant growth outcomes. The mediating effect of the exposome in the relationship between BEP supplementation and maternal health, birth outcomes and infant growth were characterized via biomonitoring markers of air pollution, mycotoxins and environmental contaminants. The results will provide holistic insight into the granular physiological effects of prenatal and postnatal BEP supplementation.
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Affiliation(s)
- Yuri Bastos-Moreira
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lionel Ouédraogo
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Centre Muraz, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Marthe De Boevre
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
| | - Alemayehu Argaw
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Brenda de Kok
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Giles T. Hanley-Cook
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lishi Deng
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Moctar Ouédraogo
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Anderson Compaoré
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Kokeb Tesfamariam
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Rasmané Ganaba
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Lieven Huybregts
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Nutrition, Diets, and Health Unit, Department of Food and Nutrition Policy, International Food Policy Research Institute (IFPRI), Washington, DC 20005, USA
| | - Laeticia Celine Toe
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Unité Nutrition et Maladies Métaboliques, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Carl Lachat
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Patrick Kolsteren
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Sarah De Saeger
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng 2028, South Africa
| | - Trenton Dailey-Chwalibóg
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
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5
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Upadhyay P, Reddy J, Proctor T, Sorel O, Veereshlingam H, Gandhi M, Wang X, Singh V. Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness. Diagnostics (Basel) 2023; 13:2014. [PMID: 37370910 DOI: 10.3390/diagnostics13122014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship.
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Affiliation(s)
| | - Jairus Reddy
- HealthTrackRx R&D Division, Denton, TX 76207, USA
| | - Teddie Proctor
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Oceane Sorel
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Harita Veereshlingam
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Manoj Gandhi
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Xuemei Wang
- Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA 94080, USA
| | - Vijay Singh
- HealthTrackRx R&D Division, Denton, TX 76207, 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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7
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Clark JA, Conway Morris A, Curran MD, White D, Daubney E, Kean IRL, Navapurkar V, Bartholdson Scott J, Maes M, Bousfield R, Török ME, Inwald D, Zhang Z, Agrawal S, Kanaris C, Khokhar F, Gouliouris T, Baker S, Pathan N. The rapid detection of respiratory pathogens in critically ill children. Crit Care 2023; 27:11. [PMID: 36627688 PMCID: PMC9831374 DOI: 10.1186/s13054-023-04303-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Respiratory infections are the most common reason for admission to paediatric intensive care units (PICU). Most patients with lower respiratory tract infection (LRTI) receive broad-spectrum antimicrobials, despite low rates of bacterial culture confirmation. Here, we evaluated a molecular diagnostic test for LRTI to inform the better use of antimicrobials. METHODS The Rapid Assay for Sick Children with Acute Lung infection Study was a single-centre, prospective, observational cohort study of mechanically ventilated children (> 37/40 weeks corrected gestation to 18 years) with suspected community acquired or ventilator-associated LRTI. We evaluated the use of a 52-pathogen custom TaqMan Array Card (TAC) to identify pathogens in non-bronchoscopic bronchoalveolar lavage (mini-BAL) samples. TAC results were compared to routine microbiology testing. Primary study outcomes were sensitivity and specificity of TAC, and time to result. RESULTS We enrolled 100 patients, all of whom were tested with TAC and 91 of whom had matching culture samples. TAC had a sensitivity of 89.5% (95% confidence interval (CI95) 66.9-98.7) and specificity of 97.9% (CI95 97.2-98.5) compared to routine bacterial and fungal culture. TAC took a median 25.8 h (IQR 9.1-29.8 h) from sample collection to result. Culture was significantly slower: median 110.4 h (IQR 85.2-141.6 h) for a positive result and median 69.4 h (IQR 52.8-78.6) for a negative result. CONCLUSIONS TAC is a reliable and rapid adjunct diagnostic approach for LRTI in critically ill children, with the potential to aid early rationalisation of antimicrobial therapy.
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Affiliation(s)
- John A Clark
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. .,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, UK.,Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - Deborah White
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Esther Daubney
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Iain R L Kean
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - M Estée Török
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Inwald
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zhenguang Zhang
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Shruti Agrawal
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Constantinos Kanaris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Blizard Institute, Queen Mary University of London, London, UK
| | - Fahad Khokhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Nazima Pathan
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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8
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Banerjee D, Hassan F, Avadhanula V, Piedra PA, Boom J, Sahni LC, Weinberg GA, Lindstrom S, Rha B, Harrison CJ, Selvarangan R. Comparative analysis of three multiplex platforms for the detection of respiratory viral pathogens. J Clin Virol 2022; 156:105274. [PMID: 36099751 DOI: 10.1016/j.jcv.2022.105274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Acute viral respiratory infections are a major health burden in children worldwide. In recent years, rapid and sensitive multiplex nucleic acid amplification tests (NAATs) have replaced conventional methods for routine virus detection in the clinical laboratory. OBJECTIVE/STUDY DESIGN We compared BioFire® FilmArray® Respiratory Panel (FilmArray V1.7), Luminex NxTag® Respiratory Pathogen Panel (NxTag RPP) and Applied Biosystems TaqMan Array Card (TAC) for the detection of eight viruses in pediatric respiratory specimens. Results from the three platforms were analyzed with a single-plex real-time RT-PCR (rRT-PCR) assay for each virus. RESULTS Of the 170/210 single-plex virus-positive samples, FilmArray detected a virus in 166 (97.6%), TAC in 163 (95.8%) and NxTag RPP in 160 (94.1%) samples. The Positive Percent Agreement (PPA) of FilmArray, NxTag RPP and TAC was highest for influenza B (100%, 100% and 95.2% respectively) and lowest for seasonal coronaviruses on both FilmArray (90.2%) and NxTag RPP (81.8%), and for parainfluenza viruses 1- 4 on TAC (84%). The Negative Percent Agreement (NPA) was lowest for rhinovirus/enterovirus (92.9%, 96.7% and 97.3%) on FilmArray, NxTag RPP and TAC respectively. NPA for all three platforms was highest (100%) for both parainfluenza viruses 1- 4 and influenza A and B, and 100% for human metapneumovirus with TAC as well. CONCLUSION All three multiplex platforms displayed high overall agreement (>90%) and high NPA (>90%), while PPA was pathogen dependent and varied among platforms; high PPA (>90%) was observed for FilmArray for all eight viruses, TAC for six viruses and NxTag RPP for 4 viruses.
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Affiliation(s)
- Dithi Banerjee
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Ferdaus Hassan
- Children's Mercy Hospital, Kansas City, MO, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America; Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America
| | - Julie Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States of America; Texas Children's Hospital, Immunization Project, Baylor College of Medicine, Houston, TX, United States of America
| | - Geoffrey A Weinberg
- University of Rochester School of Medicine & Dentistry, Rochester, NY, United States of America
| | - Stephen Lindstrom
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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9
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Pre COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. Heliyon 2022; 8:e11043. [PMID: 36247113 PMCID: PMC9551109 DOI: 10.1016/j.heliyon.2022.e11043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/24/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Epidemiological data of specific respiratory pathogens from the pre-COVID-19 period are essential to determine the effects of the COVID-19 pandemic on other respiratory infections. In this study, we revealed the pre-COVID-19 molecular epidemiology of respiratory syncytial virus (RSV) among children in Bangladesh. We tested 3170 samples collected from 2008 to 2012 for a panel of respiratory viruses; RSV, human metapneumovirus (hMPV), human parainfluenza viruses (hPIV) 1, 2, 3, and adenovirus. Five hundred fifty-five samples (17.5 %) were positive for RSV, including 2.5% having co-infections with other viruses. Genotypic characterization of RSV showed that RSV-A (82%) contributed more acute respiratory infections than RSV-B (18%). Clinical features were similar with RSV-A and RSV-B infections. However, children with RSV-B were more likely to have upper respiratory infections (URI) (10% vs. 29%, p = 0.03). Among RSV-A cases, hospitalization was higher for ON1 cases (25%, ON1 vs. 8%, NA1, p = 0.04), whereas the recovery without a disability was higher among the NA1 cases (56%, ON1 vs. 88%, NA1, p = 0.02). The time to the most recent common ancestor (TMRCA) for RSV in Bangladesh was 1949 for RSV-A and 1944 for RSV-B. This study revealed the genotypic diversity and evolutionary relatedness of RSV strains in Bangladesh and provided pre-COVID molecular epidemiology data to understand better the COVID-19 impact on upcoming RSV epidemiology in Bangladesh.
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10
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Gill CJ, Mwananyanda L, MacLeod WB, Kwenda G, Pieciak R, Mupila Z, Murphy C, Chikoti C, Forman L, Berklein F, Lapidot R, Chimoga C, Ngoma B, Larson A, Lungu J, Nakazwe R, Nzara D, Pemba L, Yankonde B, Chirwa A, Mwale M, Thea DM. Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project. Lancet Glob Health 2022; 10:e269-e277. [PMID: 35063114 PMCID: PMC8789563 DOI: 10.1016/s2214-109x(21)00518-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022]
Abstract
Background Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and a key driver of childhood mortality. Previous RSV burden of disease estimates used hospital-based surveillance data and modelled, rather than directly measured, community deaths. Given this uncertainty, we conducted a 3-year post-mortem prevalence study among young infants at a busy morgue in Lusaka, Zambia—the Zambia Pertussis RSV Infant Mortality Estimation (ZPRIME) study. Methods Infants were eligible for inclusion if they were aged between 4 days and less than 6 months and were enrolled within 48 h of death. Enrolment occurred mainly at the University Teaching Hospital of the University of Zambia Medical School (Lusaka, Zambia), the largest teaching hospital in Zambia. We extracted demographic and clinical data from medical charts and official death certificates, and we conducted verbal autopsies with the guardian or next of kin. RSV was identified using reverse transcriptase quantitative PCR and stratified by age, time of year, and setting (community vs facility deaths). By combining the PCR prevalence data with syndromic presentation, we estimated the proportion of all infant deaths that were due to RSV. Findings The ZPRIME study ran from Aug 31, 2017, to Aug 31, 2020, except for from April 1 to May 6, 2020, during which data were not collected due to restrictions on human research at this time (linked to COVID-19). We enrolled 2286 deceased infants, representing 79% of total infant deaths in Lusaka. RSV was detected in 162 (7%) of 2286 deceased infants. RSV was detected in 102 (9%) of 1176 community deaths, compared with 10 (4%) of 236 early facility deaths (<48 h from admission) and 36 (5%) of 737 late facility deaths (≥48 h from admission). RSV deaths were concentrated in infants younger than 3 months (116 [72%] of 162 infants), and were clustered in the first half of each year and in the poorest and most densely populated Lusaka townships. RSV caused at least 2·8% (95% CI 1·0–4·6) of all infant deaths and 4·7% (1·3–8·1) of community deaths. Interpretation RSV was a major seasonal cause of overall infant mortality, particularly among infants younger than 3 months of age. Because most RSV deaths occurred in the community and would have been missed through hospital-based surveillance, the global burden of fatal RSV has probably been underestimated. Funding Bill & Melinda Gates Foundation.
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Affiliation(s)
- Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA.
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA; Right to Care Zambia, Lusaka, Zambia
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Rachel Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | | | | | | | - Leah Forman
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Flora Berklein
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Rotem Lapidot
- Department of Pediatrics, Boston University School of Medicine, Boston, MA, USA
| | | | | | - Anna Larson
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | | | | | | | | | | | - Angel Chirwa
- Department of Psychiatry, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | | | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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11
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Chaves SS, Park JH, Prill MM, Whitaker B, Park R, Chew GL. Side-by-side comparison of parent vs. technician-collected respiratory swabs in low-income, multilingual, urban communities in the United States. BMC Public Health 2022; 22:103. [PMID: 35031041 PMCID: PMC8760092 DOI: 10.1186/s12889-022-12523-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Home-based swabbing has not been widely used. The objective of this analysis was to compare respiratory swabs collected by mothers of 7–12-year-olds living in low-income, multilingual communities in the United States with technician collected swabs. Methods Retrospective data analysis of respiratory samples collected at home by mothers compared to technicians. Anterior nasal and throat specimens collected using flocked swabs were combined in dry tubes. Test was done using TaqMan array cards for viral and bacterial pathogens. Cycle threshold (Ct) values of ribonuclease P (RNP) gene were used to assess specimen quality. Ct < 40 was interpreted as a positive result. Concordance of pathogen yield from mother versus technician collected swabs were analyzed using Cohen’s Kappa coefficients. Correlation analysis, paired t-test, and Wilcoxon signed-rank test for paired samples were used for RNP Ct values. Results We enrolled 36 households in Cincinnati (African American) and 44 (predominately Chinese or Latino) in Boston. In Cincinnati, eight of 32 (25%) mothers did not finish high school, and 11 (34%) had finished high school only. In Boston, 13 of 44 (30%) mothers had less than a high school diploma, 23 (52%) had finished high school only. Mother versus technician paired swabs (n = 62) had similar pathogen yield (paired t-test and Wilcoxon signed rank test p-values = 0.62 and 0.63, respectively; 95% confidence interval of the difference between the two measurements = − 0.45–0.75). Median Ct value for RNP was 22.6 (interquartile range, IQR = 2.04) for mother-collected and 22.4 (IQR = 2.39) for technician-collected swabs (p = 0.62). Agreement on pathogen yield between samples collected by mothers vs. technicians was higher for viruses than for bacterial pathogens, with high concordance for rhinovirus/enterovirus, human metapneumovirus, and adenovirus (Cohen’s kappa coefficients ≥80%, p < 0.0001). For bacterial pathogens, concordance was lower to moderate, except for Chlamydia pneumoniae, for which kappa coefficient indicated perfect agreement. Conclusion Mothers with a range of education levels from low-income communities were able to swab their children equally well as technicians. Home-swabbing using dry tubes, and less invasive collection procedures, could enhance respiratory disease surveillance. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-12523-3.
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Affiliation(s)
- Sandra S Chaves
- CDC, National Center for Immunization and Respiratory Diseases, Influenza Division, Atlanta, USA.
| | - Ju-Hyeong Park
- CDC, National Institute for Occupational Safety and Health, Respiratory Health Division, Morgantown, USA
| | - Mila M Prill
- CDC, National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Atlanta, USA
| | - Brett Whitaker
- CDC, National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Atlanta, USA
| | - Reena Park
- Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Ginger L Chew
- CDC, National Center for Environmental Health, Division of Environmental Health Science and Practice, Atlanta, USA
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12
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Cooksey GLS, Morales C, Linde L, Schildhauer S, Guevara H, Chan E, Gibb K, Wong J, Lin W, Bonin BJ, Arizmendi O, Lam-Hine T, Tzvieli O, McDowell A, Kampen KM, Lopez DL, Ennis J, Lewis LS, Oren E, Hatada A, Molinar B, Frederick M, Han GS, Sanchez M, Garcia MA, McGrath A, Le NQ, Boyd E, Bertolucci RM, Corrigan J, Brodine S, Austin M, Roach WRK, Levin RM, Tyson BM, Pry JM, Cummings KJ, Wadford DA, Jain S. Severe Acute Respiratory Syndrome Coronavirus 2 and Respiratory Virus Sentinel Surveillance, California, USA, May 10, 2020-June 12, 2021. Emerg Infect Dis 2022; 28:9-19. [PMID: 34932449 PMCID: PMC8714231 DOI: 10.3201/eid2801.211682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
State and local health departments established the California Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Respiratory Virus Sentinel Surveillance System to conduct enhanced surveillance for SARS-CoV-2 and other respiratory pathogens at sentinel outpatient testing sites in 10 counties throughout California, USA. We describe results obtained during May 10, 2020‒June 12, 2021, and compare persons with positive and negative SARS-CoV-2 PCR results by using Poisson regression. We detected SARS-CoV-2 in 1,696 (19.6%) of 8,662 specimens. Among 7,851 specimens tested by respiratory panel, rhinovirus/enterovirus was detected in 906 (11.5%) specimens and other respiratory pathogens in 136 (1.7%) specimens. We also detected 23 co-infections with SARS-CoV-2 and another pathogen. SARS-CoV-2 positivity was associated with male participants, an age of 35-49 years, Latino race/ethnicity, obesity, and work in transportation occupations. Sentinel surveillance can provide useful virologic and epidemiologic data to supplement other disease monitoring activities and might become increasingly useful as routine testing decreases.
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13
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Howard LM, Edwards KM, Zhu Y, Williams DJ, Self WH, Jain S, Ampofo K, Pavia AT, Arnold SR, McCullers JA, Anderson EJ, Wunderink RG, Grijalva CG. Parainfluenza Virus Types 1-3 Infections Among Children and Adults Hospitalized With Community-acquired Pneumonia. Clin Infect Dis 2021; 73:e4433-e4443. [PMID: 32681645 PMCID: PMC8662767 DOI: 10.1093/cid/ciaa973] [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: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Parainfluenza virus (PIV) is a leading cause of lower respiratory tract infections. Although there are several distinct PIV serotypes, few studies have compared the clinical characteristics and severity of infection among the individual PIV serotypes and between PIV and other pathogens in patients with community-acquired pneumonia. METHODS We conducted active population-based surveillance for radiographically confirmed community-acquired pneumonia hospitalizations among children and adults in 8 US hospitals with systematic collection of clinical data and respiratory, blood, and serological specimens for pathogen detection. We compared clinical features of PIV-associated pneumonia among individual serotypes 1, 2, and 3 and among all PIV infections with other viral, atypical, and bacterial pneumonias. We also compared in-hospital disease severity among groups employing an ordinal scale (mild, moderate, severe) using multivariable proportional odds regression. RESULTS PIV was more commonly detected in children (155/2354; 6.6%) than in adults (66/2297; 2.9%) (P < .001). Other pathogens were commonly co-detected among PIV cases (110/221; 50%). Clinical features of PIV-1, PIV-2, and PIV-3 infections were similar to one another in both children and adults with pneumonia. In multivariable analysis, children with PIV-associated pneumonia exhibited similar severity to children with other nonbacterial pneumonia, whereas children with bacterial pneumonia exhibited increased severity (odds ratio, 8.42; 95% confidence interval, 1.88-37.80). In adults, PIV-associated pneumonia exhibited similar severity to other pneumonia pathogens. CONCLUSIONS Clinical features did not distinguish among infection with individual PIV serotypes in patients hospitalized with community-acquired pneumonia. However, in children, PIV pneumonia was less severe than bacterial pneumonia.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Derek J Williams
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Sandra R Arnold
- University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Jonathan A McCullers
- University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Evan J Anderson
- Departments of Pediatrics and Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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14
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Huang Y, Wang C, Ma F, Guo Q, Yao L, Chen A, Luo X, Zheng L. Human adenoviruses in paediatric patients with respiratory tract infections in Beijing, China. Virol J 2021; 18:191. [PMID: 34556127 PMCID: PMC8460180 DOI: 10.1186/s12985-021-01661-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023] Open
Abstract
Background Human adenoviruse (HAdV) is a major pathogen of paediatric respiratory tract infections (RTIs). Mutation or recombination of HAdV genes may cause changes in its pathogenicity and transmission. We described the epidemiology and genotypic diversity of HAdV in hospitalized children with RTIs in Beijing, China. Methods Nasopharyngeal aspirates were collected from hospitalized children with RTIs from April 2018 to March 2019. HAdVs were detected by a quantitative real-time PCR, and the hexon gene was used for phylogenetic analysis. Results Among 1572 samples, 90 (5.72%) were HAdV-positive. The HAdV detection rate was highest in November and July. Among HAdV-positive children, 61.11% (55/90) were co-infected with other respiratory viruses, the most common of which were human respiratory syncytial virus and human rhinovirus. The main diagnosis was bronchopneumonia, most patient have cough and fever. Children with a high viral load were more likely to have a high fever (P = 0.041) and elevated WBC count (P = 0.000). Of 55 HAdV-positive specimens, HAdV-B (63.64%), HAdV-C (27.27%), and HAdV-E (9.09%) were main epidemic species. Phylogenetic analysis indicated that hexon sequences of three samples were on the same branch with the recombinant HAdV strain (CBJ113), which was circulating in Beijing since 2016. Conclusion The HAdV-B3 and HAdV-B7 are the main epidemic strains in Beijing, and the recombinant HAdV-C strain CBJ113 has formed an epidemic trend. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01661-6.
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Affiliation(s)
- Yiman Huang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Fenlian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Qiong Guo
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lihong Yao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Aijun Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Xiaoyi Luo
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lishu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
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15
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Suntarattiwong P, Mott JA, Mohanty S, Sinthuwattanawibool C, Srisantiroj N, Patamasingh Na Ayudhaya O, Klungthong C, Fernandez S, Kim L, Hunt D, Hombroek D, Brummer T, Chotpitayasunondh T, Dawood FS, Kittikraisak W. Feasibility and Performance of Self-Collected Nasal Swabs for Detection of Influenza Virus, Respiratory Syncytial Virus, and Human Metapneumovirus. J Infect Dis 2021; 224:831-838. [PMID: 34467984 DOI: 10.1093/infdis/jiab023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We assessed performance of participant-collected midturbinate nasal swabs compared to study staff-collected midturbinate nasal swabs for the detection of respiratory viruses among pregnant women in Bangkok, Thailand. METHODS We enrolled pregnant women aged ≥18 years and followed them throughout the 2018 influenza season. Women with acute respiratory illness self-collected midturbinate nasal swabs at home for influenza viruses, respiratory syncytial viruses (RSV), and human metapneumoviruses (hMPV) real-time RT-PCR testing and the study nurse collected a second midturbinate nasal swab during home visits. Paired specimens were processed and tested on the same day. RESULTS The majority (109, 60%) of 182 participants were 20-30 years old. All 200 paired swabs had optimal specimen quality. The median time from symptom onsets to participant-collected swabs was 2 days and to staff-collected swabs was also 2 days. The median time interval between the 2 swabs was 2 hours. Compared to staff-collected swabs, the participant-collected swabs were 93% sensitive and 99% specific for influenza virus detection, 94% sensitive and 99% specific for RSV detection, and 100% sensitive and 100% specific for hMPV detection. CONCLUSIONS Participant-collected midturbinate nasal swabs were a valid alternative approach for laboratory confirmation of influenza-, RSV-, and hMPV-associated illnesses among pregnant women in a community setting.
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Affiliation(s)
| | - Joshua A Mott
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarita Mohanty
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chalinthorn Sinthuwattanawibool
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | | | | | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Lindsay Kim
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | - Fatimah S Dawood
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wanitchaya Kittikraisak
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
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16
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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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17
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Chu VT, Simon E, Lu X, Rockwell P, Abedi GR, Gardner C, Kujawski SA, Schneider E, Gentile M, Ramsey LA, Liu R, Jones S, Janik C, Siniscalchi A, Landry ML, Christopher J, Lindstrom S, Steiner S, Thomas D, Gerber SI, Biggs HM. Outbreak of Acute Respiratory Illness Associated with Human Adenovirus Type 4 at the U.S. Coast Guard Academy, 2019. J Infect Dis 2021; 225:55-64. [PMID: 34139752 DOI: 10.1093/infdis/jiab322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Although a human adenovirus (HAdV) vaccine is available for military use, officers-in-training are not routinely vaccinated. We describe an HAdV-associated respiratory outbreak among unvaccinated cadets at the U.S. Coast Guard Academy and its impact on cadet training. METHODS We defined a case as a cadet with new onset cough or sore throat during August 1-October 4, 2019. We reviewed medical records and distributed a questionnaire to identify cases and to estimate impact on cadet training. We performed real-time PCR testing on patient and environmental samples and whole genome sequencing on a subset of positive patient samples. RESULTS Among the 1,072 cadets, 378 (35%) cases were identified by medical records (n=230) or additionally by the questionnaire (n=148). Of the 230 cases identified from medical records, 138 (60%) were male and 226 (98%) had no underlying conditions. From questionnaire responses, 113/228 (50%) cases reported duty restrictions. Of cases with respiratory specimens, 36/50 (72%) were HAdV positive; all 14 sequenced specimens were HAdV-4a1. Sixteen (89%) of 18 environmental specimens from the cadet dormitory were HAdV-positive. CONCLUSIONS The HAdV-4-associated outbreak infected a substantial number of cadets and significantly impacted cadet training. Routine vaccination could prevent HAdV respiratory outbreaks in this population.
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Affiliation(s)
- Victoria T Chu
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Esan Simon
- United States Coast Guard Academy, New London, Connecticut, USA.,United States Public Health Service, Rockville, Maryland, USA
| | - Xiaoyan Lu
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Glen R Abedi
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher Gardner
- United States Coast Guard Academy, New London, Connecticut, USA.,Yale-New Haven Hospital and Yale University, New Haven, Connecticut, USA
| | - Stephanie A Kujawski
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eileen Schneider
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Micah Gentile
- United States Coast Guard Academy, New London, Connecticut, USA
| | - Lee Ann Ramsey
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert Liu
- United States Coast Guard Academy, New London, Connecticut, USA
| | - Sydney Jones
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Christopher Janik
- United States Coast Guard Academy, New London, Connecticut, USA.,United States Public Health Service, Rockville, Maryland, USA
| | - Alan Siniscalchi
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Marie L Landry
- Yale-New Haven Hospital and Yale University, New Haven, Connecticut, USA
| | | | - Stephen Lindstrom
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Shane Steiner
- United States Public Health Service, Rockville, Maryland, USA.,United States Coast Guard, Washington, D.C., USA
| | - Dana Thomas
- United States Public Health Service, Rockville, Maryland, USA.,United States Coast Guard, Washington, D.C., USA
| | - Susan I Gerber
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Holly M Biggs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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18
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Lappan R, Henry R, Chown SL, Luby SP, Higginson EE, Bata L, Jirapanjawat T, Schang C, Openshaw JJ, O'Toole J, Lin A, Tela A, Turagabeci A, Wong THF, French MA, Brown RR, Leder K, Greening C, McCarthy D. Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study. Lancet Planet Health 2021; 5:e297-e308. [PMID: 33964239 PMCID: PMC8116308 DOI: 10.1016/s2542-5196(21)00051-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples. METHODS In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR. FINDINGS Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R2 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR. INTERPRETATION The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load. FUNDING Wellcome Trust Our Planet, Our Health programme.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Rebekah Henry
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Ellen E Higginson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Lamiya Bata
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Christelle Schang
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - John J Openshaw
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Joanne O'Toole
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Audrie Lin
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, CA, USA
| | - Autiko Tela
- School of Public Health, Fiji National University, Suva, Fiji
| | | | - Tony H F Wong
- Water Sensitive Cities Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A French
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Rebekah R Brown
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Karin Leder
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David McCarthy
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
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19
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Howard LM, Edwards KM, Zhu Y, Grijalva CG, Self WH, Jain S, Ampofo K, Pavia AT, Arnold SR, McCullers JA, Anderson EJ, Wunderink RG, Williams DJ. Clinical Features of Human Metapneumovirus-Associated Community-acquired Pneumonia Hospitalizations. Clin Infect Dis 2021; 72:108-117. [PMID: 32010955 DOI: 10.1093/cid/ciaa088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/28/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is a leading cause of respiratory tract infections. Few studies have compared the clinical characteristics and severity of HMPV-associated pneumonia with other pathogens. METHODS Active, population-based surveillance was previously conducted for radiographically confirmed, community-acquired pneumonia hospitalizations among children and adults in 8 United States hospitals. Clinical data and specimens for pathogen detection were systematically collected. We described clinical features of all HMPV-associated pneumonia and, after excluding codetections with other pathogen types, we compared features of HMPV-associated pneumonia with other viral, atypical, and bacterial pneumonia and modeled the severity (mild, moderate, and severe) and length of stay using multivariable proportional odds regression. RESULTS HMPV was detected in 298/2358 (12.6%) children and 88/2320 (3.8%) adults hospitalized with pneumonia and was commonly codetected with other pathogens (125/298 [42%] children and 21/88 [24%] adults). Fever and cough were the most common presenting symptoms of HMPV-associated pneumonia and were also common symptoms of other pathogens. After excluding codetections in children (n = 1778), compared to HMPV (reference), bacterial pneumonia exhibited increased severity (odds ratio [OR], 3.66; 95% confidence interval [CI], 1.43-9.40), respiratory syncytial virus (RSV; OR, 0.76; 95% CI, .59-.99) and atypical (OR, 0.39; 95% CI, .19-.81) infections exhibited decreased severity, and other viral pneumonia exhibited similar severity (OR, 0.88; 95% CI, .55-1.39). In adults (n = 2145), bacterial (OR, 3.74; 95% CI, 1.87-7.47) and RSV pneumonia (OR, 1.82; 95% CI, 1.32-2.50) were more severe than HMPV (reference), but all other pathogens had similar severity. CONCLUSIONS Clinical features did not reliably distinguish HMPV-associated pneumonia from other pathogens. HMPV-associated pneumonia was less severe than bacterial and adult RSV pneumonia, but was otherwise as or more severe than other common pathogens.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Sandra R Arnold
- University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Jonathan A McCullers
- University of Tennessee Health Sciences Center, Memphis, Tennessee, USA.,St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Evan J Anderson
- Departments of Pediatrics and Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Derek J Williams
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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20
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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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21
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Bhatnagar J, Gary J, Reagan-Steiner S, Estetter LB, Tong S, Tao Y, Denison AM, Lee E, DeLeon-Carnes M, Li Y, Uehara A, Paden CR, Leitgeb B, Uyeki TM, Martines RB, Ritter JM, Paddock CD, Shieh WJ, Zaki SR. Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. J Infect Dis 2021; 223:752-764. [PMID: 33502471 PMCID: PMC7928839 DOI: 10.1093/infdis/jiab039] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic continues to produce substantial morbidity and mortality. To understand the reasons for the wide-spectrum complications and severe outcomes of COVID-19, we aimed to identify cellular targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and replication in various tissues. Methods We evaluated RNA extracted from formalin-fixed, paraffin-embedded autopsy tissues from 64 case patients (age range, 1 month to 84 years; 21 COVID-19 confirmed, 43 suspected COVID-19) by SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR). For cellular localization of SARS-CoV-2 RNA and viral characterization, we performed in situ hybridization (ISH), subgenomic RNA RT-PCR, and whole-genome sequencing. Results SARS-CoV-2 was identified by RT-PCR in 32 case patients (21 COVID-19 confirmed, 11 suspected). ISH was positive in 20 and subgenomic RNA RT-PCR was positive in 17 of 32 RT-PCR–positive case patients. SARS-CoV-2 RNA was localized by ISH in hyaline membranes, pneumocytes, and macrophages of lungs; epithelial cells of airways; and endothelial cells and vessel walls of brain stem, leptomeninges, lung, heart, liver, kidney, and pancreas. The D614G variant was detected in 9 RT-PCR–positive case patients. Conclusions We identified cellular targets of SARS-CoV-2 tropism and replication in the lungs and airways and demonstrated its direct infection in vascular endothelium. This work provides important insights into COVID-19 pathogenesis and mechanisms of severe outcomes.
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Affiliation(s)
- Julu Bhatnagar
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Correspondence: Julu Bhatnagar, PhD, Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H18-SB, Atlanta, GA 30329-4027 ()
| | - Joy Gary
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah Reagan-Steiner
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lindsey B Estetter
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Suxiang Tong
- Respiratory Viruses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ying Tao
- Respiratory Viruses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy M Denison
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elizabeth Lee
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marlene DeLeon-Carnes
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yan Li
- Respiratory Viruses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anna Uehara
- Respiratory Viruses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Clinton R Paden
- Respiratory Viruses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brooke Leitgeb
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Roosecelis B Martines
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jana M Ritter
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher D Paddock
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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22
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Liu K, Jing H, Chen Y, Zheng X, Jiang H, Kong D, Zheng Y, Chen S, Liu P, Jiang Y. Evaluation of TaqMan Array card (TAC) for the detection of 28 respiratory pathogens. BMC Infect Dis 2020; 20:820. [PMID: 33172401 PMCID: PMC7653217 DOI: 10.1186/s12879-020-05562-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Respiratory infections are a serious threat to human health. So, rapid detection of all respiratory pathogens can facilitate prompt treatment and prevent the deterioration of respiratory disease. Previously published primers and probes of the TaqMan array card (TAC) for respiratory pathogens are not sensitive to Chinese clinical specimens. This study aimed to develop and improve the TAC assay to detect 28 respiratory viral and bacterial pathogens in a Chinese population. Methods To improve the sensitivity, we redesigned the primers and probes, and labeled the probes with minor groove binders. The amplification efficiency, sensitivity, and specificity of the primers and probes were determined using target-gene containing standard plasmids. The detection performance of the TAC was evaluated on 754 clinical specimens and the results were compared with those from conventional methods. Results The performance of the TAC assay was evaluated using 754 clinical throat swab samples and the results were compared with those from gold-standard methods. The sensitivity and specificity were 95.4 and 96.6%, respectively. The lowest detection limit of the TAC was 10 to 100 copies/μL. Conclusions TAC is an efficient, accurate, and high-throughput approach to detecting multiple respiratory pathogens simultaneously and is a promising tool for the identification of pathogen outbreaks.
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Affiliation(s)
- Keke Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Shandong Academy of Clinical Medicine, Shandong Provincial Hospital, Jinan, 250021, China
| | - Hongbo Jing
- Department of Laboratory Medicine, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Chen
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Xin Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yvling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shuiping Chen
- Department of Laboratory Medicine, the Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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23
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Milucky J, Pondo T, Gregory CJ, Iuliano D, Chaves SS, McCracken J, Mansour A, Zhang Y, Aleem MA, Wolff B, Whitaker B, Whistler T, Onyango C, Lopez MR, Liu N, Rahman MZ, Shang N, Winchell J, Chittaganpitch M, Fields B, Maldonado H, Xie Z, Lindstrom S, Sturm-Ramirez K, Montgomery J, Wu KH, Van Beneden CA. The epidemiology and estimated etiology of pathogens detected from the upper respiratory tract of adults with severe acute respiratory infections in multiple countries, 2014-2015. PLoS One 2020; 15:e0240309. [PMID: 33075098 PMCID: PMC7571682 DOI: 10.1371/journal.pone.0240309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction Etiology studies of severe acute respiratory infections (SARI) in adults are limited. We studied potential etiologies of SARI among adults in six countries using multi-pathogen diagnostics. Methods We enrolled both adults with SARI (acute respiratory illness onset with fever and cough requiring hospitalization) and asymptomatic adults (adults hospitalized with non-infectious illnesses, non-household members accompanying SARI patients, adults enrolled from outpatient departments, and community members) in each country. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from both SARI patients and asymptomatic adults. Specimens were tested for presence of 29 pathogens utilizing the Taqman® Array Card platform. We applied a non-parametric Bayesian regression extension of a partially latent class model approach to estimate proportions of SARI caused by specific pathogens. Results We enrolled 2,388 SARI patients and 1,135 asymptomatic adults from October 2013 through October 2015. We detected ≥1 pathogen in 76% of SARI patients and 67% of asymptomatic adults. Haemophilus influenzae and Streptococcus pneumoniae were most commonly detected (≥23% of SARI patients and asymptomatic adults). Through modeling, etiology was attributed to a pathogen in most SARI patients (range among countries: 57.3–93.2%); pathogens commonly attributed to SARI etiology included influenza A (14.4–54.4%), influenza B (1.9–19.1%), rhino/enterovirus (1.8–42.6%), and RSV (3.6–14.6%). Conclusions Use of multi-pathogen diagnostics and modeling enabled attribution of etiology in most adult SARI patients, despite frequent detection of multiple pathogens in the upper respiratory tract. Seasonal flu vaccination and development of RSV vaccine would likely reduce the burden of SARI in these populations.
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Affiliation(s)
- Jennifer Milucky
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
- * E-mail:
| | - Tracy Pondo
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Christopher J. Gregory
- Division of Global Health Protection, Centers for Disease Control and Prevention, Thailand Ministry of Public Health, Thailand
| | - Danielle Iuliano
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Sandra S. Chaves
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Kenya Office, Kenya
| | - John McCracken
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Adel Mansour
- Division of Global Health Protection, Centers for Disease Control and Prevention, Egypt
| | - Yuzhi Zhang
- Division of Global Health Protection, Centers for Disease Control and Prevention, China
| | | | - Bernard Wolff
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Brett Whitaker
- Division of Viral Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Toni Whistler
- Division of Global Health Protection, Centers for Disease Control and Prevention, Thailand Ministry of Public Health, Thailand
| | - Clayton Onyango
- Kenya Medical Research Institute/Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - Maria Renee Lopez
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Na Liu
- China Centers for Disease Control and Prevention, National Institute for Viral Disease, Beijing, China
| | | | - Nong Shang
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Jonas Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | | | - Barry Fields
- Division of Global Health Protection, Centers for Disease Control and Prevention, Kenya
| | - Herberth Maldonado
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Zhiping Xie
- China Centers for Disease Control and Prevention, National Institute for Viral Disease, Beijing, China
| | - Stephen Lindstrom
- Division of Viral Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Katherine Sturm-Ramirez
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Bangladesh Office, Bangladesh
| | - Joel Montgomery
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kai-Hui Wu
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Bangladesh Office, Bangladesh
| | - Chris A. Van Beneden
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
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24
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Jones NK, Conway Morris A, Curran MD, Parmar S, Sule O, Enoch DA, Aliyu SH, Zhang H, Jalal H, Navapurkar V, Murphy ME. Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care. J Med Microbiol 2020; 69:971-978. [PMID: 32552987 DOI: 10.1099/jmm.0.001218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis.Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs.Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge's Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records.Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation.Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.
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Affiliation(s)
- Nick K Jones
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Conway Morris
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Olajumoke Sule
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sani H Aliyu
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hongyi Zhang
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hamid Jalal
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Vilas Navapurkar
- The John Farman Intensive Care Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Michael E Murphy
- NHS GGC, Glasgow Royal Infirmary, Department of Clinical Microbiology, New Lister Building, Alexandra Parade, Glasgow, UK.,Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
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25
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Ordóñez-Mena JM, Fanshawe TR, Butler CC, Mant D, Longhurst D, Muir P, Vipond B, Little P, Moore M, Stuart B, Hay AD, Thornton HV, Thompson MJ, Smith S, Van den Bruel A, Hardy V, Cheah L, Crook D, Knox K. Relationship between microbiology of throat swab and clinical course among primary care patients with acute cough: a prospective cohort study. Fam Pract 2020; 37:332-339. [PMID: 31844897 PMCID: PMC7108489 DOI: 10.1093/fampra/cmz093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Acute lower respiratory tract infections (ALRTIs) account for most antibiotics prescribed in primary care despite lack of efficacy, partly due to clinician uncertainty about aetiology and patient concerns about illness course. Nucleic acid amplification tests could assist antibiotic targeting. METHODS In this prospective cohort study, 645 patients presenting to primary care with acute cough and suspected ALRTI, provided throat swabs at baseline. These were tested for respiratory pathogens by real-time polymerase chain reaction and classified as having a respiratory virus, bacteria, both or neither. Three hundred fifty-four participants scored the symptoms severity daily for 1 week in a diary (0 = absent to 4 = severe problem). RESULTS Organisms were identified in 346/645 (53.6%) participants. There were differences in the prevalence of seven symptoms between the organism groups at baseline. Those with a virus alone, and those with both virus and bacteria, had higher average severity scores of all symptoms combined during the week of follow-up than those in whom no organisms were detected [adjusted mean differences 0.204 (95% confidence interval 0.010 to 0.398) and 0.348 (0.098 to 0.598), respectively]. There were no differences in the duration of symptoms rated as moderate or severe between organism groups. CONCLUSIONS Differences in presenting symptoms and symptoms severity can be identified between patients with viruses and bacteria identified on throat swabs. The magnitude of these differences is unlikely to influence management. Most patients had mild symptoms at 7 days regardless of aetiology, which could inform patients about likely symptom duration.
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Affiliation(s)
- José M Ordóñez-Mena
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Thomas R Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Chris C Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - David Mant
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Denise Longhurst
- South West Regional Laboratory, National Infection Service, Public Health England, Bristol, UK
| | - Peter Muir
- South West Regional Laboratory, National Infection Service, Public Health England, Bristol, UK
| | - Barry Vipond
- South West Regional Laboratory, National Infection Service, Public Health England, Bristol, UK
| | - Paul Little
- University of Southampton, Primary Care and Population Sciences, Aldermoor Health Centre, Southampton, UK
| | - Michael Moore
- University of Southampton, Primary Care and Population Sciences, Aldermoor Health Centre, Southampton, UK
| | - Beth Stuart
- University of Southampton, Primary Care and Population Sciences, Aldermoor Health Centre, Southampton, UK
| | - Alastair D Hay
- Centre for Academic Primary Care, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hannah V Thornton
- Centre for Academic Primary Care, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew J Thompson
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | - Sue Smith
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Victoria Hardy
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Laikin Cheah
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
| | - Kyle Knox
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
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26
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Evaluations of the serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak. Eur J Clin Microbiol Infect Dis 2020; 39:2271-2277. [PMID: 32681308 PMCID: PMC7367508 DOI: 10.1007/s10096-020-03978-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
We developed a chemiluminescence immunoassay method based on the recombinant nucleocapsid antigen and assessed its performance for the clinical diagnosis of severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infections by detecting SARS-CoV-2–specific IgM and IgG antibodies in patients. Full-length recombinant nucleocapsid antigen and tosyl magnetic beads were used to develop the chemiluminescence immunoassay approach. Plasmas from 29 healthy cohorts, 51 tuberculosis patients, and 79 confirmed SARS-CoV-2 patients were employed to evaluate the chemiluminescence immunoassay method performance for the clinical diagnosis of SARS-CoV-2 infections. A commercial ELISA kit (Darui Biotech, China) using the same nucleocapsid antigen was used for the in-parallel comparison with our chemiluminescence immunoassay method. The IgM and IgG manner of testing in the chemiluminescence immunoassay method showed a sensitivity and specificity of 60.76% (95% CI 49.1 to 71.6) and 92.25% (95% CI 83.4 to 97.2) and 82.28% (95% CI 72.1 to 90.0) and 97.5% (95% CI 91.3 to 99.7), respectively. Higher sensitivity and specificity were observed in the chemiluminescence immunoassay method compared with the Darui Biotech ELISA kit. The developed high sensitivity and specificity chemiluminescence immunoassay IgG testing method combined with the RT-PCR approach can improve the clinical diagnosis for SARS-CoV-2 infections and thus contribute to the control of COVID-19 expansion.
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27
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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: 121] [Impact Index Per Article: 30.3] [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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28
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Caserta MT, Yang H, Bandyopadhyay S, Qiu X, Gill SR, Java J, McDavid A, Falsey AR, Topham DJ, Holden-Wiltse J, Scheible K, Pryhuber G. Measuring the Severity of Respiratory Illness in the First 2 Years of Life in Preterm and Term Infants. J Pediatr 2019; 214:12-19.e3. [PMID: 31377041 PMCID: PMC6815715 DOI: 10.1016/j.jpeds.2019.06.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/10/2019] [Accepted: 06/25/2019] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To develop a valid research tool to measure infant respiratory illness severity using parent-reported symptoms. STUDY DESIGN Nose and throat swabs were collected monthly for 1 year and during respiratory illnesses for 2 years in a prospective study of term and preterm infants in the Prematurity, Respiratory Outcomes, Immune System and Microbiome study. Viral pathogens were detected using Taqman Array Cards. Parents recorded symptoms during respiratory illnesses using a Childhood Origins of Asthma (COAST) scorecard. The COAST score was validated using linear mixed effects regression modeling to evaluate associations with hospitalization and specific infections. A data-driven method was also used to compute symptom weights and derive a new score, the Infant Research Respiratory Infection Severity Score (IRRISS). Linear mixed effects regression modeling was repeated with the IRRISS illness data. RESULTS From April 2013 to April 2017, 50 term, 40 late preterm, and 28 extremely low gestational age (<29 weeks of gestation) infants had 303 respiratory illness visits with viral testing and parent-reported symptoms. A range of illness severity was described with 39% of illness scores suggestive of severe disease. Both the COAST score and IRRISS were associated with respiratory syncytial virus infection and hospitalization. Gestational age and human rhinovirus infection were inversely associated with both scoring systems. The IRRISS and COAST scores were highly correlated (r = 0.93; P < .0001). CONCLUSIONS Using parent-reported symptoms, we validated the COAST score as a measure of respiratory illness severity in infants. The new IRRISS score performed as well as the COAST score.
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Key Words
- auc, area under the curve
- coast, childhood origins of asthma study
- ed, emergency department
- elgans, extremely low gestational age newborns
- hrv, human rhinovirus
- irriss, infant research respiratory infection severity score
- lmer, linear mixed effects regression modeling
- prism, prematurity, respiratory outcomes, immune system and microbiome
- rsv, respiratory syncytial virus
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Affiliation(s)
- Mary T. Caserta
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY,Reprint requests: Mary T. Caserta, MD, Division of Pediatric Infectious Diseases, 601 Elmwood Ave, Box 690, Rochester, NY 14642
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Sanjukta Bandyopadhyay
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Steven R. Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - James Java
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Ann R. Falsey
- Department of Medicine-Infectious Diseases, University of Rochester Medical Center, Rochester, NY
| | - David J. Topham
- Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY,UR Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY
| | - Kristin Scheible
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY,Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY
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29
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Nyawanda BO, Njuguna HN, Onyango CO, Makokha C, Lidechi S, Fields B, Winchell JM, Katieno JS, Nyaundi J, Ade F, Emukule GO, Mott JA, Otieno N, Widdowson MA, Chaves SS. Comparison of respiratory pathogen yields from Nasopharyngeal/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya. Sci Rep 2019; 9:11237. [PMID: 31375774 PMCID: PMC6677726 DOI: 10.1038/s41598-019-47713-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). However, nasopharyngeal/oropharyngeal (NP/OP) swabs may not accurately reflect etiologic agents from the lower respiratory tract where sputum specimens are considered as a more representative sample. The pathogen yields from NP/OP against sputum specimens have not been extensively explored, especially in tropical countries. We compared pathogen yields from NP/OP swabs and sputum specimens from patients ≥18 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar's test. The agreement for pathogen detection between NP/OP and sputum specimens ranged between 85-100%. More viruses were detected from NP/OP specimens whereas Klebsiella pneumoniae and Mycobacterium tuberculosis were more common in sputum specimens. There was no clear advantage in using sputum over NP/OP specimens to detect pathogens of ALRI in adults using TAC in the context of this tropical setting.
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Affiliation(s)
- Bryan O Nyawanda
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya.
| | - Henry N Njuguna
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clayton O Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Caroline Makokha
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Shirley Lidechi
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Barry Fields
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jim S Katieno
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Jeremiah Nyaundi
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Fredrick Ade
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Gideon O Emukule
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Joshua A Mott
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nancy Otieno
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra S Chaves
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
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30
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Zhou F, Wang Y, Liu Y, Liu X, Gu L, Zhang X, Pu Z, Yang G, Liu B, Nie Q, Xue B, Feng J, Guo Q, Liu J, Fan H, Chen J, Zhang Y, Xu Z, Pang M, Chen Y, Nie X, Cai Z, Xu J, Peng K, Li X, Xiang P, Zhang Z, Jiang S, Su X, Zhang J, Li Y, Jin X, Jiang R, Dong J, Song Y, Zhou H, Wang C, Cao B. Disease severity and clinical outcomes of community-acquired pneumonia caused by non-influenza respiratory viruses in adults: a multicentre prospective registry study from the CAP-China Network. Eur Respir J 2019; 54:13993003.02406-2018. [PMID: 31164430 DOI: 10.1183/13993003.02406-2018] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/02/2019] [Indexed: 02/05/2023]
Abstract
Although broad knowledge of influenza viral pneumonia has been established, the significance of non-influenza respiratory viruses in community-acquired pneumonia (CAP) and their impact on clinical outcomes remains unclear, especially in the non-immunocompromised adult population.Hospitalised immunocompetent patients with CAP were prospectively recruited from 34 hospitals in mainland China. Respiratory viruses were detected by molecular methods. Comparisons were conducted between influenza and non-influenza viral infection groups.In total, 915 out of 2336 adult patients with viral infection were enrolled in the analysis, with influenza virus (28.4%) the most frequently detected virus, followed by respiratory syncytial virus (3.6%), adenovirus (3.3%), human coronavirus (3.0%), parainfluenza virus (2.2%), human rhinovirus (1.8%) and human metapneumovirus (1.5%). Non-influenza viral infections accounted for 27.4% of viral pneumonia. Consolidation was more frequently observed in patients with adenovirus infection. The occurrence of complications such as sepsis (40.1% versus 39.6%; p=0.890) and hypoxaemia (40.1% versus 37.2%; p=0.449) during hospitalisation in the influenza viral infection group did not differ from that of the non-influenza viral infection group. Compared with influenza virus infection, the multivariable adjusted odds ratios of CURB-65 (confusion, urea >7 mmol·L-1, respiratory rate ≥30 breaths·min-1, blood pressure <90 mmHg (systolic) or ≤60 mmHg (diastolic), age ≥65 years) ≥3, arterial oxygen tension/inspiratory oxygen fraction <200 mmHg, and occurrence of sepsis and hypoxaemia for non-influenza respiratory virus infection were 0.87 (95% CI 0.26-2.84), 0.72 (95% CI 0.26-1.98), 1.00 (95% CI 0.63-1.58) and 1.05 (95% CI 0.66-1.65), respectively. The hazard ratio of 90-day mortality was 0.51 (95% CI 0.13-1.91).The high incidence of complications in non-influenza viral pneumonia and similar impact of non-influenza respiratory viruses relative to influenza virus on disease severity and outcomes suggest more attention should be given to CAP caused by non-influenza respiratory viruses.
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Affiliation(s)
- Fei Zhou
- Dept of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Institute of Respiratory Medicine Chinese Academy of Medical Science, National Clinical Research Center of Respiratory Diseases, Beijing, China.,Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.,These authors contributed equally to this work
| | - Yimin Wang
- Dept of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Institute of Respiratory Medicine Chinese Academy of Medical Science, National Clinical Research Center of Respiratory Diseases, Beijing, China.,Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.,These authors contributed equally to this work
| | - Yingmei Liu
- Dept of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Institute of Respiratory Medicine Chinese Academy of Medical Science, National Clinical Research Center of Respiratory Diseases, Beijing, China.,Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.,These authors contributed equally to this work
| | - Xuedong Liu
- Dept of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao, China.,These authors contributed equally to this work
| | - Li Gu
- Dept of Infectious Diseases, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,These authors contributed equally to this work
| | - Xiaoju Zhang
- Dept of Respiratory Medicine, Henan Provincial People's Hospital, Zhengzhou, China.,These authors contributed equally to this work
| | - Zenghui Pu
- Dept of Infectious Diseases, Yantai Yu Huang-Ding Hospital, Yantai, China.,These authors contributed equally to this work
| | - Guoru Yang
- Dept of Pulmonary and Critical Care Medicine, Weifang No. 2 People's Hospital, Weifang, China.,These authors contributed equally to this work
| | - Bo Liu
- Dept of Respiratory and Critical Care Medicine, Linzi District People's Hospital, Zibo, China.,These authors contributed equally to this work
| | - Qingrong Nie
- Dept of Respiratory and Critical Care Medicine, Liangxiang Hospital, Beijing, China
| | - Bing Xue
- Dept of Respiratory Medicine, Chuiyangliu Hospital Affiliated to Tshinghua University, Beijing, China
| | - Jing Feng
- Dept of Respiratory Medicine, General Hospital of Tianjin Medical University, Tianjin, China
| | - Qiang Guo
- Dept of Respiratory, Emergency and Critical Care Medicine, First Affiliated Hospital of Soochow University, Jiangsu, China
| | - Jianhua Liu
- Dept of Respiratory Medicine, Beijing Huairou Hospital of University of Chinese Academy of Science, Beijing, China
| | - Hong Fan
- Dept of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Chen
- Dept of Respiratory Medicine, Fuxing Hospital, Capital Medical University, Beijing, China
| | - Yongxiang Zhang
- Dept of Respiratory Medicine, Daxing Teaching Hospital, Capital Medical University, Beijing, China
| | - Zhenyang Xu
- Dept of Pulmonary and Critical Care Medicine, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Min Pang
- Dept of Respiratory Medicine, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yu Chen
- Dept of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Beijing China
| | - Xiuhong Nie
- Dept of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhigang Cai
- Dept of Pulmonary and Critical Care Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jinfu Xu
- Dept of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Shanghai, China
| | - Kun Peng
- Dept of Respiratory Medicine, Beijing No. 6 Hospital, Beijing, China
| | - Xiangxin Li
- Dept of Pulmonary and Critical Care Medicine, Beijing Changping Hospital, Beijing, China
| | - Pingchao Xiang
- Dept of Pulmonary and Critical Care Medicine, Peking University Shougang Hospital, Beijing, China
| | - Zuoqing Zhang
- Dept of Respiratory Medicine, Beijing Shijingshan Hospital, Beijing, China
| | - Shujuan Jiang
- Dept of Pulmonary and Critical Care Medicine, Shandong Province Hospital, Jinan, China
| | - Xin Su
- Dept of Respiratory Medicine, Nanjing General Hospital of Nanjing Military Command, PLA, Nanjing, China
| | - Jie Zhang
- Dept of Respiratory Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanming Li
- Dept of Pulmonary and Critical Care Medicine, Beijing Hospital, Beijing, China
| | - Xiuhong Jin
- Dept of Respiratory Medicine, Beijing Pinggu Hospital, Beijing, China
| | - Rongmeng Jiang
- Infectious Disease Diagnosis and Treatment Center, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jianping Dong
- Dept of Infectious Diseases, Beijing Haidian Hospital, Haidian Section of Peking University Third Hospital, Beijing, China
| | - Yuanlin Song
- Dept of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hong Zhou
- Dept of Respiratory Medicine, Beijing Electric Power Hospital, Beijing, China
| | - Chen Wang
- Dept of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Institute of Respiratory Medicine Chinese Academy of Medical Science, National Clinical Research Center of Respiratory Diseases, Beijing, China.,Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.,These authors contributed equally to this work
| | - Bin Cao
- Dept of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Institute of Respiratory Medicine Chinese Academy of Medical Science, National Clinical Research Center of Respiratory Diseases, Beijing, China .,Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.,These authors contributed equally to this work
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Whitaker B, Alroy KA, Guthrie E, Schildecker S, Hiers S, Woodard J, Balajee SA. Strengthening laboratory capacity for detection of respiratory viral pathogens through the Global Health Security Agenda (GHSA) framework. Afr J Lab Med 2019; 8:861. [PMID: 31392168 PMCID: PMC6676779 DOI: 10.4102/ajlm.v8i1.861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/17/2019] [Indexed: 11/26/2022] Open
Abstract
Background Endemic and emerging respiratory viruses are a threat to public health, and a robust public health laboratory system is essential to ensure global health security. Objective This program sought to expand molecular laboratory testing capacity to detect a broad range of respiratory pathogens in clinical respiratory specimens collected during disease surveillance and outbreak investigations. Methods As a part of the Global Health Security Agenda (GHSA), the United States Centers for Disease Control and Prevention utilised the equipment and training infrastructure already in place at the World Health Organization National Influenza Centers to expand testing capacity for respiratory viruses in laboratories in GHSA partner countries. This was done through the provision of quality assured reagents, including multiplex platforms and technical guidance for laboratory staff, as well as the assessment of laboratory testing accuracy. Conclusion Early findings illustrated that GHSA laboratories have been able to expand testing capacity using specimens from routine surveillance, as well as from outbreak situations.
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Affiliation(s)
- Brett Whitaker
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Karen A Alroy
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Erica Guthrie
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Sarah Schildecker
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Susan Hiers
- Office of the Director, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Jill Woodard
- Office of the Director, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - S Arunmozhi Balajee
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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32
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Yao LH, Wang C, Wei TL, Wang H, Ma FL, Zheng LS. Human adenovirus among hospitalized children with respiratory tract infections in Beijing, China, 2017-2018. Virol J 2019; 16:78. [PMID: 31196108 PMCID: PMC6567909 DOI: 10.1186/s12985-019-1185-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/24/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Human adenoviruses (HAdVs) cause a wide range of diseases. However, the genotype diversity and epidemiological information relating to HAdVs among hospitalized children with respiratory tract infections (RTIs) is limited. Here, we describe the epidemiology and genotype distribution of HAdVs associated with RTIs in Beijing, China. METHODS Nasopharyngeal aspirates (NPA) were collected from hospitalized children with RTIs from April 2017 to March 2018. HAdVs were detected by a TaqMan-based quantitative real-time polymerase chain reaction (qPCR) assay, and the hexon gene was used for phylogenetic analysis. Epidemiological data were analyzed using statistical product and service solutions (SPSS) 21.0 software. RESULTS HAdV was detected in 72 (5.64%) of the 1276 NPA specimens, with most (86.11%, 62/72) HAdV-positives cases detected among children < 6 years of age. HAdV-B3 (56.06%, 37/66) and HAdV-C2 (19.70%, 13/66) were the most frequent. Of the 72 HAdV-infected cases, 27 (37.50%) were co-infected with other respiratory viruses, most commonly parainfluenza virus (12.50%, 9/72) and rhinovirus (9.72%, 7/72). The log number of viral load ranged from 3.30 to 9.14 copies per mL of NPA, with no significant difference between the HAdV mono- and co-infection groups. The main clinical symptoms in the HAdV-infected patients were fever and cough, and 62 (86.11%, 62/72) were diagnosed with pneumonia. Additionally, HAdVs were detected throughout the year with a higher prevalence in summer. CONCLUSIONS HAdV prevalence is related to age and season. HAdV-B and HAdV-C circulated simultaneously among the hospitalized children with RTIs in Beijing, and HAdV-B type 3 and HAdV-C type 2 were the most frequent.
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Affiliation(s)
- Li-Hong Yao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Tian-Li Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Hao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Fen-Lian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China.
| | - Li-Shu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China.
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33
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Duplex real-time RT-PCR assay for detection and subgroup-specific identification of human respiratory syncytial virus. J Virol Methods 2019; 271:113676. [PMID: 31181218 PMCID: PMC7172218 DOI: 10.1016/j.jviromet.2019.113676] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023]
Abstract
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Reliable detection and identification of HRSV subgroup A and B infections are essential for accurate disease burden estimates in anticipation of licensure of novel HRSV vaccines and immunotherapies. To ensure continued reliability, molecular assays must remain current with evolving virus strains. We have developed a HRSV subgroup-specific real-time RT-PCR (rRT-PCR) assay for detection and subgroup identification using primers and subgroup-specific probes targeting a conserved region of the nucleoprotein gene combined in a single duplex reaction using all genome sequence data currently available in GenBank. The assay was validated for analytical sensitivity, specificity, reproducibility, and clinical performance with a geographically diverse collection of viral isolates and respiratory specimens in direct comparison with an established pan-HRSV rRT-PCR reference test. The assay was sensitive, reproducibly detecting as few as 5-10 copies/reaction of target RNA. The assay was specific, showing no amplification with a panel of 16 other common respiratory pathogens or predicted by in silico primer/probe analysis. The duplex rRT-PCR assay based on the most current available genome sequence data permits rapid, sensitive and specific detection and subgroup identification of HRSV.
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34
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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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Bunthi C, Baggett HC, Gregory CJ, Thamthitiwat S, Yingyong T, Paveenkittiporn W, Kerdsin A, Chittaganpitch M, Ruangchira-Urai R, Akarasewi P, Ungchusak K. Enhanced surveillance for severe pneumonia, Thailand 2010-2015. BMC Public Health 2019; 19:472. [PMID: 32326941 PMCID: PMC6696659 DOI: 10.1186/s12889-019-6774-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background The etiology of severe pneumonia is frequently not identified by routine disease surveillance in Thailand. Since 2010, the Thailand Ministry of Public Health (MOPH) and US CDC have conducted surveillance to detect known and new etiologies of severe pneumonia. Methods Surveillance for severe community-acquired pneumonia was initiated in December 2010 among 30 hospitals in 17 provinces covering all regions of Thailand. Interlinked clinical, laboratory, pathological and epidemiological components of the network were created with specialized guidelines for each to aid case investigation and notification. Severe pneumonia was defined as chest-radiograph confirmed pneumonia of unknown etiology in a patient hospitalized ≤48 h and requiring intubation with ventilator support or who died within 48 h after hospitalization; patients with underlying chronic pulmonary or neurological disease were excluded. Respiratory and pathological specimens were tested by reverse transcription polymerase chain reaction for nine viruses, including Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and 14 bacteria. Cases were reported via a secure web-based system. Results Of specimens from 972 cases available for testing during December 2010 through December 2015, 589 (60.6%) had a potential etiology identified; 399 (67.8%) were from children aged < 5 years. At least one viral agent was detected in 394 (40.5%) cases, with the most common of single vial pathogen detected being respiratory syncytial virus (RSV) (110/589, 18.7%) especially in children under 5 years. Bacterial pathogens were detected in 341 cases of which 67 cases had apparent mixed infections. The system added MERS-CoV testing in September 2012 as part of Thailand’s outbreak preparedness; no cases were identified from the 767 samples tested. Conclusions Enhanced surveillance improved the understanding of the etiology of severe pneumonia cases and improved the MOPH’s preparedness and response capacity for emerging respiratory pathogens in Thailand thereby enhanced global health security. Guidelines for investigation of severe pneumonia from this project were incorporated into surveillance and research activities within Thailand and shared for adaption by other countries.
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Affiliation(s)
- Charatdao Bunthi
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Tivanond Road, Nonthaburi, 11000, Thailand.
| | - Henry C Baggett
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Tivanond Road, Nonthaburi, 11000, Thailand.,Division of Global Health Protection, Centers for Disease Control and Prevention, Clifton Road, Atlanta, GA, 30329, USA
| | - Christopher J Gregory
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Tivanond Road, Nonthaburi, 11000, Thailand.,Division of Global Health Protection, Centers for Disease Control and Prevention, Clifton Road, Atlanta, GA, 30329, USA
| | - Somsak Thamthitiwat
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Tivanond Road, Nonthaburi, 11000, Thailand
| | - Thitipong Yingyong
- Department of Disease Control, Bureau of Epidemiology, Ministry of Public Health, Tivanond Road, Nonthaburi, 11000, Thailand
| | - Wantana Paveenkittiporn
- National Institute of Health, Ministry of Public Health, Tivanond Road, Nonthaburi, 11000, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Malinee Chittaganpitch
- National Institute of Health, Ministry of Public Health, Tivanond Road, Nonthaburi, 11000, Thailand
| | | | - Pasakorn Akarasewi
- Department of Disease Control, Bureau of Epidemiology, Ministry of Public Health, Tivanond Road, Nonthaburi, 11000, Thailand
| | - Kumnuan Ungchusak
- Department of Disease Control, Bureau of Epidemiology, Ministry of Public Health, Tivanond Road, Nonthaburi, 11000, Thailand
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Killerby ME, Rozwadowski F, Lu X, Caulcrick-Grimes M, McHugh L, Haldeman AM, Fulton T, Schneider E, Sakthivel SK, Bhatnagar J, Rabeneck DB, Zaki S, Gerber SI, Watson JT. Respiratory Illness Associated With Emergent Human Adenovirus Genome Type 7d, New Jersey, 2016-2017. Open Forum Infect Dis 2019; 6:ofz017. [PMID: 30800698 DOI: 10.1093/ofid/ofz017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/06/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background Human adenoviruses (HAdVs) are known causes of respiratory illness outbreaks in congregate settings, but cases and clusters are less well described from community settings in the United States. During December 2016-February 2017, the New Jersey Department of Health received reports of HAdV infections from 3 sources in 3 adjacent counties. We investigated to characterize the epidemiologic, laboratory, and clinical features of this HAdV outbreak. Methods A case was defined as a New Jersey resident with acute respiratory illness during December 1, 2016-March 31, 2017 with laboratory identification of HAdV genome type 7d (HAdV-7d). Human adenovirus was detected by real-time and conventional polymerase chain reaction and molecular typed by partial hexon capsid protein gene sequencing. The HAdV genome type was identified by whole genome sequencing analysis. Available medical, public health, and surveillance records were reviewed. Results We identified 12 cases, including 3 treatment facility patients, 7 college students, and 2 cases at a tertiary-care hospital. Four cases died; all had underlying comorbidities. Nine HAdV-7d whole genome sequences obtained from all 3 sites were nearly identical. Conclusions Transmission of HAdV-7d occurred in community and congregate settings across 3 counties and resulted in severe morbidity and mortality in some cases with underlying comorbidities. Clinicians and local and state health departments should consider HAdV in patients with severe respiratory infection.
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Affiliation(s)
- Marie E Killerby
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases.,Epidemic Intelligence Service, Division of Scientific Education and Professional Development
| | - Faye Rozwadowski
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development.,New Jersey Department of Health, Trenton
| | - Xiaoyan Lu
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases
| | | | | | | | | | - Eileen Schneider
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases
| | - Senthilkumar K Sakthivel
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases.,Battelle, Columbus, Ohio
| | - Julu Bhatnagar
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Demi B Rabeneck
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sherif Zaki
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susan I Gerber
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases
| | - John T Watson
- Respiratory Viruses Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases
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37
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Gaur B, Saha S, Iuliano AD, Rai SK, Krishnan A, Jain S, Whitaker B, Winchell J, Lal RB, Broor S. Use of TaqMan Array card for the detection of respiratory viral pathogens in children under 5 years old hospitalised with acute medical illness in Ballabgarh, Haryana, India. Indian J Med Microbiol 2019; 37:105-108. [PMID: 31424019 PMCID: PMC9257431 DOI: 10.4103/ijmm.ijmm_18_146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Historical specimens collected from hospitalized children were tested for the following 13 viruses: influenza A and B; respiratory syncytial virus (RSV); parainfluenza viruses 1-3; human metapneumovirus; rhinovirus; coronaviruses 229E, OC43, NL63 and HKU1 and Adenovirus using monoplex real-time reverse transcriptase polymerase chain reaction (rRT-PCR). They were retested using TaqMan Array Card (TAC), a micro-fluidic system, capable of simultaneous multi-pathogen testing, to evaluate its sensitivity and specificity against monoplex rRT-PCR. TAC showed high sensitivity (71%-100%) and specificity (98%-100%) for these viruses in comparison to monoplex rRT-PCR. Multi-specimen detection with high sensitivity and specificity makes TAC a potentially useful tool for both surveillance and outbreak investigations.
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Affiliation(s)
- Bharti Gaur
- Department of Microbiology, All Institute of Medical Sciences, New Delhi, India
| | - Siddhartha Saha
- Influenza Division, Centers for Disease Control and Prevention, U.S Embassy, New Delhi, India
| | - A Danielle Iuliano
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sanjay K Rai
- Centre for Community Medicine, All Institute of Medical Sciences, New Delhi, India
| | - Anand Krishnan
- Centre for Community Medicine, All Institute of Medical Sciences, New Delhi, India
| | - Seema Jain
- Influenza Division, Centers for Disease Control and Prevention, U.S Embassy, New Delhi, India
| | - Brett Whitaker
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Renu B Lal
- Influenza Division, Centers for Disease Control and Prevention, U.S Embassy, New Delhi, India
| | - Shobha Broor
- Department of Microbiology, All Institute of Medical Sciences, New Delhi, India
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Xie L, Zhang B, Xiao N, Zhang F, Zhao X, Liu Q, Xie Z, Gao H, Duan Z, Zhong L. Epidemiology of human adenovirus infection in children hospitalized with lower respiratory tract infections in Hunan, China. J Med Virol 2018; 91:392-400. [PMID: 30286268 PMCID: PMC7159165 DOI: 10.1002/jmv.25333] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/02/2018] [Indexed: 12/18/2022]
Abstract
To investigate the current genotypes of circulating human adenovirus (HAdV) strains, we molecularly genotyped HAdV in the nasopharyngeal aspirates (NPAs) of patients with acute lower respiratory tract infections (ALRTIs) and attempted to determine their associations with clinical symptoms. A total of 4751 NPA samples were collected from 4751 patients admitted to Hunan Provincial People's Hospital from September 2007 to March 2014, of which 447 (9.4%) samples were HAdV positive. Fourteen different HAdV types were identified; HAdV types 1 to 7 (HAdV 1‐7) were identified in 95.7% of the 447 NPA samples with HAdV‐7 and HAdV‐3 being the most prevalent. In addition, 93.3% (417 of 447) of patients were younger than 5 years. The incidence of HAdV infection peaked in summer. Different HAdV types showed a predilection for different age groups and different seasonal distribution patterns. Coinfection of HAdVs and other respiratory viruses was detected in 63.3% (283 of 447) of the HAdV‐positive samples. The most common clinical diagnosis was pneumonia and the most common symptoms were fever and cough. In comparison with children infected with HAdV‐3 alone, those infected with HAdV‐7 alone had an increased frequency of severe pneumonia involvement (11.6% vs 32.4%; P = 0.031), higher intensive care unit admission rates (7.0% vs 26.5%; P = 0.019), and a longer length of hospital stay (P = 0.03). Mixed infections in younger children were associated with a longer hospital stay (P = 0.023). Our results demonstrate the recent changes in the trends of circulating HAdV genotypes associated with ALRTIs in Hunan China.
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Affiliation(s)
- Leyun Xie
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Bing Zhang
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Niguang Xiao
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Fei Zhang
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Xin Zhao
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Qin Liu
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Zhiping Xie
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Hanchun Gao
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhaojun Duan
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lili Zhong
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
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Rotrosen E, Zaman K, Feser J, Ortiz JR, Goswami D, Sharmeen AT, Rahman M, Lewis KDC, Rahman MZ, Barin B, Brooks WA, Neuzil KM. Influenza Among Young Children in Bangladesh: Clinical Characteristics and Outcomes From a Randomized Clinical Trial. Clin Infect Dis 2018; 65:1914-1920. [PMID: 29028980 PMCID: PMC5850015 DOI: 10.1093/cid/cix674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Background Influenza causes substantial morbidity in children worldwide, although influenza vaccine is seldom used in low-resource settings. More information on the clinical presentation of influenza and the efficacy of vaccine is needed to inform policy. Methods In 2013 we conducted a randomized, placebo-controlled clinical trial of live attenuated influenza vaccine (LAIV) in children aged 24-59 months in Bangladesh (N = 1761). If participants met prespecified specimen collection criteria, we collected nasopharyngeal washes for testing by singleplex reverse-transcription polymerase chain reaction (RT-PCR) for laboratory-confirmed influenza virus infection (LCI). A panel of RT-PCR assays was used to detect noninfluenza respiratory viruses. Primary efficacy results have been reported. In this analysis of prespecified and post hoc objectives from the trial, we compared signs and symptoms between LCI and non-LCI cases and estimated the efficacy of LAIV against moderate-to-severe LCI and other prespecified non-LCI clinical outcomes including all-cause pneumonia and acute otitis media. Results The most common signs and symptoms of LCI were fever, cough, and runny nose. The combination of subjective fever and cough had a 63% sensitivity for LCI. The combination of measured fever, cough, and runny nose was most specific (90%) but had low sensitivity (32%) for LCI. The efficacy of LAIV against vaccine-strain moderate-to-severe LCI was 56.7% (95% confidence interval, 9.5%-79.2%). No statistically significant vaccine efficacy was found against the non-laboratory-confirmed clinical outcomes. Conclusions It was not possible to distinguish LCI from noninfluenza viral infections on clinical evaluations alone in this population of Bangladeshi children. LAIV was efficacious against moderate-to-severe LCI. Clinical Trials Registration NCT01797029.
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Affiliation(s)
| | - K Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - Justin R Ortiz
- Departments of Medicine and Global Health, University of Washington, Seattle
| | - Doli Goswami
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - Md Ziaur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka
| | | | - W Abdullah Brooks
- Department of International Health, Johns Hopkins University, Baltimore, Maryland
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Granade TC, Kodani M, Wells SK, Youngpairoj AS, Masciotra S, Curtis KA, Kamili S, Owen SM. Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses. J Virol Methods 2018; 259:60-65. [PMID: 29874550 DOI: 10.1016/j.jviromet.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 01/07/2023]
Abstract
Real-time PCR assays for nucleic acid testing (NAT) of hepatitis viruses A-E and for HIV-1 and HIV-2 have been developed; however, a multiplex assay that can simultaneously detect all of these agents is not yet available. Standardized TaqMan assays for detection of hepatitis viruses A-E have been described and applied to TaqMan Array Cards (TAC) which are capable of multiple pathogen detection using a single set of optimized PCR conditions. Assays for three gene regions of HIV-1 (long-terminal repeat (LTR), gag, and polymerase) and HIV-2 (overlap of LTR and gag, protease and integrase) were designed using the hepatitis assay conditions. Nucleic acid extracts of HIV-1-infected samples (44 plasma, 41 whole blood, 20 HIV-1 viral stocks) were tested on the TAC cards; 98 were reactive (92%) with 70 in multiple gene regions. Twenty-four of the 27 (89%) HIV-2 specimens (10 plasma, 1 PBMC lysate, 6 whole blood and 10 plasmids containing HIV-2 polymerase) were detected on TAC. No HIV or hepatitis virus sequences were detected in 30 HIV-negative samples (specificity 100%). Three HBV and 18 HCV co-infections were identified in the HIV-1-infected specimens. Multi-pathogen detection using TAC could provide a rapid, sensitive and more efficient method of surveying for a variety of infectious disease nucleic acids.
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Affiliation(s)
- Timothy C Granade
- Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, GA, 30333, United States.
| | - Maja Kodani
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA, 30333, United States
| | - Susan K Wells
- Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, GA, 30333, United States
| | - Ae S Youngpairoj
- Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, GA, 30333, United States
| | - Silvina Masciotra
- Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, GA, 30333, United States
| | - Kelly A Curtis
- Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, Atlanta, GA, 30333, United States
| | - Saleem Kamili
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA, 30333, United States
| | - S Michele Owen
- Centers for Disease Control and Prevention, National Center for HIV, Hepatitis, STD and TB Prevention, Atlanta, GA, 30333, United States
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Self WH, Balk RA, Grijalva CG, Williams DJ, Zhu Y, Anderson EJ, Waterer GW, Courtney DM, Bramley AM, Trabue C, Fakhran S, Blaschke AJ, Jain S, Edwards KM, Wunderink RG. Procalcitonin as a Marker of Etiology in Adults Hospitalized With Community-Acquired Pneumonia. Clin Infect Dis 2018; 65:183-190. [PMID: 28407054 PMCID: PMC5850442 DOI: 10.1093/cid/cix317] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022] Open
Abstract
Background Recent trials suggest procalcitonin-based guidelines can reduce antibiotic use for respiratory infections. However, the accuracy of procalcitonin to discriminate between viral and bacterial pneumonia requires further dissection. Methods We evaluated the association between serum procalcitonin concentration at hospital admission with pathogens detected in a multicenter prospective surveillance study of adults hospitalized with community-acquired pneumonia. Systematic pathogen testing included cultures, serology, urine antigen tests, and molecular detection. Accuracy of procalcitonin to discriminate between viral and bacterial pathogens was calculated. Results Among 1735 patients, pathogens were identified in 645 (37%), including 169 (10%) with typical bacteria, 67 (4%) with atypical bacteria, and 409 (24%) with viruses only. Median procalcitonin concentration was lower with viral pathogens (0.09 ng/mL; interquartile range [IQR], <0.05-0.54 ng/mL) than atypical bacteria (0.20 ng/mL; IQR, <0.05-0.87 ng/mL; P = .05), and typical bacteria (2.5 ng/mL; IQR, 0.29-12.2 ng/mL; P < .01). Procalcitonin discriminated bacterial pathogens, including typical and atypical bacteria, from viral pathogens with an area under the receiver operating characteristic (ROC) curve of 0.73 (95% confidence interval [CI], .69-.77). A procalcitonin threshold of 0.1 ng/mL resulted in 80.9% (95% CI, 75.3%-85.7%) sensitivity and 51.6% (95% CI, 46.6%-56.5%) specificity for identification of any bacterial pathogen. Procalcitonin discriminated between typical bacteria and the combined group of viruses and atypical bacteria with an area under the ROC curve of 0.79 (95% CI, .75-.82). Conclusions No procalcitonin threshold perfectly discriminated between viral and bacterial pathogens, but higher procalcitonin strongly correlated with increased probability of bacterial pathogens, particularly typical bacteria.
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Affiliation(s)
- Wesley H Self
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | | | - Yuwei Zhu
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Grant W Waterer
- University of Western Australia, Perth.,Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - D Mark Courtney
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Christopher Trabue
- University of Tennessee Health Science Center/Saint Thomas Health, Nashville
| | - Sherene Fakhran
- John H. Stroger, Jr Hospital of Cook County, Chicago, Illinois
| | | | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
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Ma FL, Li DD, Wei TL, Li JS, Zheng LS. Quantitative detection of human Malawi polyomavirus in nasopharyngeal aspirates, sera, and feces in Beijing, China, using real-time TaqMan-based PCR. Virol J 2017; 14:152. [PMID: 28806976 PMCID: PMC5557062 DOI: 10.1186/s12985-017-0817-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/01/2017] [Indexed: 01/02/2023] Open
Abstract
Background Human Malawi polyomavirus (MWPyV) was discovered in 2012, but its prevalence and clinical characteristics are largely unknown. Methods We used real-time TaqMan-based PCR to detect MWPyV in the feces (n = 174) of children with diarrhea, nasopharyngeal aspirates (n = 887) from children with respiratory infections, and sera (n = 200) from healthy adults, and analyzed its clinical characteristics statistically. All the MWPyV-positive specimens were also screened for other common respiratory viruses. Results Sixteen specimens were positive for MWPyV, including 13 (1.47%) respiratory samples and three (1.7%) fecal samples. The samples were all co-infected with other respiratory viruses, most commonly with influenza viruses (69.2%) and human coronaviruses (30.7%). The MWPyV-positive children were diagnosed with bronchopneumonia or viral diarrhea. They ranged in age from 12 days to 9 years, and the most frequent symptoms were cough and fever. Conclusions Real-time PCR is an effective tool for the detection of MWPyV in different types of samples. MWPyV infection mainly occurs in young children, and fecal–oral transmission is a possible route of its transmission. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0817-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fen-Lian Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Dan-di Li
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Tian-Li Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100052, China
| | - Jin-Song Li
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China
| | - Li-Shu Zheng
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, 100 Ying-Xin St., Xi-Cheng District, Beijing, 100052, China.
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Community-Acquired Pneumonia Visualized on CT Scans but Not Chest Radiographs: Pathogens, Severity, and Clinical Outcomes. Chest 2017; 153:601-610. [PMID: 28802696 PMCID: PMC5989638 DOI: 10.1016/j.chest.2017.07.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/05/2017] [Accepted: 07/26/2017] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The clinical significance of pneumonia visualized on CT scan in the setting of a normal chest radiograph is uncertain. METHODS In a multicenter prospective surveillance study of adults hospitalized with community-acquired pneumonia (CAP), we compared the presenting clinical features, pathogens present, and outcomes of patients with pneumonia visualized on a CT scan but not on a concurrent chest radiograph (CT-only pneumonia) and those with pneumonia visualized on a chest radiograph. All patients underwent chest radiography; the decision to obtain CT imaging was determined by the treating clinicians. Chest radiographs and CT images were interpreted by study-dedicated thoracic radiologists blinded to the clinical data. RESULTS The study population included 2,251 adults with CAP; 2,185 patients (97%) had pneumonia visualized on chest radiography, whereas 66 patients (3%) had pneumonia visualized on CT scan but not on concurrent chest radiography. Overall, these patients with CT-only pneumonia had a clinical profile similar to those with pneumonia visualized on chest radiography, including comorbidities, vital signs, hospital length of stay, prevalence of viral (30% vs 26%) and bacterial (12% vs 14%) pathogens, ICU admission (23% vs 21%), use of mechanical ventilation (6% vs 5%), septic shock (5% vs 4%), and inhospital mortality (0 vs 2%). CONCLUSIONS Adults hospitalized with CAP who had radiological evidence of pneumonia on CT scan but not on concurrent chest radiograph had pathogens, disease severity, and outcomes similar to patients who had signs of pneumonia on chest radiography. These findings support using the same management principles for patients with CT-only pneumonia and those with pneumonia seen on chest radiography.
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Wang L, Feng Z, Zhao M, Yang S, Yan X, Guo W, Shi Z, Li G. A comparison study between GeXP-based multiplex-PCR and serology assay for Mycoplasma pneumoniae detection in children with community acquired pneumonia. BMC Infect Dis 2017; 17:518. [PMID: 28743259 PMCID: PMC5527399 DOI: 10.1186/s12879-017-2614-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/18/2017] [Indexed: 11/18/2022] Open
Abstract
Background Diagnosis of community-acquired pneumonia (CAP) caused by Mycoplasma pneumoniae (Mp) in children has been hampered by difficulty in obtaining convalescent serum and time constraints. In this study, the two diagnostic assays that targeted respectively on Mp-antibody and Mp-DNA were retrospectively investigated. Methods A total of 3146 children were clinically diagnosed to have CAP and were confirmed by chest X-ray during March 2015 to February 2016 in Children’s hospital of Hebei Province (China). Both of the sera and sputum samples were collected in 24 h after their admission. The Mp-antibody was examined by the passive particle agglutination assay and a fourfold or greater increase of antibody titers of paired sera or≧1:160 titer of single serum was set as the serology positive. Mp-DNA in the sputum samples was tested by a multiplex-PCR method named GeXP assay (multiplex PCR combined with automated capillary electrophoresis). In order to eliminate the false positive results caused by the asymptomatic carriage after infected by M. pneumoniae, the inconsistent samples were tested by the real-time isothermal transcription-mediated RNA amplification assay (SAT). Results The inter-rated agreement test was performed in 3146 CAP patients, with a highest kappa value in the school-age children as 0.783. There were 6.29% (198/3146) cases showed inconsistent results determined by GeXP and serology assay. All of the 19 GeXP(+)/Serology (−) samples and a randomly chosen 27 from 179 GeXP(−)/Serology (+) samples were tested by SAT assay, and a 97.8% diagnosis agreement was observed between SAT and GeXP assay, but not with the serology assay. In addition, patients who were detected only by serology or only by multiplex-PCR were significantly younger than those with both methods positive (3.0 and 1.5 years vs. 5.0 years, p < 0.01). The Viral-Mp coinfection accounted for 37.0% (97/262), which was more common in winter and spring (p < 0.05) and in the infantile group (p < 0.01), compared to the pure Mp positive ones. Conclusion In some children CAP cases, the Mp laboratory diagnosis was inconsistent between serology and multiplex-PCR assay. Verified by the SAT assay, the GeXP showed a more sensitive and reliable performance compared with the serology assay. Furthermore, employing the multiplex-PCR could provide more information on the associated pathogens for clinical assessment of CAP. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2614-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Zhishan Feng
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Mengchuan Zhao
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Xiaotong Yan
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Weiwei Guo
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China
| | - Zhongren Shi
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China.
| | - Guixia Li
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, Hebei Province, 050031, China. .,Department of Laboratory Medicine, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China.
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Ryan U, Paparini A, Oskam C. New Technologies for Detection of Enteric Parasites. Trends Parasitol 2017; 33:532-546. [DOI: 10.1016/j.pt.2017.03.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/21/2022]
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Evaluation of a TaqMan Array Card for Detection of Central Nervous System Infections. J Clin Microbiol 2017; 55:2035-2044. [PMID: 28404679 DOI: 10.1128/jcm.02469-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/06/2017] [Indexed: 11/20/2022] Open
Abstract
Infections of the central nervous system (CNS) are often acute, with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan array card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid. The 21-pathogen CNS multiple-pathogen TAC (CNS-TAC) assay includes two parasites (Balamuthia mandrillaris and Acanthamoeba), six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Mycoplasma pneumoniae, Mycobacterium tuberculosis, and Bartonella), and 13 viruses (parechovirus, dengue virus, Nipah virus, varicella-zoster virus, mumps virus, measles virus, lyssavirus, herpes simplex viruses 1 and 2, Epstein-Barr virus, enterovirus, cytomegalovirus, and chikungunya virus). The card also includes human RNase P as a nucleic acid extraction control and an internal manufacturer control, GAPDH (glyceraldehyde-3-phosphate dehydrogenase). This CNS-TAC assay can test up to eight samples for all 21 agents within 2.5 h following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity, and specificity by using either live viruses (dengue, mumps, and measles viruses) or nucleic acid material (Nipah and chikungunya viruses). Of 120 samples tested by individual real-time PCR, 35 were positive for eight different targets, whereas the CNS-TAC assay detected 37 positive samples across nine different targets. The CNS-TAC assays showed 85.6% sensitivity and 96.7% specificity. Therefore, the CNS-TAC assay may be useful for outbreak investigation and surveillance of suspected neurological disease.
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Bacterial and viral pathogen spectra of acute respiratory infections in under-5 children in hospital settings in Dhaka city. PLoS One 2017; 12:e0174488. [PMID: 28346512 PMCID: PMC5367831 DOI: 10.1371/journal.pone.0174488] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/09/2017] [Indexed: 02/01/2023] Open
Abstract
The study aimed to examine for the first time the spectra of viral and bacterial pathogens along with the antibiotic susceptibility of the isolated bacteria in under-5 children with acute respiratory infections (ARIs) in hospital settings of Dhaka, Bangladesh. Nasal swabs were collected from 200 under-five children hospitalized with clinical signs of ARIs. Nasal swabs from 30 asymptomatic children were also collected. Screening of viral pathogens targeted ten respiratory viruses using RT-qPCR. Bacterial pathogens were identified by bacteriological culture methods and antimicrobial susceptibility of the isolates was determined following CLSI guidelines. About 82.5% (n = 165) of specimens were positive for pathogens. Of 165 infected cases, 3% (n = 6) had only single bacterial pathogens, whereas 43.5% (n = 87) cases had only single viral pathogens. The remaining 36% (n = 72) cases had coinfections. In symptomatic cases, human rhinovirus was detected as the predominant virus (31.5%), followed by RSV (31%), HMPV (13%), HBoV (11%), HPIV-3 (10.5%), and adenovirus (7%). Streptococcus pneumoniae was the most frequently isolated bacterial pathogen (9%), whereas Klebsiella pneumaniae, Streptococcus spp., Enterobacter agglomerans, and Haemophilus influenzae were 5.5%, 5%, 2%, and 1.5%, respectively. Of 15 multidrug-resistant bacteria, a Klebsiella pneumoniae isolate and an Enterobacter agglomerans isolate exhibited resistance against more than 10 different antibiotics. Both ARI incidence and predominant pathogen detection rates were higher during post-monsoon and winter, peaking in September. Pathogen detection rates and coinfection incidence in less than 1-year group were significantly higher (P = 0.0034 and 0.049, respectively) than in 1–5 years age group. Pathogen detection rate (43%) in asymptomatic cases was significantly lower compared to symptomatic group (P<0.0001). Human rhinovirus, HPIV-3, adenovirus, Streptococcus pneumonia, and Klebsiella pneumaniae had significant involvement in coinfections with P values of 0.0001, 0.009 and 0.0001, 0.0001 and 0.001 respectively. Further investigations are required to better understand the clinical roles of the isolated pathogens and their seasonality.
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Caserta MT, Yang H, Gill SR, Holden-Wiltse J, Pryhuber G. Viral Respiratory Infections in Preterm Infants during and after Hospitalization. J Pediatr 2017; 182:53-58.e3. [PMID: 28041669 PMCID: PMC5328856 DOI: 10.1016/j.jpeds.2016.11.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To determine the burden of viral respiratory infections in preterm infants both during and subsequent to neonatal intensive care unit (NICU) hospitalization and to compare this with term infants living in the community. STUDY DESIGN From March 2013 through March 2015, we enrolled 189 newborns (96 term and 93 preterm) into a prospective, longitudinal study obtaining nose/throat swabs within 7 days of birth, weekly while hospitalized and then monthly to 4 months after hospital discharge. Taqman array cards were used to identify 16 viral respiratory pathogens by real-time polymerase chain reaction. Demographic, clinical, and laboratory data were gathered from electronic medical records, and parent interview while hospitalized with interval histories collected at monthly visits. The hospital course of all preterm infants who underwent late-onset sepsis evaluations was reviewed. RESULTS Over 119 weeks, we collected 618 nose/throat swabs from at risk preterm infants in our level IV regional NICU. Only 4 infants had viral respiratory infections, all less than 28 weeks gestation at birth. Two infants were symptomatic with the infections recognized by the clinical team. The daily risk of acquiring a respiratory viral infection in preterm infants in the NICU was significantly lower than in the full term cohort living in the community. Once discharged from the hospital, viral respiratory infections were common in all infants. CONCLUSIONS Viral respiratory infections are infrequent in a NICU with strict infection prevention strategies and do not appear to cause unrecognized illness. Both preterm and term infants living in the community quickly acquire respiratory viral infections.
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Affiliation(s)
- Mary T Caserta
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY.
| | - Hongmei Yang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY; Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY
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Al-Abdallat MM, Rha B, Alqasrawi S, Payne DC, Iblan I, Binder AM, Haddadin A, Nsour MA, Alsanouri T, Mofleh J, Whitaker B, Lindstrom SL, Tong S, Ali SS, Dahl RM, Berman L, Zhang J, Erdman DD, Gerber SI. Acute respiratory infections among returning Hajj pilgrims-Jordan, 2014. J Clin Virol 2017; 89:34-37. [PMID: 28226273 PMCID: PMC7106359 DOI: 10.1016/j.jcv.2017.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/09/2017] [Accepted: 01/30/2017] [Indexed: 01/31/2023]
Abstract
Surveillance for respiratory illness in Hajj pilgrims took place in Jordan in 2014. 58% of the 125 subjects returning from Hajj tested positive for at least one virus. Rhino/enterovirus was the most commonly detected viral pathogen (47% of subjects). No cases of Middle East Respiratory Syndrome coronavirus were detected.
Background The emergence of Middle East Respiratory Syndrome coronavirus (MERS-CoV) has prompted enhanced surveillance for respiratory infections among pilgrims returning from the Hajj, one of the largest annual mass gatherings in the world. Objectives To describe the epidemiology and etiologies of respiratory illnesses among pilgrims returning to Jordan after the 2014 Hajj. Study design Surveillance for respiratory illness among pilgrims returning to Jordan after the 2014 Hajj was conducted at sentinel health care facilities using epidemiologic surveys and molecular diagnostic testing of upper respiratory specimens for multiple respiratory pathogens, including MERS-CoV. Results Among the 125 subjects, 58% tested positive for at least one virus; 47% tested positive for rhino/enterovirus. No cases of MERS-CoV were detected. Conclusions The majority of pilgrims returning to Jordan from the 2014 Hajj with respiratory illness were determined to have a viral etiology, but none were due to MERS-CoV. A greater understanding of the epidemiology of acute respiratory infections among returning travelers to other countries after Hajj should help optimize surveillance systems and inform public health response practices.
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Affiliation(s)
| | - Brian Rha
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Sultan Alqasrawi
- Communicable Diseases Directorate, Jordan Ministry of Health, Amman, Jordan
| | - Daniel C Payne
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ibrahim Iblan
- Jordan Field Epidemiology Training Program, Amman, Jordan
| | - Alison M Binder
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Aktham Haddadin
- Directorate of Laboratories, Jordan Ministry of Health, Amman, Jordan
| | | | - Tarek Alsanouri
- Directorate of Laboratories, Jordan Ministry of Health, Amman, Jordan
| | - Jawad Mofleh
- Eastern Mediterranean Public Health Network, Amman, Jordan
| | - Brett Whitaker
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen L Lindstrom
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sami Sheikh Ali
- Communicable Diseases Directorate, Jordan Ministry of Health, Amman, Jordan
| | | | - LaShondra Berman
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jing Zhang
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dean D Erdman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan I Gerber
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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50
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Morris SK, Pell LG, Rahman MZ, Dimitris MC, Mahmud A, Islam MM, Ahmed T, Pullenayegum E, Kashem T, Shanta SS, Gubbay J, Papp E, Science M, Zlotkin S, Roth DE. Maternal vitamin D supplementation during pregnancy and lactation to prevent acute respiratory infections in infancy in Dhaka, Bangladesh (MDARI trial): protocol for a prospective cohort study nested within a randomized controlled trial. BMC Pregnancy Childbirth 2016; 16:309. [PMID: 27737646 PMCID: PMC5064894 DOI: 10.1186/s12884-016-1103-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 10/08/2016] [Indexed: 02/08/2023] Open
Abstract
Background Early infancy is a high-risk period for severe acute respiratory infection (ARI), particularly in low-income countries with resource-limited health systems. Lower respiratory tract infection (LRTI) is commonly preceded by upper respiratory infection (URTI), and often caused by respiratory syncytial virus (RSV), influenza and other common community-acquired viral pathogens. Vitamin D status is a candidate modifiable early-life determinant of the host antiviral immune response and thus may influence the risk of ARI-associated morbidity in high-risk populations. Methods/Design In the Maternal Vitamin D for Infant Growth (MDIG) study in Dhaka, Bangladesh (NCT01924013), 1300 pregnant women are randomized to one of five groups: placebo, 4200 IU/week, 16,800 IU/week, or 28,000 IU/week from 2nd trimester to delivery plus placebo from 0–6 months postpartum; or, 28,000 IU/week prenatal and until 6-months postpartum. In the Maternal Vitamin D for ARI in Infancy (MDARI) sub-study nested within the MDIG trial, trained personnel conduct weekly postnatal home visits to inquire about ARI symptoms and conduct a standardized clinical assessment. Supplementary home visits between surveillance visits are conducted when caregivers make phone notifications of new infant symptoms. Mid-turbinate nasal swab samples are obtained from infants who meet standardized clinical ARI criteria. Specimens are tested by polymerase chain reaction (PCR) for 8 viruses (influenza A/B, parainfluenza 1/2/3, RSV, adenovirus, and human metapneumovirus), and nasal carriage density of Streptococcus pneumoniae. The primary outcome is the incidence rate of microbiologically-positive viral ARI, using incidence rate ratios to estimate between-group differences. We hypothesize that among infants 0–6 months of age, the incidence of microbiologically-confirmed viral ARI will be significantly lower in infants whose mothers received high-dose prenatal/postpartum vitamin D supplements versus placebo. Secondary outcomes include incidence of ARI associated with specific pathogens (influenza A or B, RSV), clinical ARI, and density of pneumococcal carriage. Discussion If shown to reduce the risk of viral ARI in infancy, integration of maternal prenatal/postpartum vitamin D supplementation into antenatal care programs in South Asia may be a feasible primary preventive strategy to reduce the burden of ARI-associated morbidity and mortality in young infants. Trial registration NCT02388516, registered March 9, 2015.
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Affiliation(s)
- Shaun K Morris
- Department of Paediatrics, University of Toronto and the Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada. .,Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada. .,Child Health Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada. .,Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G1X8, Canada.
| | - Lisa G Pell
- Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
| | - Mohammed Ziaur Rahman
- Zoonotic Diseases Research Group, Centre for Communicable Diseases, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Michelle C Dimitris
- Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
| | - Abdullah Mahmud
- Centre for Child and Adolescent Health, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - M Munirul Islam
- Centre for Nutrition and Food Security, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Tahmeed Ahmed
- Centre for Nutrition and Food Security, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Eleanor Pullenayegum
- Child Health Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
| | - Tahmid Kashem
- Centre for Nutrition and Food Security, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Shaila S Shanta
- Centre for Nutrition and Food Security, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Jonathan Gubbay
- Department of Paediatrics, University of Toronto and the Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada.,Public Health Ontario, 661 University Ave., Toronto, ON, Canada
| | - Eszter Papp
- Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
| | - Michelle Science
- Department of Paediatrics, University of Toronto and the Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada.,Division of Infectious Diseases, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G1X8, Canada
| | - Stanley Zlotkin
- Department of Paediatrics, University of Toronto and the Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada.,Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada.,Child Health Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
| | - Daniel E Roth
- Department of Paediatrics, University of Toronto and the Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada.,Centre for Global Child Health, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada.,Child Health Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, 686 Bay Street, Toronto, ON, Canada
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