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Emgård M, Andersson M, Gonzales-Siles L, Msuya SE, Nyombi BM, Nordén R, Muro F, Lindh M, Andersson R, Skovbjerg S. Co-occurrence of bacteria and viruses and serotype distribution of Streptococcus pneumoniae in the nasopharynx of Tanzanian children below 2 years of age following introduction of the PCV13. Front Public Health 2024; 12:1298222. [PMID: 38317802 PMCID: PMC10839969 DOI: 10.3389/fpubh.2024.1298222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Pneumococcal conjugate vaccines have reduced severe disease attributed to vaccine-type pneumococci in children. However, the effect is dependent on serotype distribution in the population and disease development may be influenced by co-occurrence of viral and bacterial pathogens in the nasopharynx. Methods Following introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Tanzania we performed repeated cross-sectional surveys, including 775 children below 2 years of age attending primary healthcare centers. All children were sampled from nasopharynx and pneumococci were detected by single-target PCR. Pneumococcal serotypes/groups and presence of viruses and other bacteria were determined by two multiplex PCR assays. Results The prevalence of PCV13 vaccine-type pneumococci decreased by 50%, but residual vaccine-types were still detected in 21% of the children 2 years after PCV13 introduction. An increase in the non-vaccine-type 15 BC was observed. Pneumococci were often co-occurring with Haemophilus influenzae, and detection of rhino/enterovirus was associated with higher pneumococcal load. Discussion We conclude that presence of residual vaccine-type and emerging non-vaccine-type pneumococci in Tanzanian children demand continued pneumococcal surveillance. High co-occurrence of viral and bacterial pathogens may contribute to the disease burden and indicate the need of multiple public health interventions to improve child health in Tanzania.
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Affiliation(s)
- Matilda Emgård
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sia E. Msuya
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Balthazar M. Nyombi
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Florida Muro
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
- Department of Community Medicine, Kilimanjaro Christian Medical Center (KCMC), Moshi, Tanzania
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rune Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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2
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Bennett JC, Emanuels A, Heimonen J, O'Hanlon J, Hughes JP, Han PD, Chow EJ, Ogokeh CE, Rolfes MA, Lockwood CM, Pfau B, Uyeki TM, Shendure J, Hoag S, Fay K, Lee J, Sibley TR, Rogers JH, Starita LM, Englund JA, Chu HY. Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic. Front Pediatr 2023; 11:1198278. [PMID: 37484765 PMCID: PMC10361771 DOI: 10.3389/fped.2023.1198278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Background Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic. Methods From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households. Results We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29). Conclusion Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults.
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Affiliation(s)
- Julia C. Bennett
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Military and Health Research Foundation, Laurel, MD, United States
| | - Eric J. Chow
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Communicable Disease Epidemiology and Immunizations Section, Prevention Division, Public Health – Seattle & King County, Seattle, WA, United States
| | - Constance E. Ogokeh
- Military and Health Research Foundation, Laurel, MD, United States
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Melissa A. Rolfes
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christine M. Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Timothy M. Uyeki
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Samara Hoag
- Student Health Services, Seattle Public Schools, Seattle, WA, United States
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Julia H. Rogers
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Janet A. Englund
- Seattle Children’s Research Institute, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, United States
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3
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Kontro MH, Kirsi M, Laitinen SK. Exposure to bacterial and fungal bioaerosols in facilities processing biodegradable waste. Front Public Health 2022; 10:789861. [PMID: 36466510 PMCID: PMC9708704 DOI: 10.3389/fpubh.2022.789861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The aim of the study was to determine the exposure of workers within biodegradable waste processing facilities to bacteria and fungi to identify any exposures of potential concern to health. Occupational measurements were performed in six composting and three bioenergy (bioethanol or methane/biogas) producing facilities. Bioaerosols were measured from breathing zones with Button aerosol or open face cassette filter samplers, and swab specimens were taken from the nasal mucous membranes of the workers. Aspergillus fumigatus, Bacillus cereus group, Campylobacter spp., Salmonella spp., Streptomyces spp., and Yersinia spp. were determined by real-time polymerase chain reaction (qPCR). A. fumigatus, and mesophilic and thermophilic actinobacteria were also cultivated from filters. Bacterial airborne endotoxins collected by IOM samplers were analyzed using a Limulus assay. Bioaerosol levels were high, especially in composting compared to bioenergy producing facilities. Endotoxin concentrations in composting often exceeded the occupational exposure value of 90 EU/m3, which may be harmful to the health. In addition to endotoxins, the concentrations of A. fumigatus (up to 2.4 × 105 copies/m3) and actinobacteria/Streptomyces spp. (up to 1.6 × 106 copies/m3) in the air of composting facilities were often high. Microbial and endotoxin concentrations were typically highest in waste reception and pre-treatment, equal or decreased during processing and handling of treated waste, and lowest in wheel loader cabins and control rooms/outdoors. Still, the parameters measured in wheel loader cabins were often higher than in the control sites, which suggests that the use of preventive measures could be improved. B. cereus group, Salmonella spp., and Yersinia spp. were rarely detected in bioaerosols or nasal swabs. Although Campylobacter spp. DNA was rarely detected in air, as a new finding, Campylobacter ureolyticus DNA was frequently detected in the nasal mucous membranes of workers, based on partial 16S rDNA sequencing. Moreover, especially A. fumigatus and C. ureolyticus spp. DNA concentrations in swabs after the work shift were significantly higher than before the shift, which indicates their inhalation or growth during the work shift. Microbial qPCR analysis of bioaerosols and swab samples of nasal mucosa allowed measuring exposure in various work operations and during the work shift, identifying problems for health risk assessment to improve working conditions, and evaluating the effectiveness of preventive measures and personal protection of workers.
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Affiliation(s)
- Merja H. Kontro
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - Maija Kirsi
- Work Environment Laboratories, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Sirpa K. Laitinen
- Department of Occupational Safety, Finnish Institute of Occupational Health, Helsinki, Finland,*Correspondence: Sirpa K. Laitinen
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Yasuda I, Suzuki M, Maeda H, Terada M, Sando E, Ng CFS, Otomaru H, Yoshida LM, Morimoto K. Respiratory virus detection in the upper respiratory tract of asymptomatic, community-dwelling older people. BMC Infect Dis 2022; 22:411. [PMID: 35484482 PMCID: PMC9047617 DOI: 10.1186/s12879-022-07355-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background The prevalence of virus positivity in the upper respiratory tract of asymptomatic community-dwelling older people remains elusive. Our objective was to investigate the prevalence of respiratory virus PCR positivity in asymptomatic community-dwelling older people using saliva samples and nasopharyngeal and oropharyngeal swabs. Methods We analyzed 504 community-dwelling adults aged ≥ 65 years who were ambulatory and enrolled in a cross-sectional study conducted from February to December 2018 in Nagasaki city, Japan. Fourteen respiratory viruses were identified in saliva, nasopharyngeal and oropharyngeal samples using multiplex PCR assays. Results The prevalences of PCR positivity for rhinovirus, influenza A, enterovirus and any respiratory virus were 12.9% (95% CI: 10.1–16.1%), 7.1% (95% CI: 5.1–9.8%), 6.9% (95% CI: 4.9–9.5%) and 25.2% (95% CI: 21.5–29.2%), respectively. Rhinovirus was detected in 21.5% of subjects, influenza A in 38.9% of subjects, enterovirus in 51.4% of subjects and any virus in 32.3% of subjects using only saliva sampling. Conclusions The prevalences of several respiratory viruses were higher than the percentages reported previously in pharyngeal samples from younger adults. Saliva sampling is a potentially useful method for respiratory virus detection in asymptomatic populations. Supplementary information The online version contains supplementary material available at 10.1186/s12879-022-07355-w.
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Affiliation(s)
- Ikkoh Yasuda
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan.,Department of General Internal Medicine and Infectious Diseases, Kita-Fukushima Medical Center, Fukushima, Japan
| | - Motoi Suzuki
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruka Maeda
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Mayumi Terada
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Nijigaoka Hospital, Nagasaki, Japan
| | - Eiichiro Sando
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan.,Department of General Internal Medicine and Infectious Diseases, Kita-Fukushima Medical Center, Fukushima, Japan
| | - Chris Fook Sheng Ng
- Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Hirono Otomaru
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Konosuke Morimoto
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Department of Respiratory Infections, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Nijigaoka Hospital, Nagasaki, Japan.
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5
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Peña B, Ochoa M, Flores O, Gil AI, Ecker L, Cornejo R, Lanata CF, Howard LM, Grijalva CG. Concordance in RT-PCR detection of SARS-CoV-2 between samples preserved in viral and bacterial transport medium. J Virol Methods 2022; 304:114522. [PMID: 35278534 PMCID: PMC8905882 DOI: 10.1016/j.jviromet.2022.114522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
Background While the detection of SARS-CoV-2 in samples preserved in viral transport medium (VTM) by RT-PCR is a standard diagnostic method, this may preclude the study of bacterial respiratory pathogens from the same specimen. It is unclear if the use of skim milk, tryptone, glucose, and glycerin (STGG) transport media, used for study of respiratory bacteria, allows an efficient and concurrent study of SARS-CoV-2 infections. Objectives To determine the concordance in SARS-CoV-2 detection by real time RT-PCR between paired nasopharyngeal (NP) swabs preserved in STGG and nasal (NS) swabs preserved in VTM. Study design Paired samples of NP and NS swabs were collected between December 2020 and March 2021 from a prospective longitudinal cohort study of 44 households and 132 participants from a peri-urban community (Lima, Peru). NP and NS swabs were taken from all participants once and twice per week, respectively, independent of respiratory symptoms. STGG medium was used for NP samples and VTM for NS samples. Samples were analyzed for SARS-CoV-2 by RT-PCR for N, S and ORF1ab targets. We calculated the concordance in detections between sample types and compared the RT-PCR cycle thresholds (Ct). Results Among the 148 paired samples, we observed a high concordance in detections between NP and NS samples (agreement = 94.59%; Kappa = 0.79). Median Ct values were statistically similar between sample types for each RT-PCR target: N, S and ORF1ab (p = 0.11, p = 0.71 and p = 0.11, respectively). Conclusions NP swabs collected in STGG medium are reliable alternatives to nasal swabs collected in VTM for the study of SARS-CoV-2.
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6
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Lopez SMC, Shaikh N, Johnson M, Liu H, Martin JM, Williams JV. Viral Coinfection and Nasal Cytokines in Children With Clinically Diagnosed Acute Sinusitis. Front Pediatr 2022; 9:783665. [PMID: 35096705 PMCID: PMC8791629 DOI: 10.3389/fped.2021.783665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Children with no pathogenic bacteria in the nasopharynx are unlikely to have acute bacterial sinusitis. We evaluated whether information on clinical presentation, viral co-detection, and mucosal cytokine levels could be used to predict presence of bacteria in the nasopharynx. Method: We obtained nasopharyngeal (NP) swabs from children diagnosed with acute sinusitis. NP swabs were processed for bacterial culture, viral PCR testing, and cytokine expression. We examined whether results of the bacterial culture could be predicted based on the presence of clinical information, presence of viruses or mucosal cytokine levels. Results: We enrolled 174 children; 123 (71%) had a positive culture for potentially pathogenic bacteria and 51 (29%) had normal flora. 122/174 (70%) tested positive for one or more viruses. Compared to children with normal flora, children with pathogenic bacteria were more likely to have viruses (p < 0.01), but this relationship disappeared when we adjusted for age. Children with pathogenic bacteria in their nasopharynx and children with normal flora had similar levels of nasal cytokines. Conclusion: In children with clinically diagnosed acute sinusitis, clinical presentation, levels of nasal cytokines, and presence of viruses do not differentiate children with and without pathogenic bacteria in their nasopharynx.
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Affiliation(s)
- Santiago M. C. Lopez
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, United States
- Sanford Research, Environmental Influences on Health and Disease Group, Sioux Falls, SD, United States
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Hui Liu
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2020; 68:e1-e47. [PMID: 30566567 DOI: 10.1093/cid/ciy866] [Citation(s) in RCA: 332] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital.,University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada.,Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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8
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Ma ZY, Deng H, Hua LD, Lei W, Zhang CB, Dai QQ, Tao WJ, Zhang L. Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection. BMC Infect Dis 2020; 20:168. [PMID: 32087697 PMCID: PMC7036252 DOI: 10.1186/s12879-020-4900-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.
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Affiliation(s)
- Zhan-Ying Ma
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Li-Dong Hua
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Chang-Bin Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Qi-Qiang Dai
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Wei-Jing Tao
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
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9
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Respiratory syncytial, parainfluenza and influenza virus infection in young children with acute lower respiratory infection in rural Gambia. Sci Rep 2019; 9:17965. [PMID: 31784567 PMCID: PMC6884537 DOI: 10.1038/s41598-019-54059-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/23/2019] [Indexed: 01/06/2023] Open
Abstract
Respiratory viral infections contribute significantly to morbidity and mortality worldwide, but representative data from sub-Saharan Africa are needed to inform vaccination strategies. We conducted population-based surveillance in rural Gambia using standardized criteria to identify and investigate children with acute lower respiratory infection (ALRI). Naso- and oropharyngeal swabs were collected. Each month from February through December 2015, specimens from 50 children aged 2–23 months were randomly selected to test for respiratory syncytial (RSV), parainfluenza (PIV) and influenza viruses. The expected number of viral-associated ALRI cases in the population was estimated using statistical simulation that accounted for the sampling design. RSV G and F proteins and influenza hemagglutinin genes were sequenced. 2385 children with ALRI were enrolled, 519 were randomly selected for viral testing. One or more viruses were detected in 303/519 children (58.4%). RSV-A was detected in 237 and RSV-B in seven. The expected incidence of ALRI associated with RSV, PIV or influenza was 140 cases (95% CI, 131–149) per 1000 person-years; RSV incidence was 112 cases (95% CI, 102–122) per 1000 person-years. Multiple strains of RSV and influenza circulated during the year. RSV circulated throughout most of the year and was associated with eight times the number of ALRI cases compared to PIV or IV. Gambian RSV viruses were closely related to viruses detected in other continents. An effective RSV vaccination strategy could have a major impact on the burden of ALRI in this setting.
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Lopez SM, Martin JM, Johnson M, Kurs-Lasky M, Horne WT, Marshall CW, Cooper VS, Williams JV, Shaikh N. A method of processing nasopharyngeal swabs to enable multiple testing. Pediatr Res 2019; 86:651-654. [PMID: 31288247 PMCID: PMC6851467 DOI: 10.1038/s41390-019-0498-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/08/2019] [Accepted: 06/08/2019] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To develop a method to perform multiple tests on a single nasopharyngeal (NP) swab. METHODS We collected a NP swab on children aged 2-12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA-sequencing, which we accomplished by cutting the tip of the swab. RESULTS Of the 174 children enrolled, 126 (72.4%) had a positive bacterial culture and 121 (69.5%) tested positive for a virus. Cytokine measurement, as judged by adequate levels of a housekeeping enzyme (glyceraldehyde 3-phosphate dehydrogenase), appeared successful. From the samples used for 16S ribosomal sequencing we recovered, on average, 16,000 sequences per sample, accounting for a total of 2646 operational taxonomic units across all samples sequenced. Samples used for RNA-sequencing had a mean RNA integrity number of 6.0. Cutting the tip of the swab did not affect the recovery yield for viruses or bacteria, nor did it affect species richness in microbiome analysis. CONCLUSION We describe a minimally invasive sample collection protocol that allows for multiple diagnostic and research investigations in young children.
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Affiliation(s)
- Santiago M.C. Lopez
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marcia Kurs-Lasky
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - William T. Horne
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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11
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Nguyen VH, Russell FM, Dance DA, Vilivong K, Phommachan S, Syladeth C, Lai J, Lim R, Morpeth M, Mayxay M, Newton PN, De Lamballerie X, Dubot-Pérès A. Nasal or throat sampling is adequate for the detection of the human respiratory syncytial virus in children with acute respiratory infections. J Med Virol 2019; 91:1602-1607. [PMID: 31050005 PMCID: PMC6772119 DOI: 10.1002/jmv.25496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 11/30/2022]
Abstract
Human respiratory syncytial virus (HRSV) is one of the most important causes of acute respiratory infections (ARI) in young children. HRSV diagnosis is based on the detection of the virus in respiratory specimens. Nasopharyngeal swabbing is considered the preferred method of sampling, although there is limited evidence of the superiority of nasopharyngeal swabs (NPS) over the less invasive nasal (NS) and throat (TS) swabs for virus detection by real‐time reverse transcription quantitative polymerase chain reaction (RT‐qPCR). In the current study, we compared the three swabbing methods for the detection of HRSV by RT‐qPCR in children hospitalized with ARI at Mahosot Hospital, Vientiane, Laos. In 2014, NS, NPS, and TS were collected from 288 children. All three samples were tested for HRSV by RT‐qPCR; 141 patients were found positive for at least one sample. Almost perfect agreements (κ > 0.8) between the swabs, compared two by two, were observed. Detection rates for the three swabs (between 93% and 95%) were not significantly different, regardless of the clinical presentation. Our findings suggest that the uncomfortable and technically more demanding NPS method is not mandatory for HRSV detection by RT‐qPCR.
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Affiliation(s)
- Van Hoan Nguyen
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Fiona M Russell
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - David Ab Dance
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Keoudomphone Vilivong
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Souphatsone Phommachan
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Chanthaphone Syladeth
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Jana Lai
- Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Ruth Lim
- Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Melinda Morpeth
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Mayfong Mayxay
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Institute of Research and Education Development, University of Health Sciences, Vientiane, Lao PDR
| | - Paul N Newton
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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12
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2019; 68. [PMID: 30566567 PMCID: PMC6653685 DOI: 10.1093/cid/ciy866 10.1093/cid/ciz044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital
- University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada
- Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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13
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Wouters Y, Keyaerts E, Rector A, Van Even E, Vissers S, Koletzki D, Pattery T, Rousseau E, Van Ranst M, Laffut W. Comparison of the Idylla™ Respiratory (IFV-RSV) panel with the GeneXpert Xpert® Flu/RSV assay: a retrospective study with nasopharyngeal and midturbinate samples. Diagn Microbiol Infect Dis 2018; 94:33-37. [PMID: 30638655 DOI: 10.1016/j.diagmicrobio.2018.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/28/2018] [Accepted: 11/23/2018] [Indexed: 11/15/2022]
Abstract
The objective of this study was to compare the performance of the Idylla™ Respiratory (IFV-RSV) panel to the GeneXpert Xpert® Flu/RSV assay and establish the performance of a midturbinate swab compared to nasopharyngeal sampling. Considering GeneXpert® assay as imperfect reference standard, a positive percentage agreement between both assays of 98-100% for influenza A and 96-99% for influenza B could be calculated when 354 nasopharyngeal and 325 midturbinate swabs were retrospectively analyzed. Comparing midturbinate samples to nasopharyngeal specimens of 321 subjects, positive percentage agreement varied from 42% to 94% depending on both target virus and assay used. Negative percentage agreements ranged from 98% to 100% for both methods and sample type comparison. The Idylla™ assay showed excellent performance compared to the GeneXpert® assay for the detection of influenza virus. The study also showed a slightly better performance for nasopharyngeal sampling compared to the use of a midturbinate swab.
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Affiliation(s)
- Yannick Wouters
- Department of Microbiology, Heilig Hart Hospital Lier, Mechelsestraat 24, 2500 Lier, Belgium
| | - Els Keyaerts
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ellen Van Even
- Department of Microbiology, Heilig Hart Hospital Lier, Mechelsestraat 24, 2500 Lier, Belgium
| | - Steven Vissers
- Department of Anaesthesiology and Reanimation, Heilig Hart Hospital Lier, Mechelsestraat 24, 2500 Lier, Belgium
| | - Diana Koletzki
- Janssen Diagnostics a division of Janssen Pharmaceutica NV, Antwerpseweg 15, 2340 Beerse, Belgium
| | - Theresa Pattery
- Janssen Diagnostics a division of Janssen Pharmaceutica NV, Antwerpseweg 15, 2340 Beerse, Belgium
| | - Els Rousseau
- Janssen Diagnostics a division of Janssen Pharmaceutica NV, Antwerpseweg 15, 2340 Beerse, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Wim Laffut
- Department of Microbiology, Heilig Hart Hospital Lier, Mechelsestraat 24, 2500 Lier, Belgium.
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14
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Comparison of Bacterial Culture Results Obtained from Nasopharyngeal and Midturbinate Swabs in Children With Upper Respiratory Tract Infection Symptoms. Pediatr Infect Dis J 2018; 37:e275-e277. [PMID: 29742648 DOI: 10.1097/inf.0000000000002027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Paired nasopharynx and midturbinate swabs were obtained from 96 children (mean age: 2.45 years) with upper respiratory tract symptoms. Of these, 38.5% were colonized with Streptococcus pneumoniae only, 16.7% with Haemophilus influenzae only and 9.4% with both bacteria. Bacterial cultures from paired nasopharynx and midturbinate swabs demonstrated agreement for S. pneumoniae (κ = 0.75), H. influenzae (κ = 0.59) and for both pathogens (κ = 0.62). This report compares the results of bacterial cultures obtained from the nasopharynx and midturbinate specimens in children with upper respiratory tract infections.
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15
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Howard LM, Johnson M, Gil AI, Pekosz A, Griffin MR, Edwards KM, Lanata CF, Grijalva CG, Williams JV. A novel real-time RT-PCR assay for influenza C tested in Peruvian children. J Clin Virol 2017; 96:12-16. [PMID: 28917132 PMCID: PMC5901714 DOI: 10.1016/j.jcv.2017.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 12/04/2022]
Abstract
BACKGROUND Influenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases. OBJECTIVES To develop a sensitive and specific real-time RT-PCR assay for ICV that allows for rapid and accurate detection in a clinical or research setting. STUDY DESIGN Multiple ICV sequences obtained from GenBank were analyzed, including 141 hemagglutinin-esterase (HE), 106 matrix (M), and 97 nucleoprotein (NP) sequences. Primers and probes were designed based on conserved regions. Multiple primer-probe sets were tested against multiple ICV strains. RESULTS The ICV M and NP genes offered the most conserved sequence regions. Primers and probes based on newer sequence data offered enhanced detection of ICV, especially for low titer specimens. An NP-targeted assay yielded the best performance and was capable of detecting 10-100 RNA copies per reaction. The NP assay detected multiple clinical isolates of ICV collected in a field epidemiology study conducted in Peru. CONCLUSIONS We report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.
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Affiliation(s)
- Leigh M Howard
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States; Vanderbilt Vaccine Research Program, Nashville, TN, United States
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, United States
| | - Ana I Gil
- Instituto de Investigacion Nutricional, Lima, Peru
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, United States
| | - Marie R Griffin
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Kathryn M Edwards
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States; Vanderbilt Vaccine Research Program, Nashville, TN, United States
| | - Claudio F Lanata
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States; Instituto de Investigacion Nutricional, Lima, Peru
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, United States.
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16
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Steens A, Milhano N, Aaberge IS, Vestrheim DF. In vitro and in vivo comparison of transport media for detecting nasopharyngeal carriage of Streptococcus pneumoniae. PeerJ 2016; 4:e2449. [PMID: 27688966 PMCID: PMC5036082 DOI: 10.7717/peerj.2449] [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: 06/27/2016] [Accepted: 08/15/2016] [Indexed: 11/20/2022] Open
Abstract
Background As a standard method for pneumococcal carriage studies, the World Health Organization recommends nasopharyngeal swabs be transported and stored at cool temperatures in a medium containing skim-milk, tryptone, glucose and glycerol (STGG). An enrichment broth used for transport at room temperature in three carriage studies performed in Norway may have a higher sensitivity than STGG. We therefore compared the media in vitro and in vivo. Methods For the in vitro component, three strains (serotype 4, 19F and 3) were suspended in STGG and enrichment broth. Recovery was compared using latex agglutination, quantification of bacterial loads by real-time PCR of the lytA gene, and counting colonies from incubated plates. For the in vivo comparison, paired swabs were obtained from 100 children and transported in STGG at cool temperatures or in enrichment broth at room temperature. Carriage was identified by latex agglutination and confirmed by Quellung reaction. Results In vitro, the cycle threshold values obtained by PCR did not differ between the two media (p = 0.853) and no clear difference in colony counts was apparent after incubation (p = 0.593). In vivo, pneumococci were recovered in 46% of swabs transported in STGG and 51% of those transported in enrichment broth (Kappa statistic 0.90, p = 0.063). Discussion Overall, no statistical differences in sensitivity were found between STGG and enrichment broth. Nevertheless, some serotype differences were observed and STGG appeared slightly less sensitive than enrichment broth for detection of nasopharyngeal carriage of pneumococci by culturing. We recommend the continued use of STGG for transport and storage of nasopharyngeal swabs in pneumococcal carriage studies for the benefit of comparability between studies and settings, including more resource-limited settings.
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Affiliation(s)
- Anneke Steens
- Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Natacha Milhano
- Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ingeborg S Aaberge
- Infection Control and Environmental Health, Norwegian Institute of Public Health , Oslo , Norway
| | - Didrik F Vestrheim
- Infection Control and Environmental Health, Norwegian Institute of Public Health , Oslo , Norway
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Abstract
Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.
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Affiliation(s)
- Stephen B Greenberg
- Department of Medicine, Ben Taub Hospital, Baylor College of Medicine, Houston, Texas
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18
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Howard LM, Johnson M, Gil AI, Griffin MR, Edwards KM, Lanata CF, Williams JV, Grijalva CG. Molecular Epidemiology of Rhinovirus Detections in Young Children. Open Forum Infect Dis 2016; 3:ofw001. [PMID: 26900577 PMCID: PMC4759584 DOI: 10.1093/ofid/ofw001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/01/2016] [Indexed: 02/06/2023] Open
Abstract
Background. Human rhinoviruses (HRVs) are frequently detected in children with acute respiratory illnesses (ARIs) but also in asymptomatic children. We compared features of ARI with HRV species (A, B, C) and determined genotypes associated with repeated HRV detections within individuals. Methods. We used clinical data and respiratory samples obtained from children <3 years old during weekly active household-based surveillance. A random subset of samples in which HRV was detected from individuals during both ARI and an asymptomatic period within 120 days of the ARI were genotyped. Features of ARI were compared among HRV species. Concordance of genotype among repeated HRV detections within individuals was assessed. Results. Among 207 ARI samples sequenced, HRV-A, HRV-B, and HRV-C were detected in 104 (50%), 20 (10%), and 83 (40%), respectively. Presence of fever, decreased appetite, and malaise were significantly higher in children with HRV-B. When codetections with other viruses were excluded (n = 155), these trends persisted, but some did not reach statistical significance. When 58 paired sequential HRV detections during asymptomatic and ARI episodes were sequenced, only 9 (16%) were identical genotypes of HRV. Conclusions. Clinical features may differ among HRV species. Repeated HRV detections in young children frequently represented acquisition of new HRV strains.
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Affiliation(s)
- Leigh M Howard
- Division of Infectious Diseases, Department of Pediatrics; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Monika Johnson
- Department of Pediatrics , University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center , Pennsylvania
| | - Ana I Gil
- Instituto de Investigacion Nutricional , Lima , Peru
| | - Marie R Griffin
- Department of Health Policy , Vanderbilt University, Tennessee
| | - Kathryn M Edwards
- Division of Infectious Diseases, Department of Pediatrics; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Claudio F Lanata
- Division of Infectious Diseases, Department of Pediatrics; Instituto de Investigacion Nutricional, Lima, Peru
| | - John V Williams
- Department of Pediatrics , University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center , Pennsylvania
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Abstract
BACKGROUND Viruses are commonly detected in children with acute respiratory illnesses (ARIs) and in asymptomatic children. Longitudinal studies of viral detections during asymptomatic periods surrounding ARI could facilitate interpretation of viral detections but are currently scant. METHODS We used reverse transcription polymerase chain reaction to analyze respiratory samples from young Andean children for viruses during asymptomatic periods within 8-120 days of index ARI (cough or fever). We compared viral detections over time within children and explored reverse transcription polymerase chain reaction cycle thresholds (CTs) as surrogates for viral loads. RESULTS At least 1 respiratory virus was detected in 367 (43%) of 859 samples collected during asymptomatic periods, with more frequent detections in periods with rhinorrhea (49%) than those without (34%, P < 0.001). Relative to index ARI with human rhinovirus (HRV), adenovirus (AdV), respiratory syncytial virus (RSV) and parainfluenza virus detected, the same viruses were also detected during 32, 22, 10 and 3% of asymptomatic periods, respectively. RSV was only detected 8-30 days after index RSV ARI, whereas HRV and AdV were detected throughout asymptomatic periods. Human metapneumovirus and influenza were rarely detected during asymptomatic periods (<3%). No significant differences were observed in the CT for HRV or AdV during asymptomatic periods relative to ARI. For RSV, CTs were significantly lower during ARI relative to the asymptomatic period (P = 0.03). CONCLUSIONS These findings indicate that influenza, human metapneumovirus, parainfluenza virus and RSV detections in children with an ARI usually indicate a causal relationship. When HRV or AdV is detected during ARI, the causal relationship is less certain.
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Detection and prediction of Streptococcus pneumoniae serotypes directly from nasopharyngeal swabs using PCR. J Med Microbiol 2015; 64:836-844. [DOI: 10.1099/jmm.0.000097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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21
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Long-term survival of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis as isolates and in nasopharyngeal specimens in frozen STGG storage medium. J Microbiol Methods 2015; 114:38-9. [PMID: 25937246 DOI: 10.1016/j.mimet.2015.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 11/22/2022]
Abstract
We evaluated survival in WHO-recommended STGG storage medium of bacteria causing respiratory-tract infection. Streptococcus pneumoniae and Moraxella catarrhalis survived as single and mixed isolates stored at -70°C for 12.5 years, but Haemophilus influenzae less than 4 years. All the bacteria survived in the nasopharyngeal specimens at -70°C for 11 years.
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