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Cane J, Sanderson N, Barnett S, Vaughan A, Pott M, Kapel N, Morgan M, Jesuthasan G, Samuel R, Ehsaan M, Boothe H, Haduli E, Studley R, Rourke E, Diamond I, Fowler T, Watson C, Stoesser N, Walker AS, Street T, Eyre DW. Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23. J Infect 2024; 88:106164. [PMID: 38692359 PMCID: PMC11101610 DOI: 10.1016/j.jinf.2024.106164] [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: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVES We evaluated Nanopore sequencing for influenza surveillance. METHODS Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification. RESULTS From 941 infections, successful sequencing was achieved in 292/388 (75 %) available Oxfordshire samples: 231 (79 %) A/H3N2, 53 (18 %) A/H1N1, and 8 (3 %) B/Victoria and in 53/113 (47 %) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141, 88 %); 36/39 (92 %) Illumina vs. Nanopore comparisons were identical, and 3 (8 %) differed by 1 variant. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941 (90 %) Oxfordshire infections were community-acquired. 63/88 (72 %) potentially healthcare-associated cases shared a hospital ward with ≥ 1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤ 5 SNPs, of these, 5 (63 %) involved potential sources that were also hospital-acquired. CONCLUSIONS Nanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.
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Affiliation(s)
- Jennifer Cane
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Sophie Barnett
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Ali Vaughan
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Megan Pott
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Natalia Kapel
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Gerald Jesuthasan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Reggie Samuel
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Muhammad Ehsaan
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Hugh Boothe
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Eric Haduli
- Berkshire and Surrey Pathology Services, Camberley, United Kingdom
| | - Ruth Studley
- Office for National Statistics, Newport, United Kingdom
| | - Emma Rourke
- Office for National Statistics, Newport, United Kingdom
| | - Ian Diamond
- Office for National Statistics, Newport, United Kingdom
| | - Tom Fowler
- UK Health Security Agency, United Kingdom; William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | | | - Nicole Stoesser
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ann Sarah Walker
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Teresa Street
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - David W Eyre
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom; Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom.
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Kim SR, Waghmare A, Hijano DR. Approach to hematopoietic cell transplant candidates with respiratory viral detection. Front Pediatr 2024; 11:1339239. [PMID: 38304442 PMCID: PMC10830789 DOI: 10.3389/fped.2023.1339239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.
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Affiliation(s)
- Sara R. Kim
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Alpana Waghmare
- Division of Pediatric Infectious Diseases, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Diego R. Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, United States
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3
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Soto R, Paul L, Porucznik CA, Xie H, Stinnett RC, Briggs B, Biggerstaff M, Stanford J, Schlaberg R. Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study. JMIR Form Res 2023; 7:e32848. [PMID: 37999952 DOI: 10.2196/32848] [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: 03/19/2022] [Revised: 02/16/2023] [Accepted: 08/09/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories. Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing, expand testing capacity, and reduce opportunities for exposure of health professionals in the context of a pandemic. OBJECTIVE We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff. METHODS Each adult participant collected 1 nasal swab, sampling both nares with the single swab, after which they collected 1 nasal swab from 1 child. After all the participant samples were collected for the household, the research staff member collected a separate single duplicate sample from each individual. Immediately after the sample collection, the adult participants completed a questionnaire about the acceptability of the sampling procedures. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis. RESULTS In total, 21 households participated in the study, each with 1 adult and 1 child, yielding 42 individuals with paired samples. Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by RNA sequencing demonstrated that adequate collection technique was achieved by brief instructions. CONCLUSIONS Our results support the feasibility of a scalable and convenient means for the identification of respiratory viruses and implementation in pandemic preparedness for novel respiratory pathogens.
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Affiliation(s)
- Raymond Soto
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Litty Paul
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Christina A Porucznik
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Heng Xie
- IDbyDNA, Salt Lake City, UT, United States
| | | | | | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joseph Stanford
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Robert Schlaberg
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
- IDbyDNA, Salt Lake City, UT, United States
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4
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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Cho SJ, Kim SH, Lee H, Lee YU, Mun J, Park S, Park J, Park JS, Lee K, Lee CM, Seo J, Kim Y, Chung YS. Re-Emergence of HMPV in Gwangju, South Korea, after the COVID-19 Pandemic. Pathogens 2023; 12:1218. [PMID: 37887734 PMCID: PMC10609798 DOI: 10.3390/pathogens12101218] [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: 07/29/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
The non-pharmaceutical interventions implemented to prevent the spread of COVID-19 have affected the epidemiology of other respiratory viruses. In South Korea, Human metapneumovirus (HMPV) typically occurs from winter to the following spring; however, it was not detected for two years during the COVID-19 pandemic and re-emerged in the fall of 2022, which is a non-epidemic season. To examine the molecular genetic characteristics of HMPV before and after the COVID-19 pandemic, we analyzed 427 HMPV-positive samples collected in the Gwangju area from 2018 to 2022. Among these, 24 samples were subjected to whole-genome sequencing. Compared to the period before the COVID-19 pandemic, the incidence rate of HMPV in 2022 increased by 2.5-fold. Especially in the age group of 6-10 years, the incidence rate increased by more than 4.5-fold. In the phylogenetic analysis results, before the COVID-19 pandemic, the A2.2.2 lineage was predominant, while in 2022, the A2.2.1 and B2 lineage were observed. The non-pharmaceutical interventions implemented after COVID-19, such as social distancing, have reduced opportunities for exposure to HMPV, subsequently leading to decreased acquisition of immunity. As a result, HMPV occurred during non-epidemic seasons, influencing the age distribution of its occurrences.
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Affiliation(s)
- Sun-Ju Cho
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Sun-Hee Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Hongsu Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yeong-Un Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jeongeun Mun
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Sujung Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jungwook Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Ji-Su Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Kwangho Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Cheong-mi Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jinjong Seo
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yonghwan Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yoon-Seok Chung
- Division of High-Risk Pathogen, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju 28159, Republic of Korea
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Williams TGS, Snell LB, Alder C, Charalampous T, Alcolea-Medina A, Sehmi JK, Al-Yaakoubi N, Humayun G, Miah S, Lackenby A, Zambon M, Batra R, Douthwaite S, Edgeworth JD, Nebbia G. Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance. Microb Genom 2023; 9:mgen001083. [PMID: 37590039 PMCID: PMC10483427 DOI: 10.1099/mgen.0.001083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Rapid respiratory viral whole genome sequencing (WGS) in a clinical setting can inform real-time outbreak and patient treatment decisions, but the feasibility and clinical utility of influenza A virus (IAV) WGS using Nanopore technology has not been demonstrated. A 24 h turnaround Nanopore IAV WGS protocol was performed on 128 reverse transcriptase PCR IAV-positive nasopharyngeal samples taken over seven weeks of the 2022-2023 winter influenza season, including 25 from patients with nosocomial IAV infections and 102 from patients attending the Emergency Department. WGS results were reviewed collectively alongside clinical details for interpretation and reported to clinical teams. All eight segments of the IAV genome were recovered for 97/128 samples (75.8 %) and the haemagglutinin gene for 117/128 samples (91.4 %). Infection prevention and control identified nosocomial IAV infections in 19 patients across five wards. IAV WGS revealed two separate clusters on one ward and excluded transmission across different wards with contemporaneous outbreaks. IAV WGS also identified neuraminidase inhibitor resistance in a persistently infected patient and excluded avian influenza in a sample taken from an immunosuppressed patient with a history of travel to Singapore which had failed PCR subtyping. Accurate IAV genomes can be generated in 24 h using a Nanopore protocol accessible to any laboratory with SARS-CoV-2 Nanopore sequencing capacity. In addition to replicating reference laboratory surveillance results, IAV WGS can identify antiviral resistance and exclude avian influenza. IAV WGS also informs management of nosocomial outbreaks, though molecular and clinical epidemiology were concordant in this study, limiting the impact on decision-making.
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Affiliation(s)
- Tom G. S. Williams
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Luke B. Snell
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Christopher Alder
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Themoula Charalampous
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Infection Sciences, Synnovis, London, UK
| | | | - Noor Al-Yaakoubi
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gul Humayun
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Shahjahan Miah
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Angie Lackenby
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Maria Zambon
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Rahul Batra
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
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7
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Miah M, Hossain ME, Hasan R, Alam MS, Puspo JA, Hasan MM, Islam A, Chowdhury S, Rahman MZ. Culture-Independent Workflow for Nanopore MinION-Based Sequencing of Influenza A Virus. Microbiol Spectr 2023; 11:e0494622. [PMID: 37212605 PMCID: PMC10269883 DOI: 10.1128/spectrum.04946-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 05/23/2023] Open
Abstract
Whole-genome sequencing (WGS) of influenza A virus (IAV) is crucial for identifying diverse subtypes and newly evolved variants and for selecting vaccine strains. In developing countries, where facilities are often inadequate, WGS is challenging to perform using conventional next-generation sequencers. In this study, we established a culture-independent, high-throughput native barcode amplicon sequencing workflow that can sequence all influenza subtypes directly from a clinical specimen. All segments of IAV in 19 clinical specimens, irrespective of their subtypes, were amplified simultaneously using a two-step reverse transcriptase PCR (RT-PCR) system. First, the library was prepared using the ligation sequencing kit, barcoded individually using the native barcodes, and sequenced on the MinION MK 1C platform with real-time base-calling. Then, subsequent data analyses were performed with the appropriate tools. WGS of 19 IAV-positive clinical samples was carried out successfully with 100% coverage and 3,975-fold mean coverage for all segments. This easy-to-install and low-cost capacity-building protocol took only 24 h complete from extracting RNA to obtaining finished sequences. Overall, we developed a high-throughput portable sequencing workflow ideal for resource-limited clinical settings, aiding in real-time surveillance, outbreak investigation, and the detection of emerging viruses and genetic reassortment events. However, further evaluation is required to compare its accuracy with other high-throughput sequencing technologies to validate the widespread application of these findings, including WGS from environmental samples. IMPORTANCE The Nanopore MinION-based influenza sequencing approach we are proposing makes it possible to sequence the influenza A virus, irrespective of its diverse serotypes, directly from clinical and environmental swab samples, so that we are not limited to virus culture. This third-generation, portable, multiplexing, and real-time sequencing strategy is highly convenient for local sequencing, particularly in low- and middle-income countries like Bangladesh. Furthermore, the cost-efficient sequencing method could provide new opportunities to respond to the early phase of an influenza pandemic and enable the timely detection of the emerging subtypes in clinical samples. Here, we meticulously described the entire process that might help the researcher who will follow this methodology in the future. Our findings suggest that this proposed method is ideal for clinical and academic settings and will aid in real-time surveillance and in the detection of potential outbreak agents and newly evolved viruses.
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Affiliation(s)
- Mojnu Miah
- Infectious Diseases Division, ICDDR,B, Dhaka, Bangladesh
| | | | - Rashedul Hasan
- Infectious Diseases Division, ICDDR,B, Dhaka, Bangladesh
| | | | | | | | - Ariful Islam
- EcoHealth Alliance, New York, New York, USA
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, Victoria, Australia
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Wan T, Lauring AS, Valesano AL, Fitzsimmons WJ, Bendall EE, Kaye KS, Petrie JG. Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan. Open Forum Infect Dis 2023; 10:ofad061. [PMID: 36861093 PMCID: PMC9969740 DOI: 10.1093/ofid/ofad061] [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: 10/13/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Background Hospital-acquired influenza virus infection (HAII) can cause severe morbidity and mortality. Identifying potential transmission routes can inform prevention strategies. Methods We identified all hospitalized patients testing positive for influenza A virus at a large, tertiary care hospital during the 2017-2018 and 2019-2020 influenza seasons. Hospital admission dates, locations of inpatient service, and clinical influenza testing information were retrieved from the electronic medical record. Time-location groups of epidemiologically linked influenza patients were defined and contained ≥1 presumed HAII case (first positive ≥48 hours after admission). Genetic relatedness within time-location groups was assessed by whole genome sequencing. Results During the 2017-2018 season, 230 patients tested positive for influenza A(H3N2) or unsubtyped influenza A including 26 HAIIs. There were 159 influenza A(H1N1)pdm09 or unsubtyped influenza A-positive patients identified during the 2019-2020 season including 33 HAIIs. Consensus sequences were obtained for 177 (77%) and 57 (36%) of influenza A cases in 2017-2018 and 2019-2020, respectively. Among all influenza A cases, there were 10 time-location groups identified in 2017-2018 and 13 in 2019-2020; 19 of 23 groups included ≤4 patients. In 2017-2018, 6 of 10 groups had ≥2 patients with sequence data, including ≥1 HAII case. Two of 13 groups met this criteria in 2019-2020. Two time-location groups from 2017-2018 each contained 3 genetically linked cases. Conclusions Our results suggest that HAIIs arise from outbreak transmission from nosocomial sources as well as single infections from unique community introductions.
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Affiliation(s)
- Tiffany Wan
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew L Valesano
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily E Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Keith S Kaye
- Division of Allergy, Immunology and Infectious Diseases, Department of Medicine, Rutgers-Robert Wood Johnson School of Medicine, New Brunswick, New Jersey, USA
| | - Joshua G Petrie
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
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9
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Snell LB, Vink JP, Verlander NQ, Miah S, Lackenby A, Williams D, Mitchell H, Beviz C, Kabia M, Cunningham E, Batra R, Edgeworth JD, Zambon M, Nebbia G. Nosocomial acquisition of influenza is associated with significant morbidity and mortality: Results of a prospective observational study. J Infect Public Health 2022; 15:1118-1123. [PMID: 36137361 PMCID: PMC10166711 DOI: 10.1016/j.jiph.2022.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/04/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022] Open
Abstract
BACKGROUND Nosocomial acquisition of influenza is known to occur but the risk after exposure to a known case and the outcomes after acquisition are poorly defined. METHODS Prospective observational study of patients exposed to influenza from another patient in a multi-site healthcare organisation, with follow-up of 7 days or until discharge, and PCR-confirmation of symptomatic disease. Multivariable analysis was used to investigate association of influenza acquisition with high dependency unit/intensive care unit (HDU/ITU) admission and in-hospital mortality. RESULTS 23/298 (7.7%) contacts of 11 cases were subsequently symptomatic and tested influenza-positive during follow-up. HDU/ITU admission was significantly higher in these secondary cases (6/23, 26%) compared to flu-negative contacts (20/275, 7.2%; p = 0.002). In-hospital mortality was significantly higher in secondary cases (5/23, 21.7%) compared to flu-negative contacts (11/275, 4%; p < 0.001). In multivariable analysis, age (OR 1.25 95% CI: 1.01-1.54, p = 0.02) and being a secondary case (OR 4.77, 95% CI: 1.63-13.9, p = 0.008) were significantly associated with HDU/ITU admission in contacts. Age (OR 1.00, 95% CI: 0.93-1.00, p = 0.02), being a secondary case after exposure to influenza (OR 3.81, 95% CI 1.09-13.3, p = 0.049) and co-morbidity (OR 1.29 per unit increment in the Charlson score, 95% CI 1.02-1.61, p = 0.03) were significantly associated with in-hospital mortality in contacts. CONCLUSIONS Nosocomial acquisition of influenza was significantly associated with increased risk of HDU/ITU admission and in-hospital mortality.
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Affiliation(s)
- L B Snell
- Centre for Clinical Infection and Diagnostics Research, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK.
| | - J P Vink
- Centre for Clinical Infection and Diagnostics Research, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - S Miah
- UK Health Security Agency, Colindale, UK
| | - A Lackenby
- UK Health Security Agency, Colindale, UK
| | - D Williams
- UK Health Security Agency, Colindale, UK
| | - H Mitchell
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK
| | - C Beviz
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK
| | - M Kabia
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK
| | | | - R Batra
- Centre for Clinical Infection and Diagnostics Research, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - J D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK
| | - M Zambon
- UK Health Security Agency, Colindale, UK
| | - G Nebbia
- Centre for Clinical Infection and Diagnostics Research, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Department of Infection, Guy's and St Thomas' NHS Foundation Trust, UK
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10
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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11
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Xi X, Spencer SEF, Hall M, Grabowski MK, Kagaayi J, Ratmann O. Inferring the sources of HIV infection in Africa from deep‐sequence data with semi‐parametric Bayesian Poisson flow models. J R Stat Soc Ser C Appl Stat 2022. [DOI: 10.1111/rssc.12544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoyue Xi
- Department of MathematicsImperial College London LondonUK
| | | | - Matthew Hall
- Big Data Institute, Nuffield Department of MedicineUniversity of Oxford OxfordUK
| | - M. Kate Grabowski
- Department of PathologyJohns Hopkins University BaltimoreMDUSA
- Rakai Health Sciences Program KalisizoUganda
| | - Joseph Kagaayi
- Rakai Health Sciences Program KalisizoUganda
- Makerere University School of Public Health KampalaUganda
| | - Oliver Ratmann
- Department of MathematicsImperial College London LondonUK
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12
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MacCannell T, Batson J, Bonin B, Astha KC, Quenelle R, Strong B, Lin W, Rudman SL, Dynerman D, Ayscue P, Han G, Kistler A, Villarino ME. Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California. Clin Infect Dis 2022; 74:829-835. [PMID: 34328176 PMCID: PMC8385848 DOI: 10.1093/cid/ciab553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between facilities by combining genomic sequencing with epidemiologic investigations enables targeting infection-control interventions. METHODS We conducted weekly surveillance of residents and staff in LTCFs in Santa Clara County, California, with ≥1 confirmed COVID-19 case between March and July 2020. Positive samples were referred for whole-genome sequencing. Epidemiological investigations and phylogenetic analyses of the largest outbreaks (>30 cases) were carried out in 6 LTCFs (Facilities A through F). RESULTS Among the 61 LTCFs in the county, 41 had ≥1 confirmed case during the study period, triggering weekly SARS-CoV-2 testing. The 6 largest outbreaks accounted for 60% of cases and 90% of deaths in LTCFs, although the bed capacity of these facilities represents only 11% of the LTCF beds in the county. Phylogenetic analysis of 196 whole-genome sequences recovered from those facilities showed that each outbreak was monophyletic, with staff and residents sharing a common viral lineage. Outbreak investigations revealed that infected staff members often worked at multiple facilities, and in 1 instance, a staff member infected while working in 1 facility was the likely index case in another. CONCLUSIONS We detected a pattern of rapid and sustained transmission after a single introduction of SARS-CoV-2 in 6 large LTCF outbreaks, with staff playing a key role in transmission within and between facilities. Infection control, testing, and occupational policies to reduce exposure and transmission risk for staff are essential components to keeping facility residents safe.
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Affiliation(s)
- Tara MacCannell
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Brandon Bonin
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - K C Astha
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Rebecca Quenelle
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Betsy Strong
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Wen Lin
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Sarah L Rudman
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | | | | | - George Han
- County of Santa Clara, Public Health Department, San Jose, California, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
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13
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Francis RV, Billam H, Clarke M, Yates C, Tsoleridis T, Berry L, Mahida N, Irving WL, Moore C, Holmes N, Ball JK, Loose M, McClure CP. The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. J Infect Dis 2022; 225:10-18. [PMID: 34555152 PMCID: PMC8522425 DOI: 10.1093/infdis/jiab483] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom's second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.
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Affiliation(s)
- Rodric V Francis
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Harriet Billam
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Mitch Clarke
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Carl Yates
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Louise Berry
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Nikunj Mahida
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - William L Irving
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Christopher Moore
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
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14
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Mathenjwa M, Khidir H, Milford C, Mosery N, Rambally Greener L, Pratt MC, O'Neil K, Harrison A, Bangsberg DR, Safren SA, Smit JA, Psaros C, Matthews LT. Acceptability of an Intervention to Promote Viral Suppression and Serostatus Disclosure for Men Living with HIV in South Africa: Qualitative Findings. AIDS Behav 2022; 26:1-12. [PMID: 34097209 PMCID: PMC8786780 DOI: 10.1007/s10461-021-03278-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 01/15/2023]
Abstract
Men living with HIV (MLWH) often have reproductive goals that can increase HIV-transmission risks to their pregnancy partners. We developed a safer conception intervention for MLWH in South Africa employing cognitive behavioral skills to promote serostatus disclosure, ART uptake, and viral suppression. MLWH were recruited from an HIV clinic near Durban, South Africa, and encouraged to include partners in follow-up visits. Exit in-depth interviews were conducted with eleven men and one female partner. The emerging over-arching theme is that safer conception care mitigates internalized and community-level HIV-stigma among MLWH. Additional related sub-themes include: (1) safer conception care acceptability is high but structural barriers challenge participation; (2) communication skills trainings helped overcome barriers to disclose serostatus; (3) feasibility and perceived effectiveness of strategies informed safer conception method selection. Our findings suggest that offering safer conception care to MLWH is a novel stigma-reducing strategy for motivating HIV prevention and treatment and serostatus disclosure to partners.
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Affiliation(s)
- Mxolisi Mathenjwa
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | | | - Cecilia Milford
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Nzwakie Mosery
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | - Letitia Rambally Greener
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
- Population Services International, South Africa, Johannesburg, South Africa
| | - Madeline C Pratt
- University of Alabama at Birmingham (UAB), Division of Infectious Disease, Birmingham, Alabama, USA
| | | | | | | | | | - Jennifer A Smit
- MRU (MatCH Research Unit), Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Durban, South Africa
| | | | - Lynn T Matthews
- University of Alabama at Birmingham (UAB), Division of Infectious Disease, Birmingham, Alabama, USA.
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15
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Javaid W, Ehni J, Gonzalez-Reiche AS, Carreño JM, Hirsch E, Tan J, Khan Z, Kriti D, Ly T, Kranitzky B, Barnett B, Cera F, Prespa L, Moss M, Albrecht RA, Mustafa A, Herbison I, Hernandez MM, Pak TR, Alshammary HA, Sebra R, Smith ML, Krammer F, Gitman MR, Sordillo EM, Simon V, van Bakel H. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. Clin Infect Dis 2021; 73:e4375-e4383. [PMID: 33252647 PMCID: PMC8653627 DOI: 10.1093/cid/ciaa1781] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures. METHODS We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation. RESULTS During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster. CONCLUSIONS We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks.
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Affiliation(s)
- Waleed Javaid
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Infection Prevention, Mount Sinai Beth Israel, New York, New York, USA
| | - Jordan Ehni
- Department of Infection Prevention, Mount Sinai Beth Israel, New York, New York, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elena Hirsch
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Tan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thanh Ly
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bethany Kranitzky
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Barbara Barnett
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Freddy Cera
- Clinical Laboratory, Mount Sinai Beth Israel, New York, New York, USA
| | - Lenny Prespa
- Clinical Laboratory, Mount Sinai Beth Israel, New York, New York, USA
| | - Marie Moss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ala Mustafa
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ilka Herbison
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew M Hernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Theodore R Pak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hala A Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa R Gitman
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia Mia Sordillo
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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16
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Antonitsch L, Gallob R, Weidinger G, Kettenbach J. New insights and antimicrobial stewardship opportunities in viral pneumonia: five lung ultrasound cases. Wien Klin Wochenschr 2021; 133:1208-1214. [PMID: 34605974 PMCID: PMC8488548 DOI: 10.1007/s00508-021-01946-4] [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: 01/23/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023]
Abstract
Background Antimicrobial stewardship is crucial to avoid antimicrobial resistance in microbes and adverse drug effects in patients. In respiratory infections, however, viral pneumonia is difficult to distinguish from bacterial pneumonia, which explains the overuse of antibiotic therapy in this indication. Cases Five cases of lung consolidation are presented. Lung ultrasound, in conjunction with procalcitonin levels, were used to exclude or corroborate bacterial pneumonia. Conclusion Lung ultrasound is easy to learn and perform and is helpful in guiding diagnosis in unclear cases of pneumonia and may also offer new insights into the spectrum of certain virus diseases. The use of lung ultrasound can raise awareness in clinicians of the need for antimicrobial stewardship and may help to avoid the unnecessary use of antibiotics. Supplementary Information The online version of this article (10.1007/s00508-021-01946-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lukas Antonitsch
- Department of Internal Medicine and Gastroenterology, Landesklinikum Wiener Neustadt, Corvinusring 3-5, 2700, Wiener Neustadt, Austria.
| | - Ronald Gallob
- Department of Anesthesia, Emergency Medicine and Intensive Care, Landesklinikum Wiener Neustadt, Corvinusring 3-5, 2700, Wiener Neustadt, Austria
| | - Gerhard Weidinger
- Department of Internal Medicine and Gastroenterology, Landesklinikum Wiener Neustadt, Corvinusring 3-5, 2700, Wiener Neustadt, Austria
| | - Joachim Kettenbach
- Institute of Diagnostic, Interventional Radiology and Nuclear Medicine, Landesklinikum Wiener Neustadt, Corvinusring 3-5, 2700, Wiener Neustadt, Austria
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17
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Braun KM, Moreno GK, Buys A, Somsen ED, Bobholz M, Accola MA, Anderson L, Rehrauer WM, Baker DA, Safdar N, Lepak AJ, O’Connor DH, Friedrich TC. Viral Sequencing to Investigate Sources of SARS-CoV-2 Infection in US Healthcare Personnel. Clin Infect Dis 2021; 73:e1329-e1336. [PMID: 33857303 PMCID: PMC8083259 DOI: 10.1093/cid/ciab281] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Healthcare personnel (HCP) are at increased risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We posit that current infection control guidelines generally protect HCP from SARS-CoV-2 infection in a healthcare setting. METHODS In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in HCP at a major academic medical institution in the Upper Midwest of the United States between 25 March and 27 December 2020. We obtained limited epidemiological data through informal interviews and review of the electronic health record and combined this information with healthcare-associated viral sequences and viral sequences collected in the broader community to infer the most likely source of infection in HCP. RESULTS We investigated SARS-CoV-2 infection clusters involving 95 HCP and 137 possible patient contact sequences. The majority of HCP infections could not be linked to a patient or coworker (55 of 95 [57.9%]) and were genetically similar to viruses circulating concurrently in the community. We found that 10.5% of HCP infections (10 of 95) could be traced to a coworker. Strikingly, only 4.2% (4 of 95) could be traced to a patient source. CONCLUSIONS Infections among HCP add further strain to the healthcare system and put patients, HCP, and communities at risk. We found no evidence for healthcare-associated transmission in the majority of HCP infections evaluated. Although we cannot rule out the possibility of cryptic healthcare-associated transmission, it appears that HCP most commonly become infected with SARS-CoV-2 via community exposure. This emphasizes the ongoing importance of mask wearing, physical distancing, robust testing programs, and rapid distribution of vaccines.
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Affiliation(s)
- Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ashley Buys
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Elizabeth D Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Max Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Laura Anderson
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Alexander J Lepak
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
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18
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Nahata KD, Bollen N, Gill MS, Layan M, Bourhy H, Dellicour S, Baele G. On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study. Viruses 2021; 13:v13081628. [PMID: 34452492 PMCID: PMC8402743 DOI: 10.3390/v13081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.
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Affiliation(s)
- Kanika D. Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Correspondence:
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
| | - Maylis Layan
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Sorbonne Université, UMR2000, CNRS, 75015 Paris, France;
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, 75015 Paris, France;
- WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, 75015 Paris, France
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, 3000 Leuven, Belgium; (N.B.); (M.S.G.); (S.D.); (G.B.)
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19
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Xu Y, Lewandowski K, Downs LO, Kavanagh J, Hender T, Lumley S, Jeffery K, Foster D, Sanderson ND, Vaughan A, Morgan M, Vipond R, Carroll M, Peto T, Crook D, Walker AS, Matthews PC, Pullan ST. Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. ACTA ACUST UNITED AC 2021; 26. [PMID: 34240696 PMCID: PMC8268652 DOI: 10.2807/1560-7917.es.2021.26.27.2000004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.
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Affiliation(s)
- Yifei Xu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Kuiama Lewandowski
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Louise O Downs
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Thomas Hender
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Ali Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Philippa C Matthews
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
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20
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Evans S, Agnew E, Vynnycky E, Stimson J, Bhattacharya A, Rooney C, Warne B, Robotham J. The impact of testing and infection prevention and control strategies on within-hospital transmission dynamics of COVID-19 in English hospitals. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200268. [PMID: 34053255 PMCID: PMC8165586 DOI: 10.1098/rstb.2020.0268] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Nosocomial transmission of SARS-CoV-2 is a key concern, and evaluating the effect of testing and infection prevention and control strategies is essential for guiding policy in this area. Using a within-hospital SEIR transition model of SARS-CoV-2 in a typical English hospital, we estimate that between 9 March 2020 and 17 July 2020 approximately 20% of infections in inpatients, and 73% of infections in healthcare workers (HCWs) were due to nosocomial transmission. Model results suggest that placing suspected COVID-19 patients in single rooms or bays has the potential to reduce hospital-acquired infections in patients by up to 35%. Periodic testing of HCWs has a smaller effect on the number of hospital-acquired COVID-19 cases in patients, but reduces infection in HCWs by as much as 37% and results in only a small proportion of staff absences (approx. 0.3% per day). This is considerably less than the 20-25% of staff that have been reported to be absent from work owing to suspected COVID-19 and self-isolation. Model-based evaluations of interventions, informed by data collected so far, can help to inform policy as the pandemic progresses and help prevent transmission in the vulnerable hospital population. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
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Affiliation(s)
- Stephanie Evans
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Emily Agnew
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Emilia Vynnycky
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
- TB Modelling Group, TB Centre and Centre for Mathematical Modelling of Infectious Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - James Stimson
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - Alex Bhattacharya
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | | | - Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Julie Robotham
- Modelling and Economics Unit, National Infection Service, Public Health England, London, UK
- Healthcare Associated Infection and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
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21
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Li KK, Woo YM, Stirrup O, Hughes J, Ho A, Filipe ADS, Johnson N, Smollett K, Mair D, Carmichael S, Tong L, Nichols J, Aranday-Cortes E, Brunker K, Parr YA, Nomikou K, McDonald SE, Niebel M, Asamaphan P, Sreenu VB, Robertson DL, Taggart A, Jesudason N, Shah R, Shepherd J, Singer J, Taylor AHM, Cousland Z, Price J, Lees JS, Jones TPW, Lopez CV, MacLean A, Starinskij I, Gunson R, Morris STW, Thomson PC, Geddes CC, Traynor JP, Breuer J, Thomson EC, Mark PB. Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface. J Infect 2021; 83:96-103. [PMID: 33895226 PMCID: PMC8061788 DOI: 10.1016/j.jinf.2021.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/18/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. METHODS We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. RESULTS Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. CONCLUSIONS Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.
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Affiliation(s)
- Kathy K Li
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Y Mun Woo
- The Glasgow Renal & Transplant Unit, Queen Elizabeth University Hospital University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Oliver Stirrup
- Institute for Global Health, University College London, London, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Stephen Carmichael
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Kirstyn Brunker
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Yasmin A Parr
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Sarah E McDonald
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Vattipally B Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Natasha Jesudason
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Rajiv Shah
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Josh Singer
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Alison H M Taylor
- Renal Unit, University Hospital Monklands, Monkscourt Ave, Airdrie ML6 0JS, Canada
| | - Zoe Cousland
- Renal Unit, University Hospital Monklands, Monkscourt Ave, Airdrie ML6 0JS, Canada
| | - Jonathan Price
- Renal Unit, University Hospital Monklands, Monkscourt Ave, Airdrie ML6 0JS, Canada
| | - Jennifer S Lees
- Renal Unit, University Hospital Monklands, Monkscourt Ave, Airdrie ML6 0JS, Canada; Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Timothy P W Jones
- Department of Infectious Diseases, University Hospital Monklands, Monkscourt Ave, Airdrie ML60JS, Canada
| | - Carlos Varon Lopez
- Department of Microbiology, University Hospital Monklands, Monkscourt Ave, Airdrie ML6 0JS, Canada
| | - Alasdair MacLean
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, UK
| | - Igor Starinskij
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, UK
| | - Scott T W Morris
- The Glasgow Renal & Transplant Unit, Queen Elizabeth University Hospital University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Peter C Thomson
- The Glasgow Renal & Transplant Unit, Queen Elizabeth University Hospital University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Colin C Geddes
- The Glasgow Renal & Transplant Unit, Queen Elizabeth University Hospital University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Jamie P Traynor
- The Glasgow Renal & Transplant Unit, Queen Elizabeth University Hospital University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK
| | - Judith Breuer
- Institute of Child Health University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK; Department of Clinical Research, London School of Hygiene and Tropical Medicine, UK.
| | - Patrick B Mark
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker building, 464 Bearsden Road, Glasgow, G61 1QH, UK; Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK.
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22
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Sansone M, Andersson M, Gustavsson L, Andersson LM, Nordén R, Westin J. Extensive Hospital In-Ward Clustering Revealed By Molecular Characterization of Influenza A Virus Infection. Clin Infect Dis 2021; 71:e377-e383. [PMID: 32011654 DOI: 10.1093/cid/ciaa108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/31/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Nosocomial transmission of influenza A virus (InfA) infection is not fully recognized. The aim of this study was to describe the characteristics of hospitalized patients with InfA infections during an entire season and to investigate in-ward transmission at a large, acute-care hospital. METHODS During the 2016-17 season, all hospitalized patients ≥18 years old with laboratory-verified (real-time polymerase chain reaction) InfA were identified. Cases were characterized according to age; sex; comorbidity; antiviral therapy; viral load, expressed as cycle threshold values; length of hospital stay; 30-day mortality; and whether the InfA infection met criteria for a health care-associated influenza A infection (HCAI). Respiratory samples positive for InfA that were collected at the same wards within 7 days were chosen for whole-genome sequencing (WGS) and a phylogenetic analysis was performed to detect clustering. For reference, concurrent InfA strains from patients with community-acquired infection were included. RESULTS We identified a total of 435 InfA cases, of which 114 (26%) met the HCAI criteria. The overall 30-day mortality rate was higher among patients with HCAI (9.6% vs 4.6% among non-HCAI patients), although the difference was not statistically significant in a multivariable analysis, where age was the only independent risk factor for death (P < .05). We identified 8 closely related clusters (involving ≥3 cases) and another 10 pairs of strains, supporting in-ward transmission. CONCLUSIONS We found that the in-ward transmission of InfA occurs frequently and that HCAI may have severe outcomes. WGS may be used for outbreak investigations, as well as for evaluations of the effects of preventive measures.
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Affiliation(s)
- Martina Sansone
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria Andersson
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lars Gustavsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johan Westin
- Department of Clinical Microbiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
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23
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An Amplicon-Based Approach for the Whole-Genome Sequencing of Human Metapneumovirus. Viruses 2021; 13:v13030499. [PMID: 33803613 PMCID: PMC8003040 DOI: 10.3390/v13030499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/29/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of five years old. Despite this burden of disease, there remain caveats in our knowledge of global genetic diversity due to a lack of HMPV sequencing, particularly at the whole-genome scale. The purpose of this study was to create a simple and robust approach for HMPV whole-genome sequencing to be used for genomic epidemiological studies. To design our assay, all available HMPV full-length genome sequences were downloaded from the National Center for Biotechnology Information (NCBI) GenBank database and used to design four primer sets to amplify long, overlapping amplicons spanning the viral genome and, importantly, specific to all known HMPV subtypes. These amplicons were then pooled and sequenced on an Illumina iSeq 100 (Illumina, San Diego, CA, USA); however, the approach is suitable to other common sequencing platforms. We demonstrate the utility of this method using a representative subset of clinical samples and examine these sequences using a phylogenetic approach. Here we present an amplicon-based method for the whole-genome sequencing of HMPV from clinical extracts that can be used to better inform genomic studies of HMPV epidemiology and evolution.
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24
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Mukwege D, Byabene AK, Akonkwa EM, Dahma H, Dauby N, Cikwanine Buhendwa JP, Le Coadou A, Montesinos I, Bruyneel M, Cadière GB, Vandenberg O, Van Laethem Y. High SARS-CoV-2 Seroprevalence in Healthcare Workers in Bukavu, Eastern Democratic Republic of Congo. Am J Trop Med Hyg 2021; 104:1526-1530. [PMID: 33591936 PMCID: PMC8045652 DOI: 10.4269/ajtmh.20-1526] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/30/2020] [Indexed: 12/22/2022] Open
Abstract
Among 359 healthcare workers (HCW) employed in Panzi General Referral Hospital located in Bukavu in the Democratic Republic of Congo, 148 (41.2%) tested positive for SARS-CoV-2 antibodies. Thirty-three (22.3%) of the 148 personnel with positive serology reported symptoms evoking a prior COVID-19 illness. None of the infected HCWs reported COVID-related hospitalization, and all of them recovered. Our findings indicate high and underestimated circulation of SARS-CoV-2 within the Bukavu area.
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Affiliation(s)
- Denis Mukwege
- 1Gynaecology and General Surgery, Panzi General Referral Hospital, Bukavu, Democratic Republic of Congo.,2Faculty of Medicine, Evangelical University in Africa, Bukavu, Democratic Republic of Congo
| | - Aline Kusinza Byabene
- 2Faculty of Medicine, Evangelical University in Africa, Bukavu, Democratic Republic of Congo
| | - Eric Mungu Akonkwa
- 1Gynaecology and General Surgery, Panzi General Referral Hospital, Bukavu, Democratic Republic of Congo.,2Faculty of Medicine, Evangelical University in Africa, Bukavu, Democratic Republic of Congo
| | - Hafid Dahma
- 3Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Dauby
- 4Department of Infectious Diseases, CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium.,5Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium.,6Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Anne Le Coadou
- 5Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Isabel Montesinos
- 3Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Bruyneel
- 7Department of Pulmonary Medicine, CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Guy-Bernard Cadière
- 8Department of Gastrointestinal Surgery, European School of Laparoscopic Surgery, Saint-Pierre University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Vandenberg
- 5Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium.,9Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Yves Van Laethem
- 4Department of Infectious Diseases, CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Hababou Y, Taleb A, Recoing A, Moreau F, Simon I, Muller de Schongor F, Gault E, Rameix-Welti MA. Molecular investigation of a RSV outbreak in a geriatric hospital. BMC Geriatr 2021; 21:120. [PMID: 33579210 PMCID: PMC7880219 DOI: 10.1186/s12877-021-02064-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acquired infections in hospitalized elderly people are a growing concern. In long-term care facilities with multiple staff and visitor contacts, virus outbreaks are a common challenge for infection prevention teams. Although several studies have reported nosocomial RSV outbreaks in long term care facilities, molecular epidemiology data are scarce. METHODS RSV RNA was detected in respiratory samples from 19 patients in a long-term care hospital for elderly in Paris in March 2019 over a 3 weeks period. Genotyping was performed using nucleotide sequencing. Sociodemographic and clinical characteristics of cases part of a unique cluster, were retrospectively reviewed. RESULTS Molecular investigation of theses RSV cases, revealed a unique cluster of 12 nosocomial cases in 2 adjacent wards. Mean age of these outbreak's cases was 89. All patients had underlying medical conditions. Seven exhibited lower respiratory symptoms and three experienced decompensation of underlying chronic heart condition. Two patients died. CONCLUSIONS This case report highlights the importance of RSV in causing substantial disease in elderly in case of nosocomial outbreak and the contributions of molecular epidemiology in investigation and management of such outbreak.
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Affiliation(s)
- Yohan Hababou
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Assia Taleb
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Amélie Recoing
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Frédérique Moreau
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | - Isabelle Simon
- AP-HP, Université Paris Saclay, Hôpital Sainte Perrine, Equipe opérationnelle d'hygiène, Paris, France
| | | | - Elyanne Gault
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France.,Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Versailles, France
| | - Marie-Anne Rameix-Welti
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France. .,Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Versailles, France.
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26
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Subbiah S, Hussain SA, Samanth Kumar M. Managing cancer during COVID pandemic - Experience of a tertiary cancer care center. Eur J Surg Oncol 2020; 47:1220-1224. [PMID: 33039295 PMCID: PMC7834458 DOI: 10.1016/j.ejso.2020.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE The COVID-19 pandemic has forced healthcare providers worldwide to bring in changes in the way cancer patients are cared for. Many cancer departments globally have brought in changes to their daily practice. This article is about our experience of evolving "COVID 19 PROTOCOL" devised in our department and taking a shape to suit a health care system with limited budget. MATERIALS AND METHODS All the patient census & details of department of surgical oncology, Royapettah cancer hospital, from month of March 2020 to July 2020, who were subjected to COVID protocol were compared to patient census of similar duration in immediate past five months of October 2019 to February 2020. The data from out-patient department, ward in-patient census and healthcare personnel data was analyzed. RESULTS There was a drop to 63.5% in OP census and 61.6% in IP census. There was a drop to 64.5% in number of major cases operated during initial phases of COVID pandemic. Health care workers were also infected with the COVID but cross infectivity can be checked if proper steps to adhere to an institutional protocol based on general measures of cleanliness are taken. CONCLUSION Adherence to an institutional protocol based on compliance to general measures of masking, hand washing and social distancing plays a major role in minimizing disease spread. The Royapettah COVID protocol, though in process of evolution, can be recommended for any health care center with limited resources.
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Affiliation(s)
- Shanmugam Subbiah
- Department of Surgical Oncology, Royapettah Govt Hospital, Chennai, 14, Tamil Nadu, India.
| | - Syed Afroze Hussain
- Department of Surgical Oncology, Royapettah Govt Hospital, Chennai, 14, Tamil Nadu, India
| | - M Samanth Kumar
- Department of Surgical Oncology, Royapettah Govt Hospital, Chennai, 14, Tamil Nadu, India
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27
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Roy S, Hartley J, Dunn H, Williams R, Williams CA, Breuer J. Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A. Clin Infect Dis 2020; 69:1649-1656. [PMID: 30993315 PMCID: PMC6821348 DOI: 10.1093/cid/ciz020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Influenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still unclear. The objective of this study was to determine the utility, if any, of whole-genome sequencing over HA/NA sequencing for infection prevention and control (IPC) in hospitals. Methods We obtained all clinical samples from influenza (H1N1)-positive patients at the Great Ormond Street Hospital between January and March 2016. Samples were sequenced using targeted enrichment on an Illumina MiSeq sequencer. Maximum likelihood trees were computed for both whole genomes and concatenated HA/NA sequences. Epidemiological data was taken from routine IPC team activity during the period. Results Complete genomes were obtained for 65/80 samples from 38 patients. Conventional IPC analysis recognized 1 outbreak, involving 3 children, and identified another potential cluster in the haemato-oncology ward. Whole-genome and HA/NA phylogeny both accurately identified the previously known outbreak cluster. However, HA/NA sequencing additionally identified unrelated strains as part of this outbreak cluster. A whole-genome analysis identified a further cluster of 2 infections that had been previously missed and refuted suspicions of transmission in the haemato-oncology wards. Conclusions Whole-genome sequencing is better at identifying outbreak clusters in a hospital setting than HA/NA sequencing. Whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine IPC team work to allow the prevention of transmission.
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Affiliation(s)
- Sunando Roy
- Division of Infection and Immunity, University College London, United Kingdom
| | - John Hartley
- Great Ormond Street Hospital for Children, United Kingdom
| | - Helen Dunn
- Great Ormond Street Hospital for Children, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, United Kingdom
| | | | - Judith Breuer
- Division of Infection and Immunity, University College London, United Kingdom.,Great Ormond Street Hospital for Children, United Kingdom.,Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College London, United Kingdom
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28
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Southgate JA, Bull MJ, Brown CM, Watkins J, Corden S, Southgate B, Moore C, Connor TR. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 2020; 36:1681-1688. [PMID: 31693070 PMCID: PMC7703727 DOI: 10.1093/bioinformatics/btz814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/18/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Motivation Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of >99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses. Availability and implementation VAPOR is available at https://github.com/connor-lab/vapor. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joel A Southgate
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Matthew J Bull
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Clare M Brown
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Joanne Watkins
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Sally Corden
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Benjamin Southgate
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
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Whyler NCA, Sherry NL, Lane CR, Seemann T, Andersson P, Sait M, Graham M, Korman TM, Howden BP, Stuart RL. Viral genomics to inform infection control response in occupational COVID-19 transmission. Clin Infect Dis 2020; 73:e1881-e1884. [PMID: 32927479 PMCID: PMC7543329 DOI: 10.1093/cid/ciaa1385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/12/2020] [Indexed: 12/02/2022] Open
Abstract
Healthcare workers are at increased risk of occupational transmission of SARS-CoV-2. We report two instances of healthcare workers contracting SARS-CoV-2 despite no known breach of personal protective equipment. Additional specific equipment cleaning was initiated. Viral genomic sequencing supported this transmission hypothesis and our subsequent response.
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Affiliation(s)
- Naomi C A Whyler
- Monash Infectious Diseases, Monash Health, Clayton, Melbourne, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Maryza Graham
- Monash Infectious Diseases, Monash Health, Clayton, Melbourne, Australia.,Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash Health, Clayton, Melbourne, Australia.,Center for Inflammatory Diseases, Monash University, Melbourne, Australia.,Department of Microbiology, Monash Health, Clayton, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,joint senior author
| | - Rhonda L Stuart
- Monash Infectious Diseases, Monash Health, Clayton, Melbourne, Australia.,Center for Inflammatory Diseases, Monash University, Melbourne, Australia.,joint senior author
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30
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Freimanis GL, Oade MS. Whole-Genome Sequencing Protocols for IBV and Other Coronaviruses Using High-Throughput Sequencing. Methods Mol Biol 2020; 2203:67-74. [PMID: 32833204 DOI: 10.1007/978-1-0716-0900-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
This chapter reports the high-throughput sequencing protocol for sequencing Coronaviruses and other positive strand viruses to produce a dataset of significant depth of coverage. The protocol describes sequencing of infectious bronchitis virus propagated in embryonated eggs and harvested in the allantoic fluid. The protocol is composed of three main steps-enrichment of the allantoic fluid using ultracentrifugation, extraction of total RNA from allantoic fluid, and library preparation from total RNA to DNA sequencing libraries. The workflow will be suitable for all coronaviruses using high-throughput sequencing platforms.
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31
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Martin C, Montesinos I, Dauby N, Gilles C, Dahma H, Van Den Wijngaert S, De Wit S, Delforge M, Clumeck N, Vandenberg O. Dynamics of SARS-CoV-2 RT-PCR positivity and seroprevalence among high-risk healthcare workers and hospital staff. J Hosp Infect 2020; 106:102-106. [PMID: 32593608 PMCID: PMC7316468 DOI: 10.1016/j.jhin.2020.06.028] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Staff working in units that were highly exposed to coronavirus disease 2019 were invited to participate in a 6-month study on the carriage and seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The results from visits on Day 1 and Day 15 show that 41 cases of SARS-CoV-2 infection were confirmed by reverse transcriptase polymerase chain reaction and/or serology in 326 participants (overall infection rate 12.6%). The presence of comorbidities or symptoms at the time of sample collection was a risk factor for infection, but working as a physician/nurse was not a risk factor. Universal screening in high-risk units, irrespective of symptoms, allowed the identification of asymptomatic and potentially contagious infected workers, enabling them to self-isolate for 7 days.
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Affiliation(s)
- C Martin
- Department of Infectious Diseases, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium.
| | - I Montesinos
- LHUB-ULB (Laboratoire Hospitalier Universitaire de Bruxelles), Microbiology, Brussels, Belgium
| | - N Dauby
- Department of Infectious Diseases, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium; Institute for Medical Immunology, Université Libre de Bruxelles, Brussels, Belgium; Environmental Health Research Centre, Public Health School, Université Libre de Bruxelles, Brussels, Belgium
| | - C Gilles
- Gynaecology-Obstetric Department, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium
| | - H Dahma
- LHUB-ULB (Laboratoire Hospitalier Universitaire de Bruxelles), Microbiology, Brussels, Belgium
| | - S Van Den Wijngaert
- LHUB-ULB (Laboratoire Hospitalier Universitaire de Bruxelles), Microbiology, Brussels, Belgium
| | - S De Wit
- Department of Infectious Diseases, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium
| | - M Delforge
- Department of Infectious Diseases, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium
| | - N Clumeck
- Department of Infectious Diseases, CHU Saint-Pierre - Université Libre de Bruxelles, Brussels, Belgium
| | - O Vandenberg
- LHUB-ULB (Laboratoire Hospitalier Universitaire de Bruxelles), Microbiology, Brussels, Belgium; Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium; Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK; Universite´ Libre de Bruxelles, Brussels, Belgium
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Sikkema RS, Pas SD, Nieuwenhuijse DF, O'Toole Á, Verweij J, van der Linden A, Chestakova I, Schapendonk C, Pronk M, Lexmond P, Bestebroer T, Overmars RJ, van Nieuwkoop S, van den Bijllaardt W, Bentvelsen RG, van Rijen MML, Buiting AGM, van Oudheusden AJG, Diederen BM, Bergmans AMC, van der Eijk A, Molenkamp R, Rambaut A, Timen A, Kluytmans JAJW, Oude Munnink BB, Kluytmans van den Bergh MFQ, Koopmans MPG. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study. THE LANCET. INFECTIOUS DISEASES 2020; 20:1273-1280. [PMID: 32622380 PMCID: PMC7332281 DOI: 10.1016/s1473-3099(20)30527-2] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 01/05/2023]
Abstract
Background 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.
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Affiliation(s)
| | - Suzan D Pas
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | | | | | - Jaco Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | | | | | - Mark Pronk
- Viroscience, Erasmus MC, Rotterdam, Netherlands
| | | | | | | | | | | | - Robbert G Bentvelsen
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Anton G M Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands; Department of Infection Control, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | - Bram M Diederen
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | - Anneke M C Bergmans
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | | | | | | | - Aura Timen
- Landelijke Coördinatie Infectieziektebestrijding, Rijksinstituut voor Volksgezondheid en Milieu, Bilthoven, Netherlands; VU University Amsterdam, Amsterdam, Netherlands
| | - Jan A J W Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
| | | | - Marjolein F Q Kluytmans van den Bergh
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
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34
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Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A. Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies. Clin Microbiol Rev 2020; 33:e00057-19. [PMID: 32102900 PMCID: PMC7048017 DOI: 10.1128/cmr.00057-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Géraldine Durand
- bioMérieux, Microbiology Research and Development, La Balme Les Grottes, France
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Patrick Murray
- BD Life Sciences Integrated Diagnostic Solutions, Scientific Affairs, Sparks, Maryland, USA
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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35
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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Marinelli T, Wee LYA, Rowe E, Chhetri R, Friel O, Higgins G, Bardy P, Singhal D, Pradhan A, Crawford L, Hiwase DK. Respiratory Viruses Cause Late Morbidity in Recipients of Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2019; 26:782-788. [PMID: 31866345 DOI: 10.1016/j.bbmt.2019.12.724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Common respiratory viral infections (CRVIs) frequently complicate hematopoietic stem cell transplantation (HSCT). We conducted a retrospective, single-center, observational cohort study to determine the incidence of CRVI in patients who received an allogeneic (allo) or autologous (auto) HSCT at the Royal Adelaide Hospital between 2009 and 2017. The median follow-up was 8.9 and 4.5 years for auto- and allo-HSCT recipients, respectively. There were 149 CRVI episodes in 74 patients, with rhinovirus being the most commonly isolated virus (n = 81, 47%). The majority of CRVIs (113/149, 75.8%) occurred more than 100 days post-HSCT and 67% were diagnosed in the outpatient setting. There was evidence of lower respiratory tract infection (LRTI) in 45.6% (68/149) of CRVIs. On multivariate logistic regression analysis, coviral infections and cytomegalovirus viremia were independent risk factors for progression of CRVI to LRTI. Ten (6.7%) CRVI episodes resulted in admission to intensive care for ventilatory support and 8 (5.4%) patients died within 30 days of CRVI diagnosis. In our study, 10.4% of HSCT recipients experienced a CRVI post-transplant, primarily causing late morbidity and potentially mortality. Prevention with strict infection control practices, vaccination, and patient education is essential.
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Affiliation(s)
- Tina Marinelli
- Department of Infectious Diseases, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia
| | - Li Yan A Wee
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Emily Rowe
- Department of Infectious Diseases, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Rakchha Chhetri
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia; Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Oisin Friel
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia
| | - Geoffrey Higgins
- Department of Infectious Diseases, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; SA Pathology, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter Bardy
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Deepak Singhal
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia; Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Alyssa Pradhan
- Department of Infectious Diseases, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia
| | - Lucy Crawford
- Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia; SA Pathology, Central Adelaide Local Health Network, Adelaide, Australia
| | - Devendra K Hiwase
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, Australia; Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia; Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.
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Kamelian K, Montoya V, Olmstead A, Dong W, Harrigan R, Morshed M, Joy JB. Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods. Sci Rep 2019; 9:16433. [PMID: 31712570 PMCID: PMC6848190 DOI: 10.1038/s41598-019-52613-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases.
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Affiliation(s)
- Kimia Kamelian
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard Harrigan
- University of British Columbia, Division of AIDS, Department of Medicine, Vancouver, BC, Canada
| | - Muhammad Morshed
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.,University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,University of British Columbia, Division of Infectious Diseases, Department of Medicine, Vancouver, BC, Canada.
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Blackburn RM, Frampton D, Smith CM, Fragaszy EB, Watson SJ, Ferns RB, Binter Š, Coen PG, Grant P, Shallcross LJ, Kozlakidis Z, Pillay D, Kellam P, Hué S, Nastouli E, Hayward AC. Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014). Influenza Other Respir Viruses 2019; 13:556-563. [PMID: 31536169 PMCID: PMC6800305 DOI: 10.1111/irv.12679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/21/2019] [Accepted: 08/25/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains. OBJECTIVES We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data. METHODS All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space-time links and assessed genetic relatedness. RESULTS We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space-time links with other cases in the same cluster. Genetic distances between pairs of cases with space-time links were lower than for pairs without spatial links (P < .001). CONCLUSIONS Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
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Affiliation(s)
| | | | | | - Ellen B. Fragaszy
- Institute of Health InformaticsUCLLondonUK
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Simon J. Watson
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - R. Bridget Ferns
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Špela Binter
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Pietro G. Coen
- Infection Control DepartmentUniversity College London HospitalsNHS Foundation TrustLondonUK
| | - Paul Grant
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
| | | | - Zisis Kozlakidis
- Institute of Health InformaticsUCLLondonUK
- International Agency for Research on CancerWorld Health OrganizationLyonFrance
| | - Deenan Pillay
- Division of Infection and ImmunityUCLLondonUK
- Africa Health Research InstituteDurbanSouth Africa
| | - Paul Kellam
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxtonUK
| | - Stéphane Hué
- Department of Infectious Disease EpidemiologyFaculty of Epidemiology and Population HealthLondon School of Hygiene and Tropical MedicineLondonUK
| | - Eleni Nastouli
- Clinical Microbiology and VirologyUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Population, Policy and PracticeUCL Institute of Child HealthLondonUK
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Van den Wijngaert S, Bossuyt N, Ferns B, Busson L, Serrano G, Wautier M, Thomas I, Byott M, Dupont Y, Nastouli E, Hallin M, Kozlakidis Z, Vandenberg O. Bigger and Better? Representativeness of the Influenza A Surveillance Using One Consolidated Clinical Microbiology Laboratory Data Set as Compared to the Belgian Sentinel Network of Laboratories. Front Public Health 2019; 7:150. [PMID: 31275914 PMCID: PMC6591264 DOI: 10.3389/fpubh.2019.00150] [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: 12/25/2018] [Accepted: 05/23/2019] [Indexed: 12/29/2022] Open
Abstract
Infectious diseases remain a serious public health concern globally, while the need for reliable and representative surveillance systems remains as acute as ever. The public health surveillance of infectious diseases uses reported positive results from sentinel clinical laboratories or laboratory networks, to survey the presence of specific microbial agents known to constitute a threat to public health in a given population. This monitoring activity is commonly based on a representative fraction of the microbiology laboratories nationally reporting to a single central reference point. However, in recent years a number of clinical microbiology laboratories (CML) have undergone a process of consolidation involving a shift toward laboratory amalgamation and closer real-time informational linkage. This report aims to investigate whether such merging activities might have a potential impact on infectious diseases surveillance. Influenza data was used from Belgian public health surveillance 2014–2017, to evaluate whether national infection trends could be estimated equally as effectively from only just one centralized CML serving the wider Brussels area (LHUB-ULB). The overall comparison reveals that there is a close correlation and representativeness of the LHUB-ULB data to the national and international data for the same time periods, both on epidemiological and molecular grounds. Notably, the effectiveness of the LHUB-ULB surveillance remains partially subject to local regional variations. A subset of the Influenza samples had their whole genome sequenced so that the observed epidemiological trends could be correlated to molecular observations from the same period, as an added-value proposition. These results illustrate that the real-time integration of high-throughput whole genome sequencing platforms available in consolidated CMLs into the public health surveillance system is not only credible but also advantageous to use for future surveillance and prediction purposes. This can be most effective when implemented for automatic detection systems that might include multiple layers of information and timely implementation of control strategies.
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Affiliation(s)
- Sigi Van den Wijngaert
- Department of Microbiology, LHUB-ULB, Pole Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Nathalie Bossuyt
- Sciensano, SD Epidemiology and Surveillance, Service 'Epidemiology of Infectious Diseases', Brussels, Belgium
| | - Bridget Ferns
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom.,UCLH/UCL Biomedical Research Centre, NIHR, London, United Kingdom
| | - Laurent Busson
- Department of Microbiology, LHUB-ULB, Pole Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Gabriela Serrano
- Research Centre on Environmental and Occupational Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, LHUB-ULB, Pole Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Matthew Byott
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Yves Dupont
- Sciensano, SD Epidemiology and Surveillance, Service 'Epidemiology of Infectious Diseases', Brussels, Belgium
| | - Eleni Nastouli
- Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom.,Department of Population, Policy and Practice, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Pole Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Zisis Kozlakidis
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom.,International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Olivier Vandenberg
- Research Centre on Environmental and Occupational Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium.,Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom.,Innovation and Business Development Unit, LHUB-ULB, Pole Hospitalier Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
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40
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Fontana L, Strasfeld L. Respiratory Virus Infections of the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient. Infect Dis Clin North Am 2019; 33:523-544. [PMID: 30940462 PMCID: PMC7126949 DOI: 10.1016/j.idc.2019.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Respiratory virus infections in hematologic stem cell transplant recipients and patients with hematologic malignancies are increasingly recognized as a cause of significant morbidity and mortality. The often overlapping clinical presentation makes molecular diagnostic strategies imperative for rapid diagnosis and to inform understanding of the changing epidemiology of each of the respiratory viruses. Most respiratory virus infections are managed with supportive therapy, although there is effective antiviral therapy for influenza. The primary focus should remain on primary prevention infection control procedures and isolation precautions, avoidance of ill contacts, and vaccination for influenza.
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Affiliation(s)
- Lauren Fontana
- Division of Infectious Disease, Department of Medicine, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Mail Code L457, Portland, OR 97239, USA.
| | - Lynne Strasfeld
- Division of Infectious Disease, Department of Medicine, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Mail Code L457, Portland, OR 97239, USA
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41
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Lizarazo E, Couto N, Vincenti-Gonzalez M, Raangs EC, Velasco Z, Bethencourt S, Jaenisch T, Friedrich AW, Tami A, Rossen JW. Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. J Biotechnol 2019; 306S:100009. [PMID: 34112375 DOI: 10.1016/j.btecx.2019.100009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
Abstract
Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Additionally, presence of DENV quasispecies (intra-host variation) was revealed by detecting single nucleotide variants. Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1-4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext® RNA to synthesize cDNA followed by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit. Libraries were sequenced using both the MiSeq and NextSeq. Bioinformatic analysis showed complete ORFs for all samples by all approaches, but longer contigs and higher sequencing depths were obtained with the TS kit. No differences were observed between MiSeq and NextSeq sequencing. Detection of multiple DENV serotypes in a single sample was feasible. Finally, results were obtained within three days with associated reagents costs between €130-170/sample. Therefore, shotgun metagenomics is suitable for identification and typing of DENV in a clinical setting.
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Affiliation(s)
- Erley Lizarazo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Maria Vincenti-Gonzalez
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Erwin C Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Zoraida Velasco
- Universidad de Carabobo, Facultad Experimental de Ciencias y Tecnología, Departamento de Biología, Valencia, Venezuela
| | - Sarah Bethencourt
- Universidad de Carabobo, Facultad de Ciencias de la Salud. Departamento de Ciencias Fisiológicas, Unidad de Investigación en Inmunología, Valencia, Venezuela
| | - Thomas Jaenisch
- University of Heidelberg, Heidelberg University Hospital, Department of Infectious Diseases, Section of Clinical Tropical Medicine, Heidelberg, Germany
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Adriana Tami
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands; Universidad de Carabobo, Facultad de Ciencias de la Salud, Departamento de Parasitología, Valencia, Venezuela
| | - John W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.
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Transmission and prevention of acute viral respiratory tract infections in hospitals. Curr Opin Pulm Med 2019; 25:220-224. [DOI: 10.1097/mcp.0000000000000566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Parkash N, Beckingham W, Andersson P, Kelly P, Senanayake S, Coatsworth N. Hospital-acquired influenza in an Australian tertiary Centre 2017: a surveillance based study. BMC Pulm Med 2019; 19:79. [PMID: 30991976 PMCID: PMC6469028 DOI: 10.1186/s12890-019-0842-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 04/01/2019] [Indexed: 11/22/2022] Open
Abstract
Background In 2017, Australia experienced its highest levels of influenza virus activity since the 2009 pandemic. This allowed detailed comparison of the characteristics of patients with community and hospital-acquired influenza, and infection control factors that contributed to influenza spread. Methods A surveillance based study was conducted on hospitalised patients with laboratory-confirmed influenza at the Canberra Hospital during April–October 2017. Differences between the hospital-acquired and community-acquired patient characteristics and outcomes were assessed by univariate analysis. Epidemiologic curves were developed and cluster distribution within the hospital was determined. Results Two hundred and ninety-two patients were included in the study. Twenty-eight (9.6%) acquired influenza in hospital, representing a higher proportion than any of the previous 5 years (range 0.9–5.8%). These patients were more likely to have influenza A (p = 0.021), had higher rates of diabetes (p = 0.015), malignancy (p = 0.046) and chronic liver disease (p = 0.043). Patients acquiring influenza in hospital met clinical criteria for influenza like illness in 25% of cases, compared with 64.4% for community-acquired cases (p < 0.001). Hospital-acquired influenza cases occurred in two distinct clusters. Patients were moved an average of 5 times after diagnosis. Mean length of stay following diagnosis was 13 days compared to 5 days for community-acquired cases (p < 0.001). Of the patients with hospital-acquired influenza, 22 were in shared rooms during their incubation period and 9 were not isolated in single rooms following diagnosis. Treatment was initiated within the recommended 48 h period following symptom onset for 62.5% of hospital-acquired cases compared with 39.8% of community-acquired cases (p = 0.033). Conclusions Our results show that clinical presentation differed between patients with hospital-acquired influenza compared with those who acquired influenza in the community. Cases occurred in two clusters suggesting intra-hospital transmission rather than random importation from the community, highlighting the importance of infection control measures to limit influenza spread. Patients with hospital-acquired influenza may present without classical features of an influenza-like illness and this should promote earlier diagnostic testing and isolation to limit spread. Movement of patients after diagnosis is likely to facilitate spread within the hospital.
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Affiliation(s)
- Nikita Parkash
- Department of Infectious Diseases, Canberra Hospital and Health Services, Canberra, Australian Capital Territory, Australia.
| | - Wendy Beckingham
- Infection Prevention and Control, Canberra Hospital and Health Services, Canberra, Australian Capital Territory, Australia
| | - Patiyan Andersson
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paul Kelly
- Australian National University Medical School, Canberra, Australian Capital Territory, Australia.,Population Health and Prevention Division, ACT Health, Canberra, Australian Capital Territory, Australia
| | - Sanjaya Senanayake
- Department of Infectious Diseases, Canberra Hospital and Health Services, Canberra, Australian Capital Territory, Australia.,Australian National University Medical School, Canberra, Australian Capital Territory, Australia
| | - Nicholas Coatsworth
- Department of Infectious Diseases, Canberra Hospital and Health Services, Canberra, Australian Capital Territory, Australia.,Australian National University Medical School, Canberra, Australian Capital Territory, Australia
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Maurier F, Beury D, Fléchon L, Varré JS, Touzet H, Goffard A, Hot D, Caboche S. A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology 2019; 531:141-148. [PMID: 30878524 PMCID: PMC7112119 DOI: 10.1016/j.virol.2019.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/31/2022]
Abstract
Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA, and to the difficulty to get an accurate genome assembly. Here we introduce a complete sequencing and analyzing protocol called V-ASAP for Virus Amplicon Sequencing Assembly Pipeline. Our protocol is able to generate the viral dominant genome sequence starting from clinical samples. It is based on a multiplex PCR amplicon sequencing coupled with a reference-free analytical pipeline. This protocol was applied to 11 clinical samples infected with coronavirus OC43 (HcoV-OC43), and led to seven complete and two nearly complete genome assemblies. The protocol introduced here is shown to be robust, to produce a reliable sequence, and could be applied to other virus.
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Affiliation(s)
- Florence Maurier
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Delphine Beury
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Léa Fléchon
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Jean-Stéphane Varré
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Hélène Touzet
- Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Anne Goffard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ségolène Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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Hijano DR, Maron G, Hayden RT. Respiratory Viral Infections in Patients With Cancer or Undergoing Hematopoietic Cell Transplant. Front Microbiol 2018; 9:3097. [PMID: 30619176 PMCID: PMC6299032 DOI: 10.3389/fmicb.2018.03097] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 12/25/2022] Open
Abstract
Survival rates for pediatric cancer have steadily improved over time but it remains a significant cause of morbidity and mortality among children. Infections are a major complication of cancer and its treatment. Community acquired respiratory viral infections (CRV) in these patients increase morbidity, mortality and can lead to delay in chemotherapy. These are the result of infections with a heterogeneous group of viruses including RNA viruses, such as respiratory syncytial virus (RSV), influenza virus (IV), parainfluenza virus (PIV), metapneumovirus (HMPV), rhinovirus (RhV), and coronavirus (CoV). These infections maintain a similar seasonal pattern to those of immunocompetent patients. Clinical manifestations vary significantly depending on the type of virus and the type and degree of immunosuppression, ranging from asymptomatic or mild disease to rapidly progressive fatal pneumonia Infections in this population are characterized by a high rate of progression from upper to lower respiratory tract infection and prolonged viral shedding. Use of corticosteroids and immunosuppressive therapy are risk factors for severe disease. The clinical course is often difficult to predict, and clinical signs are unreliable. Accurate prognostic viral and immune markers, which have become part of the standard of care for systemic viral infections, are currently lacking; and management of CRV infections remains controversial. Defining effective prophylactic and therapeutic strategies is challenging, especially considering, the spectrum of immunocompromised patients, the variety of respiratory viruses, and the presence of other opportunistic infections and medical problems. Prevention remains one of the most important strategies against these viruses. Early diagnosis, supportive care and antivirals at an early stage, when available and indicated, have proven beneficial. However, with the exception of neuraminidase inhibitors for influenza infection, there are no accepted treatments. In high-risk patients, pre-emptive treatment with antivirals for upper respiratory tract infection (URTI) to decrease progression to LRTI is a common strategy. In the future, viral load and immune markers may prove beneficial in predicting severe disease, supporting decision making and monitor treatment in this population.
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Affiliation(s)
- Diego R. Hijano
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Gabriela Maron
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Randall T. Hayden
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, United States
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Imai K, Tamura K, Tanigaki T, Takizawa M, Nakayama E, Taniguchi T, Okamoto M, Nishiyama Y, Tarumoto N, Mitsutake K, Murakami T, Maesaki S, Maeda T. Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study. Front Microbiol 2018; 9:2748. [PMID: 30483243 PMCID: PMC6243006 DOI: 10.3389/fmicb.2018.02748] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 02/01/2023] Open
Abstract
Introduction: Whole genome sequencing (WGS) of influenza viruses is important for preparing vaccines and coping with newly emerging viruses. However, WGS is difficult to perform using conventional next-generation sequencers in developing countries, where facilities are often inadequate. In this study, we developed a high-throughput WGS method for influenza viruses in clinical specimens with the MinION portable sequencer. Methods: Whole genomes of influenza A and B viruses were amplified by multiplex RT-PCR from 13 clinical specimens collected in Tokyo, Japan. Barcode tags for multiplex MinION sequencing were added with each multiplex RT-PCR amplicon by nested PCR with custom barcoded primers. All barcoded amplicons were mixed and multiplex sequencing using the MinION sequencer with 1D2 sequencing kit. In addition, multiplex RT-PCR amplicons generated from each clinical specimen were sequenced using the Illumina MiSeq platform to validate the performance of MinION sequencer. The accuracy, recall, and precision rates of MinION sequencing were calculated by comparing the results of variant calling in the Illumina MiSeq platform and MinION sequencer. Results: Whole genomes of influenza A and B viruses were successfully amplified by multiplex RT-PCR from 13 clinical samples. We identified 6 samples as influenza type A virus H3N2 subtype and 7 as influenza B virus Yamagata lineage using the Illumina MiSeq platform. The overall accuracy, recall, and precision rates of the MinION sequencer were, respectively 99.95%, 89.41%, and 97.88% from 1D reads and 99.97%, 93.28%, and 99.86% from 1D2 reads. Conclusion: We developed a novel WGS method for influenza A and B viruses. It is necessary to improve read accuracy and analytical tools in order to better utilize the MinION sequencer for real-time monitoring of genetic rearrangements and for evaluation of newly emerging viruses.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Infectious Diseases, Self-Defense Forces Central Hospital, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Kaku Tamura
- Department of Infectious Diseases, Self-Defense Forces Central Hospital, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Tomomi Tanigaki
- NBC Counter Medical Unit, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Mari Takizawa
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Eiko Nakayama
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Takahiko Taniguchi
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Misako Okamoto
- Camp Asaka Medical Office, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Yasumasa Nishiyama
- NBC Counter Medical Unit, Japan Ground Self-Defense Forces, Tokyo, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Infectious Disease and Infection Control, Saitama Medical University International Medical Center, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, Saitama, Japan
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Healthcare-Associated Viral Infections: Considerations for Nosocomial Transmission and Infection Control. HEALTHCARE-ASSOCIATED INFECTIONS IN CHILDREN 2018. [PMCID: PMC7121921 DOI: 10.1007/978-3-319-98122-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nosocomial and healthcare-associated viral infections are major contributors to patient morbidity and mortality, prolonged hospitalization, and increased healthcare costs in all pediatric age groups. Healthcare workers are also at risk of acquiring nosocomial viral infections, affecting their own health, as well as facilitating spread of the infection to other patients, their family, and the community. Healthcare-associated viral infections may occur in a variety of healthcare settings, including clinics, emergency centers, urgent care centers, procedure suites, operating rooms, hospital wards, nurseries, and intensive care units. In addition, non-patient care areas, such as the cafeteria, waiting areas, and playrooms may also be a source of viral infections that can spread in the healthcare setting. These infections may be device-related or transmitted via blood products or organ donation and respiratory droplets, through food including human milk, person to person, or via air ducts, fomites, and surfaces. They most commonly involve the respiratory and gastrointestinal tracts; however, all organ systems may potentially be involved. Both DNA and RNA viruses, either common or exotic, may contribute to healthcare-associated viral infections. Advances in molecular viral diagnostics have enabled rapid detection and routine surveillance for viral infections and now allow early identification of viruses. Prompt identification allows timely containment measures to minimize transmission to other patients or healthcare workers and avoids hospital, community, and global outbreaks.
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