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Chang AB, Yerkovich ST, Baines KJ, Burr L, Champion A, Chatfield MD, Eg KP, Goyal V, Marsh RL, McCallum GB, McElrea M, McPhail S, Morgan LC, Morris PS, Nathan AM, O'Farrell H, Sanchez MO, Parsons M, Schultz A, Torzillo PJ, West NP, Versteegh L, Marchant JM, Grimwood K. Erdosteine in children and adults with bronchiectasis (BETTER trial): study protocol for a multicentre, double-blind, randomised controlled trial. BMJ Open Respir Res 2024; 11:e002216. [PMID: 38719503 PMCID: PMC11086403 DOI: 10.1136/bmjresp-2023-002216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
INTRODUCTION Bronchiectasis is a worldwide chronic lung disorder where exacerbations are common. It affects people of all ages, but especially Indigenous populations in high-income nations. Despite being a major contributor to chronic lung disease, there are no licensed therapies for bronchiectasis and there remain relatively few randomised controlled trials (RCTs) conducted in children and adults. Our RCT will address some of these unmet needs by evaluating whether the novel mucoactive agent, erdosteine, has a therapeutic role in children and adults with bronchiectasis.Our primary aim is to determine in children and adults aged 2-49 years with bronchiectasis whether regular erdosteine over a 12-month period reduces acute respiratory exacerbations compared with placebo. Our primary hypothesis is that people with bronchiectasis who regularly use erdosteine will have fewer exacerbations than those receiving placebo.Our secondary aims are to determine the effect of the trial medications on quality of life (QoL) and other clinical outcomes (exacerbation duration, time-to-next exacerbation, hospitalisations, lung function, adverse events). We will also assess the cost-effectiveness of the intervention. METHODS AND ANALYSIS We are undertaking an international multicentre, double-blind, placebo-RCT to evaluate whether 12 months of erdosteine is beneficial for children and adults with bronchiectasis. We will recruit 194 children and adults with bronchiectasis to a parallel, superiority RCT at eight sites across Australia, Malaysia and Philippines. Our primary endpoint is the rate of exacerbations over 12 months. Our main secondary outcomes are QoL, exacerbation duration, time-to-next exacerbation, hospitalisations and lung function. ETHICS AND DISSEMINATION The Human Research Ethics Committees (HREC) of Children's Health Queensland (for all Australian sites), University of Malaya Medical Centre (Malaysia) and St. Luke's Medical Centre (Philippines) approved the study. We will publish the results and share the outcomes with the academic and medical community, funding and relevant patient organisations. TRIAL REGISTRATION NUMBER ACTRN12621000315819.
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Affiliation(s)
- Anne B Chang
- Department of Respiratory Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Stephanie T Yerkovich
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Katherine J Baines
- School of Medicine and Public Health, The University of Newcastle, Newcastle, New South Wales, Australia
- Immune Health Research Program, Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Lucy Burr
- Mater Health Services, South Brisbane, Queensland, Australia
| | - Anita Champion
- Department of Pharmacy, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | | | - Kah P Eg
- Department of Paediatrics, Universiti Malaya Faculty of Medicine, Kuala Lumpur, Malaysia
| | - Vikas Goyal
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia
| | - Robyn L Marsh
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Gabrielle B McCallum
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Margaret McElrea
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
| | - Steven McPhail
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
- School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, Brisbane, Queensland, Australia
- Metro South Health, Clinical Informatics Directorate, Woollongabba, Queensland, Australia
| | - Lucy C Morgan
- Department of Respiratory Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Peter S Morris
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Anne M Nathan
- Department of Paediatrics, Universiti Malaya Faculty of Medicine, Kuala Lumpur, Malaysia
| | - Hannah O'Farrell
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Marion O Sanchez
- Section of Pediatric Pulmonology, Institute of Pulmonary Medicine, St. Luke's Medical Center, Quezon City, Philippines
| | - Marianne Parsons
- Parent Advisory Group, Cough, Asthma and Airways Group, Queensland University of Technology Faculty of Health, Kelvin Grove, Queensland, Australia
| | - André Schultz
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
- Wal-yan Respiratory Research Centre, Telethon Kids Institute & Division of Paediatrics, Faculty of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Paul J Torzillo
- Respiratory Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- Sydney Medical School, The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Nicholas P West
- School of Medicine and Dentistry, Griffith University Griffith Health, Gold Coast, Queensland, Australia
| | - Lesley Versteegh
- Child and Maternal Health Division and andand NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Julie M Marchant
- Department of Respiratory Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- The Australian Centre for Health Services Innovation (AusHSI), Queensland University of Technology, Brisbane, Queensland, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry, Griffith University Griffith Health, Gold Coast, Queensland, Australia
- Departments of Infectious Disease and Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia
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Fulte S, Atto B, McCarty A, Horn KJ, Redzic JS, Eisenmesser E, Yang M, Marsh RL, Tristram S, Clark SE. Heme sequestration by hemophilin from Haemophilus haemolyticus reduces respiratory tract colonization and infection with non-typeable Haemophilus influenzae. mSphere 2024; 9:e0000624. [PMID: 38380941 PMCID: PMC10964412 DOI: 10.1128/msphere.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
Iron acquisition is a key feature dictating the success of pathogen colonization and infection. Pathogens scavenging iron from the host must contend with other members of the microbiome similarly competing for the limited pool of bioavailable iron, often in the form of heme. In this study, we identify a beneficial role for the heme-binding protein hemophilin (Hpl) produced by the non-pathogenic bacterium Haemophilus haemolyticus against its close relative, the opportunistic respiratory tract pathogen non-typeable Haemophilus influenzae (NTHi). Using a mouse model, we found that pre-exposure to H. haemolyticus significantly reduced NTHi colonization of the upper airway and impaired NTHi infection of the lungs in an Hpl-dependent manner. Further, treatment with recombinant Hpl was sufficient to decrease airway burdens of NTHi without exacerbating lung immunopathology or systemic inflammation. Instead, mucosal production of the neutrophil chemokine CXCL2, lung myeloperoxidase, and serum pro-inflammatory cytokines IL-6 and TNFα were lower in Hpl-treated mice. Mechanistically, H. haemolyticus suppressed NTHi growth and adherence to human respiratory tract epithelial cells through the expression of Hpl, and recombinant Hpl could recapitulate these effects. Together, these findings indicate that heme sequestration by non-pathogenic, Hpl-producing H. haemolyticus is protective against NTHi colonization and infection. IMPORTANCE The microbiome provides a critical layer of protection against infection with bacterial pathogens. This protection is accomplished through a variety of mechanisms, including interference with pathogen growth and adherence to host cells. In terms of immune defense, another way to prevent pathogens from establishing infections is by limiting the availability of nutrients, referred to as nutritional immunity. Restricting pathogen access to iron is a central component of this approach. Here, we uncovered an example where these two strategies intersect to impede infection with the respiratory tract bacterial pathogen Haemophilus influenzae. Specifically, we find that a non-pathogenic (commensal) bacterium closely related to H. influenzae called Haemophilus haemolyticus improves protection against H. influenzae by limiting the ability of this pathogen to access iron. These findings suggest that beneficial members of the microbiome improve protection against pathogen infection by effectively contributing to host nutritional immunity.
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Affiliation(s)
- Sam Fulte
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Arianna McCarty
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kadi J. Horn
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Michael Yang
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Sarah E. Clark
- Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Mandal PK, Cleanthous A, Rigas V, Kleinecke M, Lawrence K, Leach AJ, Smith-Vaughan H, Morris PS, Beissbarth J, Marsh RL. Complete genome sequence of Oligella urethralis MSHR-50412PR, isolated from an ear discharge swab of a child with chronic suppurative otitis media. Microbiol Resour Announc 2024; 13:e0107123. [PMID: 38275301 PMCID: PMC10868213 DOI: 10.1128/mra.01071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Oligella urethralis are opportunistic pathogens typically associated with genitourinary infections. Here, we report the complete genome for an Oligella urethralis isolate recovered from ear discharge of a child with chronic suppurative otitis media (strain MSHR-50412PR). The genome comprises 2.58 Mb, with 2,448 coding sequences and 46.26% average GC content.
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Affiliation(s)
- Pappu K. Mandal
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Alexander Cleanthous
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Vanessa Rigas
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mariana Kleinecke
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Katrina Lawrence
- Health and Human Science, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Amanda J. Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Peter S. Morris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Robyn L. Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
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Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
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Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
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Bleakley AS, Kho S, Binks MJ, Pizzutto S, Chang AB, Beissbarth J, Minigo G, Marsh RL. Extracellular traps are evident in Romanowsky-stained smears of bronchoalveolar lavage from children with non-cystic fibrosis bronchiectasis. Respirology 2023; 28:1126-1135. [PMID: 37648649 PMCID: PMC10947271 DOI: 10.1111/resp.14587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND AND OBJECTIVE The importance of extracellular traps (ETs) in chronic respiratory conditions is increasingly recognized but their role in paediatric bronchiectasis is poorly understood. The specialized techniques currently required to study ETs preclude routine clinical use. A simple and cost-effective ETs detection method is needed to support diagnostic applications. We aimed to determine whether ETs could be detected using light microscopy-based assessment of Romanowsky-stained bronchoalveolar lavage (BAL) slides from children with bronchiectasis, and whether the ETs cellular origin could be determined. METHODS Archived Romanowsky-stained BAL slides from a cross-sectional study of children with bronchiectasis were examined for ETs using light microscopy. The cellular origin of individual ETs was determined based on morphology and physical contact with surrounding cell(s). RESULTS ETs were observed in 78.7% (70/89) of BAL slides with neutrophil (NETs), macrophage (METs), eosinophil (EETs) and lymphocyte (LETs) ETs observed in 32.6%, 51.7%, 4.5% and 9%, respectively. ETs of indeterminate cellular origin were present in 59.6% of slides. Identifiable and indeterminate ETs were co-detected in 43.8% of slides. CONCLUSION BAL from children with bronchiectasis commonly contains multiple ET types that are detectable using Romanowsky-stained slides. While specialist techniques remain necessary to determining the cellular origin of all ETs, screening of Romanowsky-stained slides presents a cost-effective method that is well-suited to diagnostic settings. Our findings support further research to determine whether ETs can be used to define respiratory endotypes and to understand whether ETs-specific therapies may be required to resolve airway inflammation among children with bronchiectasis.
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Affiliation(s)
- Amy S. Bleakley
- Child and Maternal Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Steven Kho
- Global and Tropical Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Michael J. Binks
- Child and Maternal Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Susan Pizzutto
- Research Institute for the Environment and Livelihoods, Faculty of Science and TechnologyCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Anne B. Chang
- Child and Maternal Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
- Department of Respiratory and Sleep MedicineQueensland Children's Hospital and Australian Centre for Health Services Innovation, Queensland University of TechnologyBrisbaneQueenslandAustralia
| | - Jemima Beissbarth
- Child and Maternal Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Gabriela Minigo
- Global and Tropical Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
- School of Medicine, Faculty of HealthCharles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Robyn L. Marsh
- Child and Maternal Health DivisionMenzies School of Health Research, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
- School of Health SciencesUniversity of TasmaniaLauncestonTasmaniaAustralia
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Tamir SO, Bialasiewicz S, Brennan-Jones CG, Der C, Kariv L, Macharia I, Marsh RL, Seguya A, Thornton R. ISOM 2023 research Panel 4 - Diagnostics and microbiology of otitis media. Int J Pediatr Otorhinolaryngol 2023; 174:111741. [PMID: 37788516 DOI: 10.1016/j.ijporl.2023.111741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023]
Abstract
OBJECTIVES To identify and review key research advances from the literature published between 2019 and 2023 on the diagnosis and microbiology of otitis media (OM) including acute otitis media (AOM), recurrent AOM (rAOM), otitis media with effusion (OME), chronic suppurative otitis media (CSOM) and AOM complications (mastoiditis). DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS All relevant original articles published in Medline in English between July 2019 and February 2023 were identified. Studies that were reviews, case studies, relating to OM complications (other than mastoiditis), and studies focusing on guideline adherence, and consensus statements were excluded. Members of the panel drafted the report based on these search results. MAIN FINDINGS For the diagnosis section, 2294 unique records screened, 55 were eligible for inclusion. For the microbiology section 705 unique records were screened and 137 articles were eligible for inclusion. The main themes that arose in OM diagnosis were the need to incorporate multiple modalities including video-otoscopy, tympanometry, telemedicine and artificial intelligence for accurate diagnoses in all diagnostic settings. Further to this, was the use of new, cheap, readily available tools which may improve access in rural and lowmiddle income (LMIC) settings. For OM aetiology, PCR remains the most sensitive method for detecting middle ear pathogens with microbiome analysis still largely restricted to research use. The global pandemic response reduced rates of OM in children, but post-pandemic shifts should be monitored. IMPLICATION FOR PRACTICE AND FUTURE RESEARCH Cheap, easy to use multi-technique assessments combined with artificial intelligence and/or telemedicine should be integrated into future practice to improve diagnosis and treatment pathways in OM diagnosis. Longitudinal studies investigating the in-vivo process of OM development, timings and in-depth interactions between the triad of bacteria, viruses and the host immune response are still required. Standardized methods of collection and analysis for microbiome studies to enable inter-study comparisons are required. There is a need to target underlying biofilms if going to effectively prevent rAOM and OME and possibly enhance ventilation tube retention.
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Affiliation(s)
- Sharon Ovnat Tamir
- Department of Otolaryngology-Head and Neck Surgery, Sasmon Assuta Ashdod University Hospital, Faculty of Health Sciences, Ben Gurion University of the Negev, Israel.
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Christopher G Brennan-Jones
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia; Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - Carolina Der
- Facultad de Medicina, Universidad Del Desarrollo, Dr Luis Calvo Mackenna Hospital, Santiago, Chile
| | - Liron Kariv
- Hearing, Speech and Language Institute, Sasmon Assuta Ashdod University Hospital, Israel
| | - Ian Macharia
- Kenyatta University Teaching, Referral & Research Hospital, Kenya
| | - Robyn L Marsh
- Menzies School of Health Research, Darwin, Australia; School of Health Sciences, University of Tasmania, Launceston, Australia
| | - Amina Seguya
- Department of Otolaryngology - Head and Neck Surgery, Mulago National Referral Hospital, Kampala, Uganda
| | - Ruth Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia; Centre for Child Health Research, University of Western Australia, Perth, Australia
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Salter SJ, Marsh RL, Parkhill J. Complete Genome Sequence of Ornithobacterium hominis Type Strain MSHR-COH1 (ATCC TSD-185). Microbiol Resour Announc 2023:e0037923. [PMID: 37382534 DOI: 10.1128/mra.00379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
We report the complete genome sequence of the Ornithobacterium hominis type strain MSHR-COH1 (ATCC TSD-185/NCTC 14317), a bacterial species isolated from the human nasopharynx. Long-read sequencing reveals that the genome is 2,036,909 bp in length, with a GC content of 35.72%.
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Affiliation(s)
- Susannah J Salter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- School of Health Sciences, University of Tasmania, Hobart, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Bowman‐Derrick S, Harris TM, Beissbarth J, Kleinecke M, Lawrence K, Wozniak TM, Bleakley A, Rumaseb A, Binks MJ, Marsh RL, Morris PS, Leach AJ, Smith‐Vaughan H. Can non‐typeable
Haemophilus influenzae
carriage surveillance data infer antimicrobial resistance associated with otitis media? Pediatr Investig 2023; 7:13-22. [PMID: 36967743 PMCID: PMC10030701 DOI: 10.1002/ped4.12364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/29/2022] [Indexed: 02/10/2023] Open
Abstract
Importance In remote communities of the Northern Territory, Australia, children experience high rates of otitis media (OM), commonly caused by non-typeable Haemophilus influenzae (NTHi). Few data exist on antibiotic susceptibility of NTHi from OM. Objective To determine whether population-level nasopharyngeal NTHi antibiotic susceptibility data could inform antibiotic treatment for OM. Methods NTHi isolates (n = 92) collected from ear discharge between 2003 and 2013 were selected to time- and age-match NTHi isolates from the nasopharyngeal carriage (n = 95). Antimicrobial susceptibility were tested. Phylogenomic trees and a genome-wide association study (GWAS) were performed to determine the similarity of nasopharyngeal and ear isolates at a population level. Results Among 174 NTHi isolates available for antimicrobial susceptibility testing, 10.3% (18/174) were resistant to ampicillin and 9.2% (16/174) were resistant to trimethoprim-sulfamethoxazole. Small numbers of isolates (≤3) were resistant to tetracycline, chloramphenicol, or amoxicillin-clavulanic acid. There was no statistical difference in the proportion of ampicillin-resistant (P = 0.11) or trimethoprim-sulfamethoxazole-resistant isolates (P = 0.70) between ear discharge and nasopharynx-derived NTHi isolates. Three multi-drug resistant NTHi isolates were identified. Phylogenomic trees showed no clustering of 187 Haemophilus influenzae isolates based on anatomical niche (nasopharynx or ear discharge), and no genetic variations that distinguished NTHi derived from ear discharge and nasopharyngeal carriage were evident in the GWAS. Interpretation In this population-level study, nasopharyngeal and ear discharge isolates did not represent distinct microbial populations. These results support tracking of population-level nasopharyngeal NTHi antibiotic resistance patterns to inform clinical management of OM in this population.
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Affiliation(s)
| | - Tegan M. Harris
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Jemima Beissbarth
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Mariana Kleinecke
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Katrina Lawrence
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Teresa M. Wozniak
- Menzies School of Health Research Charles Darwin University Darwin Australia
- Australian e‐Health Research Centre CSIRO Brisbane Australia
| | - Amy Bleakley
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Angela Rumaseb
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Michael J. Binks
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Robyn L. Marsh
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Peter S. Morris
- Menzies School of Health Research Charles Darwin University Darwin Australia
- Royal Darwin Hospital Darwin Australia
| | - Amanda J. Leach
- Menzies School of Health Research Charles Darwin University Darwin Australia
| | - Heidi Smith‐Vaughan
- Menzies School of Health Research Charles Darwin University Darwin Australia
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Mason KM, Marsh RL, Pelton SI, Harvill ET. Editorial: Otitis media. Front Cell Infect Microbiol 2022; 12:1063153. [PMID: 36506022 PMCID: PMC9733949 DOI: 10.3389/fcimb.2022.1063153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Kevin M. Mason
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, United States,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States,*Correspondence: Kevin M. Mason, ; Robyn L. Marsh, ; Stephen I. Pelton, ; Eric T. Harvill,
| | - Robyn L. Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia,*Correspondence: Kevin M. Mason, ; Robyn L. Marsh, ; Stephen I. Pelton, ; Eric T. Harvill,
| | - Stephen I. Pelton
- Boston University Chobanian & Avedisian School of Medicine, Boston, MA, United States,Department of Pediatrics, Boston Medical Center, Boston, MA, United States,*Correspondence: Kevin M. Mason, ; Robyn L. Marsh, ; Stephen I. Pelton, ; Eric T. Harvill,
| | - Eric T. Harvill
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States,*Correspondence: Kevin M. Mason, ; Robyn L. Marsh, ; Stephen I. Pelton, ; Eric T. Harvill,
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10
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Marsh RL, Binks MJ, Smith-Vaughan HC, Janka M, Clark S, Richmond P, Chang AB, Thornton RB. Prevalence and subtyping of biofilms present in bronchoalveolar lavage from children with protracted bacterial bronchitis or non-cystic fibrosis bronchiectasis: a cross-sectional study. The Lancet Microbe 2022; 3:e215-e223. [DOI: 10.1016/s2666-5247(21)00300-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022] Open
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11
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Broderick DTJ, Waite DW, Marsh RL, Camargo CA, Cardenas P, Chang AB, Cookson WOC, Cuthbertson L, Dai W, Everard ML, Gervaix A, Harris JK, Hasegawa K, Hoffman LR, Hong SJ, Josset L, Kelly MS, Kim BS, Kong Y, Li SC, Mansbach JM, Mejias A, O’Toole GA, Paalanen L, Pérez-Losada M, Pettigrew MM, Pichon M, Ramilo O, Ruokolainen L, Sakwinska O, Seed PC, van der Gast CJ, Wagner BD, Yi H, Zemanick ET, Zheng Y, Pillarisetti N, Taylor MW. Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis. Front Microbiol 2021; 12:711134. [PMID: 35002989 PMCID: PMC8733647 DOI: 10.3389/fmicb.2021.711134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.
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Affiliation(s)
| | - David W. Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Robyn L. Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Paul Cardenas
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Anne B. Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Queensland Children’s Hospital, Brisbane, QLD, Australia
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - William O. C. Cookson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Leah Cuthbertson
- Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Wenkui Dai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Mark L. Everard
- School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Alain Gervaix
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lucas R. Hoffman
- Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics and Microbiology, University of Washington, Seattle, WA, United States
| | - Soo-Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University, Durham, NC, United States
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, South Korea
| | - Yong Kong
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Shuai C. Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jonathan M. Mansbach
- Harvard Medical School, Boston, MA, United States
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Asuncion Mejias
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Laura Paalanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Melinda M. Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Maxime Pichon
- CHU Poitiers, Infectious Agents Department, Poitiers, France
- University of Poitiers, INSERM U1070, Poitiers, France
| | - Octavio Ramilo
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lasse Ruokolainen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Patrick C. Seed
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Aurora, CO, United States
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | | | - Michael W. Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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12
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Bates AE, Primack RB, Biggar BS, Bird TJ, Clinton ME, Command RJ, Richards C, Shellard M, Geraldi NR, Vergara V, Acevedo-Charry O, Colón-Piñeiro Z, Ocampo D, Ocampo-Peñuela N, Sánchez-Clavijo LM, Adamescu CM, Cheval S, Racoviceanu T, Adams MD, Kalisa E, Kuuire VZ, Aditya V, Anderwald P, Wiesmann S, Wipf S, Badihi G, Henderson MG, Loetscher H, Baerenfaller K, Benedetti-Cecchi L, Bulleri F, Bertocci I, Maggi E, Rindi L, Ravaglioli C, Boerder K, Bonnel J, Mathias D, Archambault P, Chauvaud L, Braun CD, Thorrold SR, Brownscombe JW, Midwood JD, Boston CM, Brooks JL, Cooke SJ, China V, Roll U, Belmaker J, Zvuloni A, Coll M, Ortega M, Connors B, Lacko L, Jayathilake DRM, Costello MJ, Crimmins TM, Barnett L, Denny EG, Gerst KL, Marsh RL, Posthumus EE, Rodriguez R, Rosemartin A, Schaffer SN, Switzer JR, Wong K, Cunningham SJ, Sumasgutner P, Amar A, Thomson RL, Stofberg M, Hofmeyr S, Suri J, Stuart-Smith RD, Day PB, Edgar GJ, Cooper AT, De Leo FC, Garner G, Des Brisay PG, Schrimpf MB, Koper N, Diamond MS, Dwyer RG, Baker CJ, Franklin CE, Efrat R, Berger-Tal O, Hatzofe O, Eguíluz VM, Rodríguez JP, Fernández-Gracia J, Elustondo D, Calatayud V, English PA, Archer SK, Dudas SE, Haggarty DR, Gallagher AJ, Shea BD, Shipley ON, Gilby BL, Ballantyne J, Olds AD, Henderson CJ, Schlacher TA, Halliday WD, Brown NAW, Woods MB, Balshine S, Juanes F, Rider MJ, Albano PS, Hammerschlag N, Hays GC, Esteban N, Pan Y, He G, Tanaka T, Hensel MJS, Orth RJ, Patrick CJ, Hentati-Sundberg J, Olsson O, Hessing-Lewis ML, Higgs ND, Hindell MA, McMahon CR, Harcourt R, Guinet C, Hirsch SE, Perrault JR, Hoover SR, Reilly JD, Hobaiter C, Gruber T, Huveneers C, Udyawer V, Clarke TM, Kroesen LP, Hik DS, Cherry SG, Del Bel Belluz JA, Jackson JM, Lai S, Lamb CT, LeClair GD, Parmelee JR, Chatfield MWH, Frederick CA, Lee S, Park H, Choi J, LeTourneux F, Grandmont T, de-Broin FD, Bêty J, Gauthier G, Legagneux P, Lewis JS, Haight J, Liu Z, Lyon JP, Hale R, D'Silva D, MacGregor-Fors I, Arbeláez-Cortés E, Estela FA, Sánchez-Sarria CE, García-Arroyo M, Aguirre-Samboní GK, Franco Morales JC, Malamud S, Gavriel T, Buba Y, Salingré S, Lazarus M, Yahel R, Ari YB, Miller E, Sade R, Lavian G, Birman Z, Gury M, Baz H, Baskin I, Penn A, Dolev A, Licht O, Karkom T, Davidzon S, Berkovitch A, Yaakov O, Manenti R, Mori E, Ficetola GF, Lunghi E, March D, Godley BJ, Martin C, Mihaly SF, Barclay DR, Thomson DJM, Dewey R, Bedard J, Miller A, Dearden A, Chapman J, Dares L, Borden L, Gibbs D, Schultz J, Sergeenko N, Francis F, Weltman A, Moity N, Ramírez-González J, Mucientes G, Alonso-Fernández A, Namir I, Bar-Massada A, Chen R, Yedvab S, Okey TA, Oppel S, Arkumarev V, Bakari S, Dobrev V, Saravia-Mullin V, Bounas A, Dobrev D, Kret E, Mengistu S, Pourchier C, Ruffo A, Tesfaye M, Wondafrash M, Nikolov SC, Palmer C, Sileci L, Rex PT, Lowe CG, Peters F, Pine MK, Radford CA, Wilson L, McWhinnie L, Scuderi A, Jeffs AG, Prudic KL, Larrivée M, McFarland KP, Solis R, Hutchinson RA, Queiroz N, Furtado MA, Sims DW, Southall E, Quesada-Rodriguez CA, Diaz-Orozco JP, Rodgers KS, Severino SJL, Graham AT, Stefanak MP, Madin EMP, Ryan PG, Maclean K, Weideman EA, Şekercioğlu ÇH, Kittelberger KD, Kusak J, Seminoff JA, Hanna ME, Shimada T, Meekan MG, Smith MKS, Mokhatla MM, Soh MCK, Pang RYT, Ng BXK, Lee BPYH, Loo AHB, Er KBH, Souza GBG, Stallings CD, Curtis JS, Faletti ME, Peake JA, Schram MJ, Wall KR, Terry C, Rothendler M, Zipf L, Ulloa JS, Hernández-Palma A, Gómez-Valencia B, Cruz-Rodríguez C, Herrera-Varón Y, Roa M, Rodríguez-Buriticá S, Ochoa-Quintero JM, Vardi R, Vázquez V, Requena-Mesa C, Warrington MH, Taylor ME, Woodall LC, Stefanoudis PV, Zhang X, Yang Q, Zukerman Y, Sigal Z, Ayali A, Clua EEG, Carzon P, Seguine C, Corradini A, Pedrotti L, Foley CM, Gagnon CA, Panipakoochoo E, Milanes CB, Botero CM, Velázquez YR, Milchakova NA, Morley SA, Martin SM, Nanni V, Otero T, Wakeling J, Abarro S, Piou C, Sobral AFL, Soto EH, Weigel EG, Bernal-Ibáñez A, Gestoso I, Cacabelos E, Cagnacci F, Devassy RP, Loretto MC, Moraga P, Rutz C, Duarte CM. Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biol Conserv 2021; 263:109175. [PMID: 34035536 PMCID: PMC8135229 DOI: 10.1016/j.biocon.2021.109175] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 05/19/2023]
Abstract
The global lockdown to mitigate COVID-19 pandemic health risks has altered human interactions with nature. Here, we report immediate impacts of changes in human activities on wildlife and environmental threats during the early lockdown months of 2020, based on 877 qualitative reports and 332 quantitative assessments from 89 different studies. Hundreds of reports of unusual species observations from around the world suggest that animals quickly responded to the reductions in human presence. However, negative effects of lockdown on conservation also emerged, as confinement resulted in some park officials being unable to perform conservation, restoration and enforcement tasks, resulting in local increases in illegal activities such as hunting. Overall, there is a complex mixture of positive and negative effects of the pandemic lockdown on nature, all of which have the potential to lead to cascading responses which in turn impact wildlife and nature conservation. While the net effect of the lockdown will need to be assessed over years as data becomes available and persistent effects emerge, immediate responses were detected across the world. Thus, initial qualitative and quantitative data arising from this serendipitous global quasi-experimental perturbation highlights the dual role that humans play in threatening and protecting species and ecosystems. Pathways to favorably tilt this delicate balance include reducing impacts and increasing conservation effectiveness.
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Affiliation(s)
- Amanda E Bates
- Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Road, St. John's A1K 3E6, Canada
| | - Richard B Primack
- Biology Department, Boston University, 881 Commonwealth Avenue, Boston, MA 02215, United States
| | - Brandy S Biggar
- Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Road, St. John's A1K 3E6, Canada
| | - Tomas J Bird
- Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's A1A 5J7, Canada
| | - Mary E Clinton
- Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Road, St. John's A1K 3E6, Canada
| | - Rylan J Command
- School of Ocean Technology, Fisheries and Marine Institute, Memorial University of Newfoundland, 155 Ridge Rd, St. John's, NL A1C 5R3, Canada
| | - Cerren Richards
- Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Road, St. John's A1K 3E6, Canada
| | - Marc Shellard
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Nathan R Geraldi
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Valeria Vergara
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Orlando Acevedo-Charry
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
| | | | - David Ocampo
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
| | - Natalia Ocampo-Peñuela
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Lina M Sánchez-Clavijo
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Cristian M Adamescu
- Research Center for Systems Ecology and Sustainability, University of Bucharest, 050095 Bucharest, Romania
| | - Sorin Cheval
- National Meteorological Administration, 013686 Bucharest, Romania
| | - Tudor Racoviceanu
- Research Center for Systems Ecology and Sustainability, University of Bucharest, 050095 Bucharest, Romania
| | - Matthew D Adams
- Department of Geography, Geomatics and Environment, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Egide Kalisa
- Department of Geography, Geomatics and Environment, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Vincent Z Kuuire
- Department of Geography, Geomatics and Environment, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Vikram Aditya
- Ashoka Trust for Research in Ecology and the Environment, PO, Royal Enclave, Bengaluru, Karnataka 560064, India
| | - Pia Anderwald
- Swiss National Park, Chastè Planta-Wildenberg, Runatsch 124, 7530 Zernez, Switzerland
| | - Samuel Wiesmann
- Swiss National Park, Chastè Planta-Wildenberg, Runatsch 124, 7530 Zernez, Switzerland
| | - Sonja Wipf
- Swiss National Park, Chastè Planta-Wildenberg, Runatsch 124, 7530 Zernez, Switzerland
| | - Gal Badihi
- Origins of Mind, School of Psychology, University of St Andrews, St Marys Quad, St Andrews, Fife KY16 9JP, Scotland, United Kingdom
| | - Matthew G Henderson
- Origins of Mind, School of Psychology, University of St Andrews, St Marys Quad, St Andrews, Fife KY16 9JP, Scotland, United Kingdom
| | - Hanspeter Loetscher
- Office for Nature and Environment of the Grisons, Ringstrasse 10, 7001 Chur, Switzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich and Swiss Institute of Bioinformatics (SIB), 7265 Davos, Switzerland
| | | | - Fabio Bulleri
- Department of Biology, University of Pisa, Via Derna 1, I-56126 Pisa, Italy
| | - Iacopo Bertocci
- Department of Biology, University of Pisa, Via Derna 1, I-56126 Pisa, Italy
| | - Elena Maggi
- Department of Biology, University of Pisa, Via Derna 1, I-56126 Pisa, Italy
| | - Luca Rindi
- Department of Biology, University of Pisa, Via Derna 1, I-56126 Pisa, Italy
| | - Chiara Ravaglioli
- Department of Biology, University of Pisa, Via Derna 1, I-56126 Pisa, Italy
| | - Kristina Boerder
- Biology Department, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4J1, Canada
| | - Julien Bonnel
- Woods Hole Oceanographic Institution, Applied Ocean Physics and Engineering Department, Woods Hole, MA 02543, USA
| | - Delphine Mathias
- Société d'Observation Multi-Modale de l'Environnement, 115 Rue Claude Chappe, 29280 Plouzané, France
| | - Philippe Archambault
- ArcticNet, Département de Biologie, Québec-Océan, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | - Laurent Chauvaud
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 CNRS, UBO, IRD, Ifremer, Institut Universitaire Européen de la Mer (IUEM), LIA BeBEST, rue Dumont D'Urville, 29280 Plouzané, France
| | - Camrin D Braun
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Simon R Thorrold
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Jacob W Brownscombe
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Jonathan D Midwood
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Christine M Boston
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Jill L Brooks
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Victor China
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Jonathan Belmaker
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
- The Steinhardt Museum of Natural History, Tel Aviv University, P.O. Box 39040, Tel Aviv 6139001, Israel
| | - Assaf Zvuloni
- Israel Nature and Parks Authority, Am V'Olamo 3, 95463 Jerusalem, Israel
| | - Marta Coll
- Institute of Marine Science (CSIC), Passeig Maritim de la Barceloneta 37-49 & Ecopath International Initiative (EII), Barcelona 08003, Spain
| | - Miquel Ortega
- Fundació ENT, Carrer Josep Llanza, 1-7, 2-3, Vilanova i la Geltrú, Barcelona, 08800 & Institut de Ciència i Tecnologia Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Valles, Spain
| | - Brendan Connors
- Quantitative Assessment Methods Section, Stock Assessment and Research Division, Pacific Region, Fisheries and Oceans Canada, 401 Burrard St Suite 200, Vancouver, BC V6C 3L6, Canada
| | - Lisa Lacko
- Quantitative Assessment Methods Section, Stock Assessment and Research Division, Pacific Region, Fisheries and Oceans Canada, 401 Burrard St Suite 200, Vancouver, BC V6C 3L6, Canada
| | | | - Mark J Costello
- Faculty of Biosciences and Aquaculture, Nord University, Bodo 1049, Norway
| | - Theresa M Crimmins
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - LoriAnne Barnett
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Ellen G Denny
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Katharine L Gerst
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - R L Marsh
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Erin E Posthumus
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Reilly Rodriguez
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Alyssa Rosemartin
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Sara N Schaffer
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Jeff R Switzer
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Kevin Wong
- USA National Phenology Network, School of Natural Resources and the Environment, University of Arizona, 1200 E. University Blvd, Tucson, AZ 85721, USA
| | - Susan J Cunningham
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Petra Sumasgutner
- Core Facility Konrad Lorenz Research Center for Behaviour and Cognition, University of Vienna, Fischerau 11, A-4645 Grünau im Almtal, Austria
| | - Arjun Amar
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Robert L Thomson
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Miqkayla Stofberg
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Sally Hofmeyr
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Jessleena Suri
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Rick D Stuart-Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Paul B Day
- Carijoa - Marine Environmental Consulting, 29 Sydenham Street, Rivervale, Perth, Western Australia 6103, Australia
| | - Graham J Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Antonia T Cooper
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Fabio Cabrera De Leo
- Ocean Networks Canada, University of Victoria, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Grant Garner
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Paulson G Des Brisay
- Environment and Climate Change Canada, 150-123 Main St, Winnipeg, MB R3C 4W2, Canada
| | - Michael B Schrimpf
- Natural Resources Institute, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Nicola Koper
- Natural Resources Institute, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | | | - Ross G Dwyer
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Cameron J Baker
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ron Efrat
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Oded Berger-Tal
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Ohad Hatzofe
- Science Division, Israel Nature and Parks Authority, Am V'Olamo 3, 95463 Jerusalem, Israel
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), E07122 Palma de Mallorca, Spain
| | - Jorge P Rodríguez
- Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), 07190 Esporles, Spain
| | - Juan Fernández-Gracia
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), E07122 Palma de Mallorca, Spain
| | - David Elustondo
- Instituto de Biodiversidad y Medioambiente (BIOMA), Universidad de Navarra, Pamplona 31080, Spain
| | - Vicent Calatayud
- Fundación CEAM, C/Charles R. Darwin 14, Parque Tecnológico, Paterna, Valencia 46980, Spain
| | - Philina A English
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Stephanie K Archer
- Louisiana Universities Marine Consortium, 8124 LA-56, Chauvin, LA 70344, United States
| | - Sarah E Dudas
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | - Dana R Haggarty
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
| | | | | | | | - Ben L Gilby
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Jasmine Ballantyne
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Andrew D Olds
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Christopher J Henderson
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Thomas A Schlacher
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - William D Halliday
- Wildlife Conservation Society Canada, P.O. Box 606, 202 B Ave, Kaslo, British Columbia V0G 1M0, Canada
| | - Nicholas A W Brown
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Mackenzie B Woods
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Sigal Balshine
- Department of Psychology, Neuroscience, and Behaviour, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Mitchell J Rider
- Rosenstiel School of Marine & Atmospheric Science, University of Miami, 1320 S Dixie Hwy, Coral Gables, FL 33146, United States
| | - Patricia S Albano
- Rosenstiel School of Marine & Atmospheric Science, University of Miami, 1320 S Dixie Hwy, Coral Gables, FL 33146, United States
| | - Neil Hammerschlag
- Rosenstiel School of Marine & Atmospheric Science, University of Miami, 1320 S Dixie Hwy, Coral Gables, FL 33146, United States
| | - Graeme C Hays
- Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, Australia
| | - Nicole Esteban
- Department of Biosciences, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Yuhang Pan
- Division of Social Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Guojun He
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Takanao Tanaka
- Division of Social Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Marc J S Hensel
- Virginia Institute of Marine Science, College of William and Mary, Sadler Center, 200 Stadium Dr, Williamsburg, VA 23185, United States
| | - Robert J Orth
- Virginia Institute of Marine Science, College of William and Mary, Sadler Center, 200 Stadium Dr, Williamsburg, VA 23185, United States
| | - Christopher J Patrick
- Virginia Institute of Marine Science, College of William and Mary, Sadler Center, 200 Stadium Dr, Williamsburg, VA 23185, United States
| | - Jonas Hentati-Sundberg
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Turistgatan 5, 453 30 Lysekil, Sweden
| | - Olof Olsson
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | - Nicholas D Higgs
- Cape Eleuthera Institute, Cape Eleuthera Island School, PO Box EL-26029, Rock Sound, Eleuthera, The Bahamas
| | - Mark A Hindell
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS 7005, Australia
| | - Clive R McMahon
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW 2088, Australia
| | - Rob Harcourt
- Department of Biological Sciences, Macquarie University, Balaclava Rd, Macquarie Park, NSW 2109, Australia
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé, Station d'Écologie de Chizé-La Rochelle Université, CNRS UMR7372, Villiers-en-Bois, France
| | - Sarah E Hirsch
- Loggerhead Marinelife Center, 14200 US-1, Juno Beach, FL 33408, United States
| | - Justin R Perrault
- Loggerhead Marinelife Center, 14200 US-1, Juno Beach, FL 33408, United States
| | - Shelby R Hoover
- Loggerhead Marinelife Center, 14200 US-1, Juno Beach, FL 33408, United States
| | - Jennifer D Reilly
- Loggerhead Marinelife Center, 14200 US-1, Juno Beach, FL 33408, United States
| | - Catherine Hobaiter
- Origins of Mind, School of Psychology, University of St Andrews, St Marys Quad, St Andrews, Fife KY16 9JP, Scotland, United Kingdom
| | - Thibaud Gruber
- Faculty of Psychology and Educational Sciences, Swiss Center for Affective Sciences, Chemin des Mines 9, 1202 Geneva, Switzerland
| | - Charlie Huveneers
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Vinay Udyawer
- Arafura Timor Research Facility, Australian Institute of Marine Science, Darwin, NT 0810, Australia
| | - Thomas M Clarke
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Laura P Kroesen
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada
| | - David S Hik
- Department of Biological Sciences, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada
| | - Seth G Cherry
- Parks Canada Agency, 5420 Highway 93, Radium Hot Springs, BC V0A 1M0, Canada
| | | | | | - Shengjie Lai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Hartley Library B12, University Rd, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Clayton T Lamb
- Department of Biology, University of British Columbia, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Gregory D LeClair
- University of Maine, 168 College Ave, Orono, ME 04469, United States
| | - Jeffrey R Parmelee
- University of New England, Department of Biology, Biddeford, ME 04005, United States
| | | | | | - Sangdon Lee
- Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, South Korea
| | - Hyomin Park
- Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, South Korea
| | - Jaein Choi
- Ewha Womans University, 52 Ewhayeodae-gil, Daehyeon-dong, Seodaemun-gu, Seoul, South Korea
| | - Frédéric LeTourneux
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | - Thierry Grandmont
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | - Frédéric Dulude de-Broin
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | - Joël Bêty
- Département de Biologie, Centre d'Études Nordiques, Université du Québec à Rimouski, 300 Allée des Ursulines, QC G5L 3A1, Canada
| | - Gilles Gauthier
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | - Pierre Legagneux
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
- Centre d'Etudes Biologiques de Chizé, Station d'Écologie de Chizé-La Rochelle Université, CNRS UMR7372, Villiers-en-Bois, France
| | - Jesse S Lewis
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, United States
| | - Jeffrey Haight
- School of Life Science, Arizona State University, 1151 S. Forest Ave, Tempe, AZ 85281, Canada
| | - Zhu Liu
- Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Jarod P Lyon
- Arthur Rylah Institute for Environmental Research, Department of Environment, Land, Water and Planning, Heidelberg, Victoria, Australia
| | - Robin Hale
- Arthur Rylah Institute for Environmental Research, Department of Environment, Land, Water and Planning, Heidelberg, Victoria, Australia
| | | | - Ian MacGregor-Fors
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland
| | - Enrique Arbeláez-Cortés
- Grupo de Estudios en Biodiversidad, Escuela de Biología, Universidad Industrial de Santander, Ciudad Universitaria Carrera 27 Calle 9, Bucaramanga, Santander, Colombia
| | - Felipe A Estela
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana-Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Camilo E Sánchez-Sarria
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana-Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Michelle García-Arroyo
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland
| | - Giann K Aguirre-Samboní
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana-Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Juan C Franco Morales
- Facultad de Ciencias Básicas, Universidad Autónoma de Occidente, Calle 25, Vía Cali - Puerto Tejada 115-85 Km 2, Jamundí, Cali, Valle del Cauca, Colombia
| | - Shahar Malamud
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Tal Gavriel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Yehezkel Buba
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Shira Salingré
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Mai Lazarus
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Ruthy Yahel
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Yigael Ben Ari
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Eyal Miller
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Rotem Sade
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Guy Lavian
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Ziv Birman
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Manor Gury
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Harel Baz
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Ilia Baskin
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Alon Penn
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Amit Dolev
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Ogen Licht
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Tabi Karkom
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Sharon Davidzon
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Avi Berkovitch
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Ofer Yaakov
- Israel Nature and Parks Authority, Am V'Olamo 3, Jerusalem 95463, Israel
| | - Raoul Manenti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, I-20133 Milano, Italy
| | - Emiliano Mori
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, I-20133 Milano, Italy
| | - Enrico Lunghi
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1, 100101 Beijing, China
| | - David March
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Brendan J Godley
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Cecilia Martin
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Steven F Mihaly
- Ocean Networks Canada, University of Victoria Queenswood Campus, 2474 Arbutus Road, Victoria, BC V8N 1V8, Canada
| | - David R Barclay
- Department of Oceanography, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B4H 4R2, Canada
| | - Dugald J M Thomson
- Department of Oceanography, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B4H 4R2, Canada
| | - Richard Dewey
- Ocean Networks Canada, University of Victoria Queenswood Campus, 2474 Arbutus Road, Victoria, BC V8N 1V8, Canada
| | - Jeannette Bedard
- Ocean Networks Canada, University of Victoria Queenswood Campus, 2474 Arbutus Road, Victoria, BC V8N 1V8, Canada
| | - Aroha Miller
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Amber Dearden
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Jennifer Chapman
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Lauren Dares
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Laura Borden
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Donna Gibbs
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Jessica Schultz
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Nikita Sergeenko
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Fiona Francis
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Amanda Weltman
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver V6B 3X8, Canada
| | - Nicolas Moity
- Charles Darwin Research Station, Charles Darwin Foundation, Av. Charles Darwin, Santa Cruz, Galapagos, Ecuador
| | - Jorge Ramírez-González
- Charles Darwin Research Station, Charles Darwin Foundation, Av. Charles Darwin, Santa Cruz, Galapagos, Ecuador
| | - Gonzalo Mucientes
- Instituto de Investigaciones Marinas (IIM-CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | | | - Itai Namir
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Avi Bar-Massada
- Department of Biology and Environment, University of Haifa at Oranim, 36006 Tivon, Israel
| | - Ron Chen
- Hamaarag, The Steinhardt Museum of Natural History, Tel Aviv University, P.O. Box 39040, Tel Aviv 6139001, Israel
| | - Shmulik Yedvab
- The Mammal Center, Society for the Protection of Nature in Israel, Israel
| | - Thomas A Okey
- School of Environmental Studies, University of Victoria, PO Box 1700 STN CSC, Victoria, BC V8W 2Y2, Canada
| | - Steffen Oppel
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Cambridge, United Kingdom
| | | | - Samuel Bakari
- BirdLife International, Africa Partnership Secretariat, Nairobi, Kenya
| | | | | | | | | | | | - Solomon Mengistu
- Ethiopia Wildlife and Natural History Society, Addis Ababa, Ethiopia/Dilla University, Natural and Computational Sciences, Department of Biology, P.O. Box, 419, Dilla, Ethiopia
| | | | - Alazar Ruffo
- Faculty of Natural Science, Department of Zoological Science, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Mengistu Wondafrash
- Ethiopia Wildlife and Natural History Society, Addis Ababa, Ethiopia/Dilla University, Natural and Computational Sciences, Department of Biology, P.O. Box, 419, Dilla, Ethiopia
| | | | - Charles Palmer
- Department of Geography and Environment, London School of Economics and Political Science, UK
| | - Lorenzo Sileci
- Department of Geography and Environment, London School of Economics and Political Science, UK
| | - Patrick T Rex
- Dept of Biological Sciences, California State University Long Beach, Long Beach, CA, USA
| | - Christopher G Lowe
- Dept of Biological Sciences, California State University Long Beach, Long Beach, CA, USA
| | - Francesc Peters
- Institute of Marine Sciences (CSIC), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Matthew K Pine
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Craig A Radford
- Institute of Marine Science, University of Auckland, New Zealand
| | - Louise Wilson
- Institute of Marine Science, University of Auckland, New Zealand
| | - Lauren McWhinnie
- School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, Scotland, United Kingdom
| | - Alessia Scuderi
- Marine and Environmental Science Faculty, University of Cádiz, Cádiz, Spain
| | - Andrew G Jeffs
- Institute of Marine Science, University of Auckland, New Zealand
| | - Kathleen L Prudic
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Maxim Larrivée
- Montreal Space for Life, Insectarium, Montreal, QC, Canada
| | | | - Rodrigo Solis
- Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Rebecca A Hutchinson
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Nuno Queiroz
- Centro de Investigação em Biodiversidade e Recursos Genéticos/Research Network in Biodiversity and Evolutionary Biology, Campus Agrário de Vairão, Universidade do Porto, 4485-668 Vairão, Portugal
| | - Miguel A Furtado
- Centro de Investigação em Biodiversidade e Recursos Genéticos/Research Network in Biodiversity and Evolutionary Biology, Campus Agrário de Vairão, Universidade do Porto, 4485-668 Vairão, Portugal
| | - David W Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Emily Southall
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | | | - Ku'ulei S Rodgers
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Sarah J L Severino
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Andrew T Graham
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Matthew P Stefanak
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Elizabeth M P Madin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Kyle Maclean
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Eleanor A Weideman
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Çağan H Şekercioğlu
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112-0840, USA
| | - Kyle D Kittelberger
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112-0840, USA
| | - Josip Kusak
- Department of Veterinary Biology, Veterinary Faculty, University of Zagreb, Zagreb, Croatia
| | - Jeffrey A Seminoff
- NOAA-National Marine Fisheries Service, 8901 La Jolla Shores Dr., La Jolla, CA 92037, USA
| | - Megan E Hanna
- Scripps Institution of Oceanography, 8622 Kennel Way, La Jolla, CA 92037, USA
| | - Takahiro Shimada
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mark G Meekan
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre (M096), University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Martin K S Smith
- Rondevlei Scientific Services, South African National Parks, Garden Route 6570, South Africa
| | - Mohlamatsane M Mokhatla
- Rondevlei Scientific Services, South African National Parks, Garden Route 6570, South Africa
| | - Malcolm C K Soh
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Roanna Y T Pang
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Breyl X K Ng
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Benjamin P Y-H Lee
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Adrian H B Loo
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Kenneth B H Er
- National Parks Board, 1 Cluny Rd, Singapore Botanic Gardens, Singapore 259569, Singapore
| | - Gabriel B G Souza
- Postgraduate Program in Ecology, Federal University of Rio de Janeiro, Av. Pedro Calmon, 550 Cidade Universitária da Universidade Federal do Rio de Janeiro, RJ 21941-901, Brazil
| | | | - Joseph S Curtis
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Meaghan E Faletti
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Jonathan A Peake
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Michael J Schram
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Kara R Wall
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA
| | - Carina Terry
- Biology Department, Boston University, 881 Commonwealth Avenue, Boston, MA 02215, United States
| | - Matt Rothendler
- Biology Department, Boston University, 881 Commonwealth Avenue, Boston, MA 02215, United States
| | - Lucy Zipf
- Biology Department, Boston University, 881 Commonwealth Avenue, Boston, MA 02215, United States
| | - Juan Sebastián Ulloa
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Angélica Hernández-Palma
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Bibiana Gómez-Valencia
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Cristian Cruz-Rodríguez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Yenifer Herrera-Varón
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Margarita Roa
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Susana Rodríguez-Buriticá
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Jose Manuel Ochoa-Quintero
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar 16-20, Bogotá D.C., Colombia
| | - Reut Vardi
- The Albert Katz International School for Desert Studies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Víctor Vázquez
- Department of Research and Development, Coccosphere Environmental Analysis, C/Cruz 39, 29120 Alhaurín el Grande, Málaga, Spain
| | - Christian Requena-Mesa
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Miyako H Warrington
- Natural Resources Institute, University of Manitoba, 317 Sinnott Bldg., 70 Dysart Rd., Winnipeg, MB R3T 2M6, Canada
| | - Michelle E Taylor
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Lucy C Woodall
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, United Kingdom
| | - Paris V Stefanoudis
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, United Kingdom
| | - Xiangliang Zhang
- Computational Biosciences Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Qiang Yang
- Computational Biosciences Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Yuval Zukerman
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Zehava Sigal
- Science Division, Israel Nature and Parks Authority, Am V'Olamo 3, 95463 Jerusalem, Israel
| | - Amir Ayali
- School of Zoology, Tel aviv University, Tel Aviv 6997802, Israel
| | - Eric E G Clua
- PSL Research University CRIOBE USR3278 EPHE-CNRS-UPVD BP1013, 98729 Papetoai, French Polynesia
| | - Pamela Carzon
- PSL Research University CRIOBE USR3278 EPHE-CNRS-UPVD BP1013, 98729 Papetoai, French Polynesia
| | - Clementine Seguine
- PSL Research University CRIOBE USR3278 EPHE-CNRS-UPVD BP1013, 98729 Papetoai, French Polynesia
| | - Andrea Corradini
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Calepina, 14, 38122 Trento, Italy
| | | | - Catherine M Foley
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA
| | - Catherine Alexandra Gagnon
- Département de Biologie, Centre d'Études Nordiques, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
| | | | - Celene B Milanes
- Civil and Environmental Department, Universidad de La Costa, Cl. 58 #55 - 66, Barranquilla, Atlántico, Colombia
| | - Camilo M Botero
- School of Law, Universidad Sergio Arboleda, Santa Marta, Colombia
| | - Yunior R Velázquez
- Multidisciplinary Studies Center of Coastal Zone, Universidad de Oriente, Avenida Patricio Lumumba S/N, Santiago de Cuba 90500, Cuba
| | - Nataliya A Milchakova
- Institute of Biology of the Southern Seas, Russian Academian Science, Sevastopol 299011, Russia
| | - Simon A Morley
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, Cambridgeshire CB30ET, UK
| | - Stephanie M Martin
- Government of Tristan da Cunha, Jamestown STHL 1ZZ, Saint Helena, Ascension and Tristan da Cunha
| | - Veronica Nanni
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di Genova, Corso Europa 26, 16132 Genova, Italy
| | - Tanya Otero
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver, BC V6B 3X8, Canada
| | - Julia Wakeling
- Ocean Wise Conservation Association, 845 Avison Way, Vancouver, BC V6B 3X8, Canada
| | - Sarah Abarro
- WWF-Canada, 60 St Jacques St, Montreal, Quebec H2Y 1L5, Canada
| | - Cyril Piou
- CIRAD, UMR CBGP, INRAE, IRD, Montpellier SupAgro, Univ. Montpellier, F-34398 Montpellier, France
| | - Ana F L Sobral
- Okeanos Research Centre of the University of the Azores, Rua Prof. Dr. Frederico Machado, 9901-862 Horta, Azores, Portugal
| | - Eulogio H Soto
- Centro de Observación Marino para Estudios de Riesgos del Ambiente Costero (COSTAR), Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Viña del Mar, Chile
| | - Emily G Weigel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alejandro Bernal-Ibáñez
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Funchal, Portugal
| | - Ignacio Gestoso
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Funchal, Portugal
| | - Eva Cacabelos
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Funchal, Portugal
| | - Francesca Cagnacci
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Italy
| | - Reny P Devassy
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
| | - Matthias-Claudio Loretto
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
| | - Paula Moraga
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, Sir Harold Mitchell Building, St Andrews KY16 9TH, UK
| | - Carlos M Duarte
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology, 23955 Thuwal, Saudi Arabia
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Smith‐Vaughan HC, Cheng AC, Tabrizi SN, Wurzel DF, Beissbarth J, Leach AJ, Morris PS, Binks MJ, Torzillo PJ, Chang AB, Marsh RL. Absence of human papillomavirus in nasopharyngeal swabs from infants in a population at high risk of human papillomavirus infection. Pediatr Investig 2021; 5:136-139. [PMID: 34179711 PMCID: PMC8212721 DOI: 10.1002/ped4.12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/02/2020] [Indexed: 11/09/2022] Open
Abstract
Maternal urogenital human papillomavirus (HPV) infection may place neonates at risk of HPV acquisition and subsequently lower respiratory infections as HPV can influence development of immunity. The respiratory HPV prevalence is not known in remote-dwelling Aboriginal infants, who are at high risk of respiratory infection and where the population prevalence of urogenital HPV in women is high. These data are necessary to inform HPV vaccination regimens. A retrospective analysis using PCR specific for HPV was performed on 64 stored nasopharyngeal swabs from remote-dwelling Aboriginal infants < 6 months of age, with and without hospitalised pneumonia. HPV DNA was not detected in any specimen. Despite the negative result, we cannot exclude a role for HPV in respiratory infections affecting infants in this population; however, our data do not support HPV as an important contributor to acute respiratory infection in remote-dwelling Aboriginal children.
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Affiliation(s)
- Heidi C Smith‐Vaughan
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
- School of MedicineGriffith UniversityGold CoastAustralia
| | | | - Sepehr N. Tabrizi
- Murdoch Children’s Research InstituteThe Royal Children’s HospitalMelbourneAustralia
- Department of Obstetrics and GynaecologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Danielle F Wurzel
- Murdoch Children’s Research InstituteThe Royal Children’s HospitalMelbourneAustralia
| | - Jemima Beissbarth
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
| | - Amanda J Leach
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
| | - Peter S Morris
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
- Royal Darwin HospitalDarwinAustralia
| | - Michael J Binks
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
| | | | - Anne B Chang
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
- Dept of Respiratory and Sleep MedicineQueensland Children’s HospitalBrisbaneAustralia
| | - Robyn L Marsh
- Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
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14
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Coleman A, Bialasiewicz S, Marsh RL, Grahn Håkansson E, Cottrell K, Wood A, Jayasundara N, Ware RS, Zaugg J, Sidjabat HE, Adams J, Ferguson J, Brown M, Roos K, Cervin A. Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children. J Pediatric Infect Dis Soc 2021; 10:468-476. [PMID: 33393596 DOI: 10.1093/jpids/piaa141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health. METHODS In total, 103 Indigenous Australian children aged 2-7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children's ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis. RESULTS Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children. CONCLUSIONS Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.
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Affiliation(s)
- Andrea Coleman
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia.,Department of Surgery-Otolaryngology, Head and Neck Surgery, Townsville University Hospital, Townsville, Australia
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Eva Grahn Håkansson
- Department of Clinical Microbiology, Umeå University and Essum AB, Umeå, Sweden
| | - Kyra Cottrell
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Amanda Wood
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | - Nadeesha Jayasundara
- Queensland Pediatric Infectious Diseases Laboratory, Queensland Children's Hospital, South Brisbane, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
| | - Julian Zaugg
- Children's Health Research Centre, The University of Queensland Centre for Clinical Research, South Brisbane, Australia
| | - Hanna E Sidjabat
- The University of Queensland Centre for Clinical Research, Herston, Australia
| | - Jasmyn Adams
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Matthew Brown
- Queensland Health Deadly Ears Program, Brisbane, Australia
| | | | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Herston, Australia.,Department of Otolaryngology, Head and Neck Surgery, The Royal Brisbane and Women's Hospital, Brisbane, Australia
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15
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Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR. Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. Cell Rep 2020; 26:2227-2240.e5. [PMID: 30784601 PMCID: PMC6435281 DOI: 10.1016/j.celrep.2019.01.091] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 01/25/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in micro-biological analyses of complex, chronic infection specimens. Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.
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Affiliation(s)
- Maria T Nelson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Christopher E Pope
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0811, Australia
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Anh T Vo
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Mitchell J Brittnacher
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Computer Science and Engineering, University of Washington School of Medicine, Seattle, WA 98105, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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16
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Marsh RL, Aho C, Beissbarth J, Bialasiewicz S, Binks M, Cervin A, Kirkham LAS, Lemon KP, Slack MPE, Smith-Vaughan HC. Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109836. [PMID: 31879084 PMCID: PMC7085411 DOI: 10.1016/j.ijporl.2019.109836] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019. DATA SOURCES PubMed database, National Library of Medicine. REVIEW METHODS Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members. CONCLUSIONS Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data. IMPLICATIONS FOR PRACTICE Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.
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Affiliation(s)
- Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia.
| | - Celestine Aho
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Seweryn Bialasiewicz
- The University of Queensland, Australian Centre for Ecogenomics, Queensland, Australia; Children's Health Queensland, Centre for Children's Health Research, Queensland, Australia
| | - Michael Binks
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Lea-Ann S Kirkham
- Centre for Child Health Research, University of Western Australia, Western Australia, Australia; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Western Australia, Australia
| | - Katherine P Lemon
- Forsyth Institute (Microbiology), USA and Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Massachusetts, USA; Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology and Pediatrics, Infectious Diseases Section, Texas Children's Hospital, Baylor College of Medicine, Texas, USA
| | - Mary P E Slack
- School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia; School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
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17
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Cox SM, Easton KL, Lear MC, Marsh RL, Delp SL, Rubenson J. The Interaction of Compliance and Activation on the Force-Length Operating Range and Force Generating Capacity of Skeletal Muscle: A Computational Study using a Guinea Fowl Musculoskeletal Model. Integr Org Biol 2019; 1:obz022. [PMID: 32510037 PMCID: PMC7259458 DOI: 10.1093/iob/obz022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A muscle’s performance is influenced by where it operates on its force–length (F–L) curve. Here we explore how activation and tendon compliance interact to influence muscle operating lengths and force-generating capacity. To study this, we built a musculoskeletal model of the lower limb of the guinea fowl and simulated the F–L operating range during fixed-end fixed-posture contractions for 39 actuators under thousands of combinations of activation and posture using three different muscle models: Muscles with non-compliant tendons, muscles with compliant tendons but no activation-dependent shift in optimal fiber length (L0), and muscles with both compliant tendons and activation-dependent shifts in L0. We found that activation-dependent effects altered muscle fiber lengths up to 40% and increased or decreased force capacity by up to 50% during fixed-end contractions. Typically, activation-compliance effects reduce muscle force and are dominated by the effects of tendon compliance at high activations. At low activation, however, activation-dependent shifts in L0 are equally important and can result in relative force changes for low compliance muscles of up to 60%. There are regions of the F–L curve in which muscles are most sensitive to compliance and there are troughs of influence where these factors have little effect. These regions are hard to predict, though, because the magnitude and location of these areas of high and low sensitivity shift with compliance level. In this study we provide a map for when these effects will meaningfully influence force capacity and an example of their contributions to force production during a static task, namely standing.
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Affiliation(s)
- S M Cox
- Biomechanics Laboratory, Kinesiology Department, The Pennsylvania State University, University Park, PA 16802, USA.,Biomechanics Laboratory, Kinesiology Department, The Pennsylvania State University, University Park, PA 16802, USA
| | - K L Easton
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - M Cromie Lear
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - R L Marsh
- Department of Biology, Northeastern University, Boston, MA 02115, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - S L Delp
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.,Departments of Bioengineering and Orthopedic Surgery, Stanford University, Stanford, CA 94305, USA
| | - J Rubenson
- Biomechanics Laboratory, Kinesiology Department, The Pennsylvania State University, University Park, PA 16802, USA.,School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
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18
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Lawrence KA, Harris TM, Salter SJ, Hall RW, Smith-Vaughan HC, Chang AB, Marsh RL. Method for culturing Candidatus Ornithobacterium hominis. J Microbiol Methods 2019; 159:157-160. [DOI: 10.1016/j.mimet.2019.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
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19
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Marsh RL, Smith-Vaughan HC, Chen AC, Marchant JM, Yerkovich ST, Gibson PG, Pizzutto SJ, Hodge S, Upham JW, Chang AB. Multiple Respiratory Microbiota Profiles Are Associated With Lower Airway Inflammation in Children With Protracted Bacterial Bronchitis. Chest 2019; 155:778-786. [DOI: 10.1016/j.chest.2019.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/01/2022] Open
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20
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Coleman A, Wood A, Bialasiewicz S, Ware RS, Marsh RL, Cervin A. The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media. Microbiome 2018; 6:199. [PMID: 30396360 PMCID: PMC6219068 DOI: 10.1186/s40168-018-0577-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic review of the literature exploring the upper airway and middle ear microbiota in relation to OM in indigenous children. METHODS Papers targeting microbiota in relation to OM in children < 18 years indigenous to Australia, New Zealand, North America, and Greenland were sought. MEDLINE, CINAHL, EMBASE, Cochrane Library, and Informit databases were searched using key words. Two independent reviewers screened titles, abstracts, and then full-text papers against inclusion criteria according to PRISMA guidelines. RESULTS Twenty-five papers considering indigenous Australian, Alaskan, and Greenlandic children were included. There were high rates of nasopharyngeal colonization with the three main otopathogens (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) in indigenous children with OM. Middle ear samples had lower rates of otopathogen detection, although detection rates increased when molecular methods were used. Pseudomonas aeruginosa and Staphylococcus aureus were commonly detected in middle ear discharge of children with chronic suppurative OM. There was a significant heterogeneity between studies, particularly in microbiological methods, which were largely limited to culture-based detection of the main otopathogens. CONCLUSIONS There are high rates of otopathogen colonization in indigenous children with OM. Chronic suppurative OM appears to be associated with a different microbial profile. Beyond the main otopathogens, the data are limited. Further research is required to explore the entire upper respiratory tract/middle ear microbiota in relation to OM, with the inclusion of healthy indigenous peers as controls.
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Affiliation(s)
- Andrea Coleman
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland Australia
- Queensland Pediatric Infectious Disease Laboratory, Centre for Children’s Health Research, Children’s Health Queensland Hospital, Queensland University of Technology, Child Health Research Centre, The University of Queensland, 62 Graham Street, South Brisbane, Queensland 4101 Australia
| | - Amanda Wood
- The Deadly Ears Program, Children’s Health Queensland Hospital and Health Service, Brisbane, Queensland Australia
| | - Seweryn Bialasiewicz
- Queensland Pediatric Infectious Disease Laboratory, Centre for Children’s Health Research, Children’s Health Queensland Hospital, Queensland University of Technology, Child Health Research Centre, The University of Queensland, 62 Graham Street, South Brisbane, Queensland 4101 Australia
| | - Robert S. Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland Australia
| | - Robyn L. Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Anders Cervin
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland Australia
- Head & Neck Surgery, Department of Otolaryngology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland Australia
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Marsh RL, Nelson MT, Pope CE, Leach AJ, Hoffman LR, Chang AB, Smith-Vaughan HC. How low can we go? The implications of low bacterial load in respiratory microbiota studies. Pneumonia (Nathan) 2018; 10:7. [PMID: 30003009 PMCID: PMC6033291 DOI: 10.1186/s41479-018-0051-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Background Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present. Main body Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed. Conclusion Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.
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Affiliation(s)
- Robyn L Marsh
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Maria T Nelson
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Chris E Pope
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Amanda J Leach
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Lucas R Hoffman
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Anne B Chang
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia.,3Department of Respiratory and Sleep Medicine, Children's Health Queensland and Queensland University of Technology, Brisbane, QLD Australia
| | - Heidi C Smith-Vaughan
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
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22
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Smith-Vaughan HC, Binks MJ, Beissbarth J, Chang AB, McCallum GB, Mackay IM, Morris PS, Marsh RL, Torzillo PJ, Wurzel DF, Grimwood K, Nosworthy E, Gaydon JE, Leach AJ, MacHunter B, Chatfield MD, Sloots TP, Cheng AC. Bacteria and viruses in the nasopharynx immediately prior to onset of acute lower respiratory infections in Indigenous Australian children. Eur J Clin Microbiol Infect Dis 2018; 37:1785-1794. [PMID: 29959609 PMCID: PMC7088242 DOI: 10.1007/s10096-018-3314-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/21/2018] [Indexed: 12/16/2022]
Abstract
Acute lower respiratory infection (ALRI) is a major cause of hospitalization for Indigenous children in remote regions of Australia. The associated microbiology remains unclear. Our aim was to determine whether the microbes present in the nasopharynx before an ALRI were associated with its onset. A retrospective case-control/crossover study among Indigenous children aged up to 2 years. ALRI cases identified by medical note review were eligible where nasopharyngeal swabs were available: (1) 0–21 days before ALRI onset (case); (2) 90–180 days before ALRI onset (same child controls); and (3) from time and age-matched children without ALRI (different child controls). PCR assays determined the presence and/or load of selected respiratory pathogens. Among 104 children (182 recorded ALRI episodes), 120 case-same child control and 170 case-different child control swab pairs were identified. Human adenoviruses (HAdV) were more prevalent in cases compared to same child controls (18 vs 7%; OR = 3.08, 95% CI 1.22–7.76, p = 0.017), but this association was not significant in cases versus different child controls (15 vs 10%; OR = 1.93, 95% CI 0.97–3.87 (p = 0.063). No other microbes were more prevalent in cases compared to controls. Streptococcus pneumoniae (74%), Haemophilus influenzae (75%) and Moraxella catarrhalis (88%) were commonly identified across all swabs. In a pediatric population with a high detection rate of nasopharyngeal microbes, HAdV was the only pathogen detected in the period before illness presentation that was significantly associated with ALRI onset. Detection of other potential ALRI pathogens was similar between cases and controls.
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Affiliation(s)
- Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia. .,School of Medicine, Griffith University, Gold Coast, 4222, Australia.
| | - Michael J Binks
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Anne B Chang
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia.,Lady Cilento Children's Hospital, Queensland University of Technology, Brisbane, 4101, Australia
| | - Gabrielle B McCallum
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Ian M Mackay
- Faculty of Medicine, Child Health Research Centre, The University of Queensland, Brisbane, 4101, Australia.,Department of Health, Public and Environmental Health Virology Laboratory, Forensic and Scientific Services, Archerfield, 4108, Australia
| | - Peter S Morris
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia.,Royal Darwin Hospital, Darwin, 0810, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | | | - Danielle F Wurzel
- Murdoch Childrens Research Institute, The Royal Children's Hospital, Melbourne, 3052, Australia
| | - Keith Grimwood
- School of Medicine, Griffith University, Gold Coast, 4222, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, 4222, Australia.,Departments of Infectious Disease and Paediatrics, Gold Coast Health, Gold Coast, 4215, Australia
| | - Elizabeth Nosworthy
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Jane E Gaydon
- QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Amanda J Leach
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Barbara MacHunter
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia
| | - Mark D Chatfield
- Menzies School of Health Research, Charles Darwin University, Building 58, Royal Darwin Hospital, Rocklands Drive, Darwin, Northern Territory, 0810, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - Theo P Sloots
- UQ Centre for Child Health Research, The University of Queensland, Brisbane, 4101, Australia
| | - Allen C Cheng
- Department of Infectious Diseases, Alfred Health, Melbourne, 3004, Australia. .,School of Public Health and Preventive Medicine, Monash University, Melbourne, 3800, Australia.
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Beissbarth J, Binks MJ, Marsh RL, Chang AB, Leach AJ, Smith-Vaughan HC. Recommendations for application of Haemophilus influenzae PCR diagnostics to respiratory specimens for children living in northern Australia: a retrospective re-analysis. BMC Res Notes 2018; 11:323. [PMID: 29784027 PMCID: PMC5963172 DOI: 10.1186/s13104-018-3429-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/10/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Haemophilus haemolyticus can be misidentified as nontypeable Haemophilus influenzae (NTHi) due to their phenotypic similarities in microbiological culture. This study aimed to determine the prevalence of misidentified NTHi in respiratory specimens from children living in northern Australia. RESULTS Among respiratory specimens collected in studies between 2010 and 2013, retrospective PCR analysis found that routine culture misidentified H. haemolyticus as NTHi in 0.3% (3/879) of nasal specimens, 25% (14/55) of bronchoalveolar lavage and 40% (12/30) of throat specimens. Therefore, in this population, PCR-based NTHi diagnostics are indicated for throat and bronchoalveolar specimens, but not for nasal specimens.
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Affiliation(s)
- Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia.
| | - Michael J Binks
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia
| | - Anne B Chang
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia.,Department of Respiratory Medicine, Lady Cilento Children's Hospital, PO Box 3474, South Brisbane, QLD, 4101, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, Brisbane, QLD, 4001, Australia
| | - Amanda J Leach
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia
| | - Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Australia
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Smith-Vaughan HC, Beissbarth J, Bowman J, Hare KM, Price EP, Pickering J, Lehmann D, Chang AB, Morris PS, Marsh RL, Leach AJ. Geographic consistency in dominant, non-typeable Haemophilus influenzae genotypes colonising four distinct Australian paediatric groups: a cohort study. Pneumonia (Nathan) 2016; 8:13. [PMID: 28702292 PMCID: PMC5471799 DOI: 10.1186/s41479-016-0013-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 08/08/2016] [Indexed: 11/10/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi)-associated ear and respiratory diseases (including pneumonia) represent a major health burden in many parts of the world. NTHi strains retrieved from the upper airways commonly reflect those found in the lower airways. Despite growing genomic and genotyping data on NTHi, there remains a limited understanding of global and regional NTHi population structures. The aim of this study was to determine whether nasopharyngeal carriage in four Australian paediatric groups at varying risk of NTHi colonisation was dominated by the same NTHi genotypes. Genotyping data generated by PCR-ribotyping were evaluated for 3070 NTHi isolates colonising the nasopharynges of Aboriginal and non-Aboriginal children enrolled in four longitudinal studies in three separate urban and remote regions of Australia. Several NTHi PCR-ribotypes dominated in nasopharyngeal carriage, irrespective of study setting. Principal coordinates analysis confirmed a cluster of common PCR-ribotypes among all cohorts. In conclusion, we identified dominant PCR-ribotypes common to geographically disparate Australian paediatric populations. Future genomic analyses will shed further light on the precise factors underlying the dominance of certain NTHi strains in nasopharyngeal carriage.
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Affiliation(s)
- Heidi C. Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
- School of Medicine, Griffith University, Gold Coast, Queensland Australia
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Jacinta Bowman
- Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Perth, Western Australia Australia
| | - Kim M. Hare
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Erin P. Price
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Janessa Pickering
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia Australia
| | - Deborah Lehmann
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia Australia
| | - Anne B. Chang
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
- Department of Respiratory and Sleep Medicine, Queensland Children’s Medical Research Institute, Children’s Health, Queensland University of Technology, Brisbane, Queensland Australia
| | - Peter S. Morris
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
- Royal Darwin Hospital, Darwin, Northern Territory Australia
| | - Robyn L. Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Amanda J. Leach
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
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Hare KM, Marsh RL, Smith-Vaughan HC, Bauert P, Chang AB. Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough. J Med Microbiol 2015; 64:1353-1360. [PMID: 26399701 DOI: 10.1099/jmm.0.000173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. Flexible bronchoscopy with bronchoalveolar lavage (BAL) is used to obtain lower-airway specimens in young children. The first lavage (lavage-1) is typically used for bacterial culture. However, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. BAL fluid was collected from two sequential lavages of the same lobe in 79 children enrolled in our prospective studies of chronic cough. The respiratory bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Haemophilus parainfluenzae were isolated and identified using standard published methods. H. influenzae was differentiated from Haemophilus haemolyticus using PCR assays. Lower-airway infection was defined as ≥ 104 c.f.u. ml- 1 BAL fluid. We compared cultivable bacteria from lavage-1 with those from the second lavage (lavage-2) using the κ statistic. Lower-airway infections by any pathogen were detected in 46% of first lavages and 39% of second lavages. Detection was similar in both lavages for all pathogens; the κ statistic was 0.7-0.8 for all bacteria except H. parainfluenzae. Of all infections detected in either lavage, 90% were detected in lavage-1 and 78 in lavage-2. However, culture of lavage-2 identified infections that would have been missed in 8% of children, including infections by additional Streptococcus pneumoniae serotypes. Our findings support the continued use of lavage-1 for bacterial culture; however, culture of lavage-2 may yield additional identifications of bacterial pathogens in lower-airway infections.
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Affiliation(s)
- K M Hare
- Menzies School of Health Research, Rocklands Drive, Tiwi, NT 0810, Australia
| | - R L Marsh
- Menzies School of Health Research, Rocklands Drive, Tiwi, NT 0810, Australia
| | - H C Smith-Vaughan
- Menzies School of Health Research, Rocklands Drive, Tiwi, NT 0810, Australia
| | - P Bauert
- Menzies School of Health Research, Rocklands Drive, Tiwi, NT 0810, Australia
| | - A B Chang
- Menzies School of Health Research, Rocklands Drive, Tiwi, NT 0810, Australia
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26
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Jervis-Bardy J, Rogers GB, Morris PS, Smith-Vaughan HC, Nosworthy E, Leong LEX, Smith RJ, Weyrich LS, De Haan J, Carney AS, Leach AJ, O'Leary S, Marsh RL. The microbiome of otitis media with effusion in Indigenous Australian children. Int J Pediatr Otorhinolaryngol 2015; 79:1548-55. [PMID: 26228497 DOI: 10.1016/j.ijporl.2015.07.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Indigenous Australian children have a high prevalence of otitis media with effusion (OME) and associated conductive hearing loss. Only three microbiological studies of middle ear fluid (MEF) from Indigenous Australian children with OME have been reported. All of these were reliant on culture or species-specific PCR assays. The aim of this study was to characterise the middle ear fluid (MEF), adenoid and nasopharyngeal (NP) microbiomes of Indigenous Australian children, using culture-independent 16S rRNA gene sequencing. METHODS MEF, NP swabs and adenoid specimens were collected from 11 children in the Alice Springs region of Central Australia. Bacterial communities in these specimens were characterised using 16S rRNA gene sequencing. RESULTS The microbiota in MEF samples were dominated (>50% relative abundance) by operational taxonomic units (OTUs) consistent with Alloiococcus otitidis (6/11), Haemophilus influenzae (3/11) or Streptococcus sp. (specifically, Mitis group streptococci which includes Streptococcus pneumoniae) (1/11). Anatomical site selectivity was indicated by the presence of a single conserved Haemophilus OTU in 7/11 MEF samples. In comparison, there were ten distinct Haemophilus OTUs observed across the NP and adenoid samples. Despite significant differences between the MEF and NP/adenoid microbiomes, Streptococcus sp., H. influenzae and Moraxella catarrhalis OTUs were common to all sample types. Co-occurrence of classical otopathogens in paired MEF and NP/Adenoid samples is consistent with earlier culture-based studies. CONCLUSION These data highlight the need to further assess H. influenzae traits important in otitis media and to understand the role of canal flora, especially A. otitidis, in populations with a high prevalence of tympanic membrane perforation.
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Affiliation(s)
- Jake Jervis-Bardy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; School of Medicine, Flinders University, Adelaide, SA, Australia
| | - Geraint B Rogers
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia
| | - Peter S Morris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Lex E X Leong
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia
| | - Renee J Smith
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia; School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia
| | - Jacques De Haan
- Department of Otolaryngology, Alice Springs Hospital, Alice Springs, NT, Australia
| | - A Simon Carney
- Department of Otolaryngology-Head & Neck Surgery, Flinders University, Adelaide, SA, Australia
| | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Stephen O'Leary
- Department of Otolaryngology, University of Melbourne, Melbourne, VIC, Australia
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
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Price EP, Sarovich DS, Nosworthy E, Beissbarth J, Marsh RL, Pickering J, Kirkham LAS, Keil AD, Chang AB, Smith-Vaughan HC. Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. BMC Genomics 2015; 16:641. [PMID: 26311542 PMCID: PMC4551764 DOI: 10.1186/s12864-015-1857-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance, accurate identification of H. influenzae is a non-trivial endeavour. H. haemolyticus can be misidentified as H. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. On the molecular level, frequent genetic exchange amongst Haemophilus spp. has confounded accurate identification of H. influenzae, leading to both false-positive and false-negative results with existing speciation assays. Results Whole-genome single-nucleotide polymorphism data from 246 closely related global Haemophilus isolates, including 107 Australian isolate genomes generated in this study, were used to construct a whole-genome phylogeny. Based on this phylogeny, H. influenzae could be differentiated from closely related species. Next, a H. influenzae-specific locus, fucP, was identified, and a novel TaqMan real-time PCR assay targeting fucP was designed. PCR specificity screening across a panel of clinically relevant species, coupled with in silico analysis of all species within the order Pasteurellales, demonstrated that the fucP assay was 100 % specific for H. influenzae; all other examined species failed to amplify. Conclusions This study is the first of its kind to use large-scale comparative genomic analysis of Haemophilus spp. to accurately delineate H. influenzae and to identify a species-specific molecular signature for this species. The fucP assay outperforms existing H. influenzae targets, most of which were identified prior to the next-generation genomics era and thus lack validation across a large number of Haemophilus spp. We recommend use of the fucP assay in clinical and research laboratories for the most accurate detection and diagnosis of H. influenzae infection and colonisation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1857-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. .,Menzies School of Health Research, PO Box 41096, Casuarina, NT, 0811, Australia.
| | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | | | | | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Perth, WA, Australia.
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Republished: Respiratory microbiota: addressing clinical questions, informing clinical practice. Postgrad Med J 2015; 91:463-70. [PMID: 26304986 PMCID: PMC4552901 DOI: 10.1136/postgradmedj-2014-205826rep] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/30/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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Marsh RL, Thornton RB, Smith-Vaughan HC, Richmond P, Pizzutto SJ, Chang AB. Detection of biofilm in bronchoalveolar lavage from children with non-cystic fibrosis bronchiectasis. Pediatr Pulmonol 2015; 50:284-292. [PMID: 24644254 DOI: 10.1002/ppul.23031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 02/03/2014] [Indexed: 01/28/2023]
Abstract
BACKGROUND The presence of Pseudomonas aeruginosa biofilms in lower airway specimens from cystic fibrosis (CF) patients is well established. To date, biofilm has not been demonstrated in bronchoalveolar lavage (BAL) from people with non-CF bronchiectasis. The aim of this study was to determine (i) if biofilm was present in BAL from children with and without bronchiectasis, and (ii) if biofilm detection differed between sequentially collected BAL. METHODS Testing for biofilm in two sequentially collected BAL from children with and without bronchiectasis was done using BacLight™ live-dead staining and lectin staining for extracellular polymeric biofilm matrices. Bacterial culture and cytological measures were performed on the first and second lavages, respectively. Clinically important BAL infection was defined as >104 cfu of respiratory pathogens/ml BAL. RESULTS Biofilm was detected in BAL from seven of eight (87.5%) children with bronchiectasis (aged 0.8-6.9 years), but was not detected in any of three controls (aged 1.3-8.6 years). The biofilms contained both live and dead bacteria irrespective of antibiotic use prior to bronchoscopy. Biofilm was detected more frequently in the second lavage than the first. Three of the seven biofilm-positive BAL were culture-positive for respiratory pathogens at clinically important levels. CONCLUSIONS Biofilm is present in BAL from children with non-CF bronchiectasis even when BAL-defined clinically important infection was absent. Studies to characterize lower airway biofilms and determine how biofilm contributes to bronchiectasis disease progression and treatment outcomes are necessary. Pediatr Pulmonol. 2015; 50:284-292. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Ruth B Thornton
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Western Australia, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Peter Richmond
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Western Australia, Australia
| | - Susan J Pizzutto
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Queensland Children's Respiratory Centre, Queensland Children's Medical Research Institute, Royal Children's Hospital, Brisbane, Queensland, Australia
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Chang AB, Marsh RL, Upham JW, Hoffman LR, Smith-Vaughan H, Holt D, Toombs M, Byrnes C, Yerkovich ST, Torzillo PJ, O'Grady KAF, Grimwood K. Toward making inroads in reducing the disparity of lung health in Australian indigenous and new zealand māori children. Front Pediatr 2015; 3:9. [PMID: 25741502 PMCID: PMC4327127 DOI: 10.3389/fped.2015.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - John W Upham
- Department of Respiratory Medicine, Princess Alexandra Hospital , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
| | - Lucas R Hoffman
- Department of Pediatrics, University of Washington , Seattle, WA , USA ; Department of Microbiology, University of Washington , Seattle, WA , USA
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Deborah Holt
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia
| | - Maree Toombs
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; Indigenous Health, Toowoomba Rural Clinical School, The University of Queensland , Toowoomba, QLD , Australia
| | - Catherine Byrnes
- Paediatric Department, University of Auckland & Starship Children's Hospital , Auckland , New Zealand
| | - Stephanie T Yerkovich
- Child Health Division, Menzies School of Health Research, Charles Darwin University , Darwin, NT , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia ; Queensland Lung Transplant Service, The Prince Charles Hospital , Chermside, QLD , Australia
| | - Paul J Torzillo
- Nganampa Health Council, Alice Springs and Royal Prince Alfred Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Kerry-Ann F O'Grady
- Queensland Children's Medical Research Institute, Queensland University of Technology , Brisbane, QLD , Australia
| | - Keith Grimwood
- Gold Coast University Hospital, Griffith University , Gold Coast, QLD , Australia
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Jervis-Bardy J, Leong LEX, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O’Leary S, Rogers GB, Marsh RL. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome 2015; 3:19. [PMID: 25969736 PMCID: PMC4428251 DOI: 10.1186/s40168-015-0083-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spurious signal that is characteristic of samples with low levels of bacteria and high levels of non-bacterial DNA. We have developed a workflow based on the paired-end read Illumina MiSeq-based approach, which enables significant improvement in data quality, post-sequencing. We demonstrate the efficacy of this methodology through its application to paediatric upper-respiratory samples from several anatomical sites. RESULTS A workflow for processing sequence data was developed based on commonly available tools. Data generated from different sample types showed a marked variation in levels of non-bacterial signal and 'contaminant' bacterial reads. Significant differences in the ability of reference databases to accurately assign identity to operational taxonomic units (OTU) were observed. Three OTU-picking strategies were trialled as follows: de novo, open-reference and closed-reference, with open-reference performing substantially better. Relative abundance of OTUs identified as potential reagent contamination showed a strong inverse correlation with amplicon concentration allowing their objective removal. The removal of the spurious signal showed the greatest improvement in sample types typically containing low levels of bacteria and high levels of human DNA. A substantial impact of pre-filtering data and spurious signal removal was demonstrated by principal coordinate and co-occurrence analysis. For example, analysis of taxon co-occurrence in adenoid swab and middle ear fluid samples indicated that failure to remove the spurious signal resulted in the inclusion of six out of eleven bacterial genera that accounted for 80% of similarity between the sample types. CONCLUSIONS The application of the presented workflow to a set of challenging clinical samples demonstrates its utility in removing the spurious signal from the dataset, allowing clinical insight to be derived from what would otherwise be highly misleading output. While other approaches could potentially achieve similar improvements, the methodology employed here represents an accessible means to exclude the signal from contamination and other artefacts.
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Affiliation(s)
- Jake Jervis-Bardy
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Lex E X Leong
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Shashikanth Marri
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
| | - Renee J Smith
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
- />School of Biological Sciences, Flinders University, Adelaide, South Australia 5001 Australia
| | - Jocelyn M Choo
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Heidi C Smith-Vaughan
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Elizabeth Nosworthy
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Peter S Morris
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Stephen O’Leary
- />Department of Otolaryngology, University of Melbourne, Melbourne, VIC Australia
| | - Geraint B Rogers
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Robyn L Marsh
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Respiratory microbiota: addressing clinical questions, informing clinical practice. Thorax 2015; 70:74-81. [PMID: 25035125 PMCID: PMC4283665 DOI: 10.1136/thoraxjnl-2014-205826] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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Abstract
Children in indigenous populations have substantially higher respiratory morbidity than non-indigenous children. Indigenous children have more frequent respiratory infections that are, more severe and, associated with long-term sequelae. Post-infectious sequelae such as chronic suppurative lung disease and bronchiectasis are especially prevalent among indigenous groups and have lifelong impact on lung function. Also, although estimates of asthma prevalence among indigenous children are similar to non-indigenous groups the morbidity of asthma is higher in indigenous children. To reduce the morbidity of respiratory illness, best-practice medicine is essential in addition to improving socio-economic factors, (eg household crowding), tobacco smoke exposure, and access to health care and illness prevention programs that likely contribute to these issues. Although each indigenous group may have unique health beliefs and interfaces with modern health care, a culturally sensitive and community-based comprehensive care system of preventive and long term care can improve outcomes for all these conditions. This article focuses on common respiratory conditions encountered by indigenous children living in affluent countries where data is available.
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Affiliation(s)
- A B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Brisbane, Australia; Queensland Respiratory Centre, Royal Children's Hospital, Brisbane, Queensland Medical Research Institute, Queensland University of Technology, Brisbane, Australia.
| | - N Brown
- National Aboriginal Community Controlled Health Organisation and University of Wollongong, Wollongong, New South Wales, Australia
| | - M Toombs
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Brisbane, Australia; Indigenous Health, Toowoomba Rural Clinical School, University of Queensland
| | - R L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Brisbane, Australia
| | - G J Redding
- University of Washington School of Medicine, Pediatric Pulmonary Division, Children's Hospital and Regional Medical Center, Seattle, Washington, USA
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Astley HC, Abbott EM, Azizi E, Marsh RL, Roberts TJ. Chasing maximal performance: a cautionary tale from the celebrated jumping frogs of Calaveras County. ACTA ACUST UNITED AC 2014; 216:3947-53. [PMID: 24133149 DOI: 10.1242/jeb.090357] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Maximal performance is an essential metric for understanding many aspects of an organism's biology, but it can be difficult to determine because a measured maximum may reflect only a peak level of effort, not a physiological limit. We used a unique opportunity provided by a frog jumping contest to evaluate the validity of existing laboratory estimates of maximum jumping performance in bullfrogs (Rana catesbeiana). We recorded video of 3124 bullfrog jumps over the course of the 4-day contest at the Calaveras County Jumping Frog Jubilee, and determined jump distance from these images and a calibration of the jump arena. Frogs were divided into two groups: 'rental' frogs collected by fair organizers and jumped by the general public, and frogs collected and jumped by experienced, 'professional' teams. A total of 58% of recorded jumps surpassed the maximum jump distance in the literature (1.295 m), and the longest jump was 2.2 m. Compared with rental frogs, professionally jumped frogs jumped farther, and the distribution of jump distances for this group was skewed towards long jumps. Calculated muscular work, historical records and the skewed distribution of jump distances all suggest that the longest jumps represent the true performance limit for this species. Using resampling, we estimated the probability of observing a given jump distance for various sample sizes, showing that large sample sizes are required to detect rare maximal jumps. These results show the importance of sample size, animal motivation and physiological conditions for accurate maximal performance estimates.
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Affiliation(s)
- H C Astley
- Brown University, Department of Ecology and Evolutionary Biology, Providence, RI 02912, USA
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Smith-Vaughan HC, Binks MJ, Marsh RL, Kaestli M, Ward L, Hare KM, Pizzutto SJ, Thornton RB, Morris PS, Leach AJ. Dominance of Haemophilus influenzae in ear discharge from Indigenous Australian children with acute otitis media with tympanic membrane perforation. BMC Ear Nose Throat Disord 2013; 13:12. [PMID: 24099576 PMCID: PMC3852835 DOI: 10.1186/1472-6815-13-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/01/2013] [Indexed: 11/10/2022]
Abstract
Background Indigenous Australian children living in remote communities experience high rates of acute otitis media with tympanic membrane perforation (AOMwiP). Otitis media in this population is associated with dense nasopharyngeal colonization of three primary otopathogens; Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis. Little is known about the relative abundance of these pathogens during infection. The objective of this study was to estimate the abundance and concordance of otopathogens in ear discharge and paired nasopharyngeal swabs from children with AOMwiP (discharge of not more than 6 weeks’ duration and perforation size <2%). Methods Culture and quantitative PCR (qPCR) estimation of H. influenzae, S. pneumoniae, M. catarrhalis and total bacterial load were performed on paired nasopharyngeal and ear discharge swabs from 55 Indigenous children with AOMwiP aged 3.5 – 45.6 months and resident in remote communities. Results By culture, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 80%, 84% and 91% of nasopharyngeal swabs, and 49%, 33% and 4% of ear discharge swabs, respectively. Using qPCR, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 82%, 82%, and 93% of nasopharyngeal swabs, and 89%, 41% and 18% of ear discharge swabs, respectively. Relative abundance of H. influenzae in ear discharge swabs was 0-68% of the total bacterial load (median 2.8%); whereas S. pneumoniae and M. catarrhalis relative abundances were consistently <2% of the total bacterial load. S. pneumoniae and M. catarrhalis abundances were significantly lower in ear discharge compared with nasopharyngeal swabs (p = 0.001, p < 0.001); no significant difference was observed in H. influenzae mean abundance at the two sites. Conclusions H. influenzae was the dominant otopathogen detected in ear discharge swabs collected from children with AOMwiP. High prevalence and abundance of S. pneumoniae and M. catarrhalis in the nasopharynx did not predict ear discharge prevalence and abundances of these pathogens. PCR was substantially more sensitive than culture for ear discharge, and a necessary adjunct to standard microbiology. Quantitative methods are required to understand species abundance in polymicrobial infections and may be needed to measure accurately the microbiological impact of interventions and to provide a better understanding of clinical failure in these children.
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Affiliation(s)
- Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
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Hare KM, Marsh RL, Binks MJ, Grimwood K, Pizzutto SJ, Leach AJ, Chang AB, Smith-Vaughan HC. Quantitative PCR confirms culture as the gold standard for detection of lower airway infection by nontypeable Haemophilus influenzae in Australian Indigenous children with bronchiectasis. J Microbiol Methods 2012; 92:270-2. [PMID: 23266579 DOI: 10.1016/j.mimet.2012.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
Abstract
Correlation was observed between quantitative PCR and semi-quantitative culture for definition of Haemophilus influenzae infection in bronchoalveolar lavage specimens from 81 children with bronchiectasis. However, qPCR data correlated less well with airway neutrophilia, and supports continued use of culture as the gold standard for defining H. influenzae lower airway infection.
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Affiliation(s)
- Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, Northern Territory 0811, Australia.
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Marsh RL, Binks MJ, Beissbarth J, Christensen P, Morris PS, Leach AJ, Smith-Vaughan HC. Quantitative PCR of ear discharge from Indigenous Australian children with acute otitis media with perforation supports a role for Alloiococcus otitidis as a secondary pathogen. BMC Ear Nose Throat Disord 2012; 12:11. [PMID: 23033913 PMCID: PMC3546424 DOI: 10.1186/1472-6815-12-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/21/2012] [Indexed: 11/29/2022]
Abstract
Background Otitis media is endemic in remote Indigenous communities of Australia’s Northern Territory. Alloiococcus otitidis is an outer ear commensal and putative middle ear pathogen that has not previously been described in acute otitis media (AOM) in this population. The aims of this study were to determine the presence, antibiotic susceptibility and bacterial load of A. otitidis in nasopharyngeal and ear discharge swabs collected from Indigenous Australian children with AOM with perforation. Methods Paired nasopharyngeal and ear discharge swabs from 27 children with AOM with perforation were tested by A. otitidis quantitative PCR (qPCR). Positive swabs were cultured for 21 days. Total and respiratory pathogen bacterial loads in A. otitidis-positive swabs were determined by qPCR. Results A. otitidis was detected by qPCR in 11 ear discharge swabs from 10 of 27 (37%) children, but was not detected in paired nasopharyngeal swabs. A. otitidis was cultured from 5 of 11 qPCR-positive swabs from four children. All A. otitidis isolates had minimum inhibitory concentrations consistent with macrolide resistance. All A. otitidis qPCR-positive swabs were culture-positive for other bacteria. A. otitidis bacterial load ranged from 2.2 × 104-1.1 × 108 cells/swab (median 1.8 × 105 cells/swab). The relative abundance of A. otitidis ranged from 0.01% to 34% of the total bacterial load (median 0.7%). In 6 of 11 qPCR-positive swabs the A. otitidis relative abundance was <1% and in 5 of 11 it was between 2% and 34%. The A. otitidis bacterial load and relative abundance measures were comparable to that of Haemophilus influenzae. Conclusions A. otitidis can be a dominant species in the bacterial communities present in the ear discharge of Indigenous children with AOM with perforation. The absence of A. otitidis in nasopharyngeal swabs suggests the ear canal as the likely primary reservoir. The significance of A. otitidis at low relative abundance is unclear; however, at higher relative abundance it may be contributing to the associated inflammation. Further studies to better understand A. otitidis as a secondary otopathogen are warranted, particularly in populations at high-risk of progression to chronic suppurative otitis media and where macrolide therapies are being used.
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Affiliation(s)
- Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Darwin, Australia.
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Kirkham LAS, Wiertsema SP, Smith-Vaughan HC, Thornton RB, Marsh RL, Lehmann D, Leach AJ, Morris PS, Richmond PC. Are you listening? The inaugural Australian Otitis Media (OMOZ) workshop--towards a better understanding of otitis media. Med J Aust 2010; 193:569-71. [PMID: 21077811 DOI: 10.5694/j.1326-5377.2010.tb04063.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 09/20/2010] [Indexed: 11/17/2022]
Affiliation(s)
- Lea-Ann S Kirkham
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
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Marsh RL, Smith-Vaughan H, Beissbarth J, Hare K, Kennedy M, Wigger C, Mellon G, Stubbs E, Gadil JR, Pettit A, Mackenzie G, Tipakalippa P, Morris PS, Leach AJ. Molecular characterisation of pneumococcal serotype 16F: Established predominant carriage and otitis media serotype in the 7vPCV era. Vaccine 2007; 25:2434-6. [PMID: 17028080 DOI: 10.1016/j.vaccine.2006.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Young Australian Aboriginal children in remote communities experience very high rates of pneumococcal carriage and otitis media. Prior to introduction of the 7-valent pneumococcal conjugate vaccine (7vPCV, Prevenar), serotype 16F was an important type found in nasal and ear discharge swabs. Since commencement of pneumococcal immunisation for Aboriginal infants in 2001, 16F has become the predominant established serotype in carriage and otitis media in young Aboriginal children. BOX typing and multi-locus sequence typing revealed a diverse population of serotype 16F strains, and evidence of potential capsule switching from a vaccine serotype 4 to a serotype 16F.
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Affiliation(s)
- R L Marsh
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
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Wagner H, Siebert T, Ellerby DJ, Marsh RL, Blickhan R. ISOFIT: a model-based method to measure muscle–tendon properties simultaneously. Biomech Model Mechanobiol 2005; 4:10-9. [PMID: 15895262 DOI: 10.1007/s10237-005-0068-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 12/08/2004] [Indexed: 11/26/2022]
Abstract
Estimation of muscle parameters specifying force-length and force-velocity behavior requires in general a large number of sophisticated experiments often including a combination of isometric, isokinetic, isotonic, and quick-release experiments. This study validates a simpler method (ISOFIT) to determine muscle properties by fitting a Hill-type muscle model to a set of isovelocity data. Muscle properties resulting from the ISOFIT method agreed well with muscle properties determined separately in in vitro measurements using frog semitendinosus muscles. The force-length curve was described well by the results of the model. The force-velocity curve resulting from the model coincided with the experimentally determined curve above approximately 20% of maximum isometric force (correlation coefficient R>0.99). At lower forces and thus higher velocities the predicted curve underestimated velocity. The stiffness of the series elastic component determined with direct experiments was approximately 10% lower than that determined by the ISOFIT method. Use of the ISOFIT method can decrease experimental time up to 80% and reduce potential changes in muscle parameters due to fatigue.
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Affiliation(s)
- H Wagner
- Department Science of Motion, Friedrich-Schiller-University Jena, 07749 Jena, Germany.
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Nabi G, Asterlings S, Greene DR, Marsh RL. Percutaneous embolization of varicoceles: outcomes and correlation of semen improvement with pregnancy. Urology 2004; 63:359-63. [PMID: 14972491 DOI: 10.1016/j.urology.2003.09.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Accepted: 09/09/2003] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To assess the technical feasibility and compare the semen quality in men with or without pregnancy after percutaneous embolization of varicoceles in the management of infertility. METHODS The records of 102 patients who underwent retrograde varicocele embolization between January 1997 and January 2002 were reviewed through the Hospital Information Support System. Infertility was the indication for embolization in 71 cases. The present study consisted of this group of patients. The size of the varicoceles, the size of the testis, the pre-embolization semen analysis parameters, the technical details of embolization procedure, any anomalous vessels seen on venography, and, if unsuccessful, the reason for failure of the procedure were noted. A record of postembolization semen parameters (at least two) was made. Patients were divided into four groups depending on the pre-embolization semen density, and a correlation of this was assessed with improvements in morphology and motility. Follow-up was performed using a questionnaire to evaluate the success rate of the procedure, complications, and any treatment for infertility by the patient or his partner after the procedure. Patients who had a successful pregnancy were compared with those who did not to determine the correlation between the changes in semen quality and pregnancy rate. RESULTS Between January 1997 and January 2002, 71 patients underwent retrograde varicocele embolization, using an embolizing coil, for infertility. In 68 (95.7%), it was technically successful. Nineteen patients (26.7%) had various anomalous vessels on venography. A statistically significant improvement (P = 0.002) was noted in the motility parameters in patients with a pre-embolization semen density between 10 and 30 million/mL. All patients were followed up by questionnaire. Follow-up was possible in 51 patients (75%). One patient had varicocele recurrence and underwent open inguinal surgical ligation. Of 45 patients, the partners of 18 (40%) had a successful pregnancy. A comparison of the postembolization semen quality between those with and without a successful pregnancy found no correlation between the changes in the semen parameters and the pregnancy rate. CONCLUSIONS Varicocele embolization is a technically feasible, minimally invasive, outpatient procedure that improves semen quality significantly in patients with a pre-embolization semen density of 10 to 30 million/mL. However, no correlation was found between the improvements in semen quality and the pregnancy rate.
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Affiliation(s)
- G Nabi
- Academic Unit of Urology, Department of Surgery, University of Aberdeen, Foresterhill, Scotland, United Kingdom
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Boutlis CS, Hobbs MR, Marsh RL, Misukonis MA, Tkachuk AN, Lagog M, Booth J, Granger DL, Bockarie MJ, Mgone CS, Levesque MC, Weinberg JB, Anstey NM. Inducible nitric oxide synthase (NOS2) promoter CCTTT repeat polymorphism: relationship to in vivo nitric oxide production/NOS activity in an asymptomatic malaria-endemic population. Am J Trop Med Hyg 2003; 69:569-73. [PMID: 14740870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Polymorphisms in the inducible nitric oxide synthase gene (NOS2) promoter have been associated with clinical outcome from malaria. These include a CCTTT repeat (CCTTTn) 2.5 kilobases upstream from the NOS2 transcription start site, and two single nucleotide substitutions: G-->C at position -954 (G-954C), and C-->T at position -1173 (C-1173T). Although hypothesized to influence NO production in vivo, the functional relevance of (CCTTT)n and G-954C is uncertain because disease association studies have yielded inconsistent results. This study found no association between CCTTT repeat number and levels of plasma NO metabolites or peripheral blood mononuclear cell NOS activity in a cohort of asymptomatic malaria-exposed coastal Papua New Guineans 1-60 years old. This suggests that (CCTTT)n does not independently influence NOS2 transcription in vivo. Neither the G-954C nor the C-1173T polymorphisms were identified in this population, indicating the variability and complexity of selection for NOS2 promoter polymorphisms in different malaria-endemic populations.
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Affiliation(s)
- Craig S Boutlis
- International Health Program, Infectious Diseases Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
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Ramachandran K, Arunachalam PS, Hurren A, Marsh RL, Samuel PR. Botulinum toxin injection for failed tracheo-oesophageal voice in laryngectomees: the Sunderland experience. J Laryngol Otol 2003; 117:544-8. [PMID: 12901809 DOI: 10.1258/002221503322112978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Spasm of the pharyngo-oesophageal segment is one of the important causes of tracheo-oesophageal voice failure. Traditionally it has been managed by either prolonged speech therapy, surgical pharyngeal myotomy or pharyngeal plexus neurectomy with varying degrees of success. Botulinum neurotoxin has been found to be effective in relieving pharyngo-oesophageal segment spasm. Since 1995, we have used botulinum toxin injection on 10 laryngectomees with either aphonia or hypertonicity due to pharyngo-oesophageal segment spasm. Early results were analysed by the Sunderland Surgical Voice Restoration Rating scale. Seven of the 10 patients, who were previously completely aphonic, developed voice following this therapy and are using their valve choice as their only method of communication. Out of the three patients who were treated for hypertonic voice, two did derive some benefit from the procedure. One patient developed a hypotonic voice, which lasted for a few months.
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Affiliation(s)
- K Ramachandran
- Department of Otolaryngology and Head and Neck Surgery, Sunderland Royal Hospital, Sunderland
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Askew GN, Marsh RL. The mechanical power output of the pectoralis muscle of blue-breasted quail (Coturnix chinensis): thein vivolength cycle and its implications for muscle performance. J Exp Biol 2001; 204:3587-600. [PMID: 11719526 DOI: 10.1242/jeb.204.21.3587] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYSonomicrometry and electromyographic (EMG) recordings were made for the pectoralis muscle of blue-breasted quail (Coturnix chinensis) during take-off and horizontal flight. In both modes of flight, the pectoralis strain trajectory was asymmetrical, with 70 % of the total cycle time spent shortening. EMG activity was found to start just before mid-upstroke and continued into the downstroke. The wingbeat frequency was 23 Hz, and the total strain was 23 % of the mean resting length.Bundles of fibres were dissected from the pectoralis and subjected in vitro to the in vivo length and activity patterns, whilst measuring force. The net power output was only 80 W kg–1 because of a large artefact in the force record during lengthening. For more realistic estimates of the pectoralis power output, we ignored the power absorbed by the muscle bundles during lengthening. The net power output during shortening averaged over the entire cycle was approximately 350 W kg–1, and in several preparations over 400 W kg–1. Sawtooth cycles were also examined for comparison with the simulation cycles, which were identical in all respects apart from the velocity profile. The power output during these cycles was found to be 14 % lower than during the in vivo strain trajectory. This difference was due to a higher velocity of stretch, which resulted in greater activation and higher power output throughout the later part of shortening, and the increase in shortening velocity towards the end of shortening, which facilitated deactivation.The muscle was found to operate at a mean length shorter than the plateau of the length/force relationship, which resulted in the isometric stress measured at the mean resting length being lower than is typically reported for striated muscle.
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Affiliation(s)
- G N Askew
- Department of Zoology, Downing Street, University of Cambridge, Cambridge CB2 3EJ, UK.
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Abstract
SUMMARYBlue-breasted quail (Coturnix chinensis) were filmed during take-off flights. By tracking the position of the centre of mass of the bird in three dimensions, we were able to calculate the power required to increase the potential and kinetic energy. In addition, high-speed video recordings of the position of the wings over the course of the wing stroke, and morphological measurements, allowed us to calculate the aerodynamic and inertial power requirements. The total power output required from the pectoralis muscle was, on average, 390 W kg–1, which was similar to the highest measurements made on bundles of muscle fibres in vitro (433 W kg–1), although for one individual a power output of 530 W kg–1 was calculated. The majority of the power was required to increase the potential energy of the body. The power output of these muscles is the highest yet found for any muscle in repetitive contractions.We also calculated the power requirements during take-off flights in four other species in the family Phasianidae. Power output was found to be independent of body mass in this family. However, the precise scaling of burst power output within this group must await a better assessment of whether similar levels of performance were measured across the group. We extended our analysis to one species of hawk, several species of hummingbird and two species of bee. Remarkably, we concluded that, over a broad range of body size (0.0002–5 kg) and contractile frequency (5–186 Hz), the myofibrillar power output of flight muscles during short maximal bursts is very high (360–460 W kg–1) and shows very little scaling with body mass. The approximate constancy of power output means that the work output varies inversely with wingbeat frequency and reaches values of approximately 30–60 J kg–1 in the largest species.
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Affiliation(s)
- G N Askew
- Department of Zoology, Downing Street, University of Cambridge, Cambridge CB2 3EJ, UK.
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Landau JD, Marsh RL, Parsons TE. Dissociation of two kinds of source attributions. Am J Psychol 2001; 113:539-51. [PMID: 11232539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
We examined the relationship between two different source attribution errors. One error found primarily in the cognitive psychology literature is the belief that one is an author of an idea when one is not. The other error, reported in the social psychology literature, occurs when people overestimate how long they have known an idea. Although somewhat different, both errors are a form of misappropriation of ideas to oneself. We investigated both attributions and found that when participants performed a more elaborate encoding task, erroneous claims of authorship were reduced but length-of-knowing judgments increased. The results are discussed in terms of the cognitive processing that is likely to give rise to each source attribution.
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Affiliation(s)
- J D Landau
- Department of Psychology, York College of Pennsylvania, York, PA 17404, USA.
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Abstract
A number of recent reports have investigated false memories using variants of the Deese-Roediger-McDermott (DRM) paradigm. Because these false memories have been difficult to eliminate, this study investigated whether false recognition could be reduced by incorporating source-monitoring criteria into decision processes. Making claims about the manner in which items were learned should require more careful scrutiny of memories, and therefore false recognition should be minimized with source instructions as compared with old-new recognition instructions. In 3 experiments that varied the combination of sources, false recognition was increased rather than reduced by applying source-monitoring processes. The theoretical implications of these counterintuitive results are discussed in terms of the old-new detection component of source judgments.
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Affiliation(s)
- J L Hicks
- Department of Psychology, Louisiana State University, Baton Rouge 70803-5501, USA.
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Abstract
Previous studies have concluded that recognition memory is immune to disruption from divided attention and therefore is a relatively automatic process (A. Baddeley, V. Lewis, M. Eldridge, & N. Thomson, 1984; F. I. M. Craik, R. Govoni, M. Naveh-Benjamin, & N. D. Anderson, 1996). Because costs have been found on the concurrent task used to divide attention, recognition may nevertheless require some attentional resources (M. Naveh-Benjamin, F. I. M. Craik, J. Guez, & H. Dori, 1998). The present authors used attention-demanding concurrent tasks to demonstrate significant costs on both the concurrent task and recognition memory performance. Decrements in recognition accuracy were found for classes of items that were studied deeply but not for more shallowly learned materials. The present findings suggest that recognition processes can require significant attentional resources when tested under the appropriate conditions. The results are discussed in terms of the requirements both at encoding and at test that are needed to observe dual-task decrements to recognition accuracy.
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Affiliation(s)
- J L Hicks
- Department of Psychology, Louisiana State University, Baton Rouge 70803-5501, USA.
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