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Frumence E, Wilkinson DA, Klitting R, Vincent M, Mnemosyme N, Grard G, Traversier N, Li-Pat-Yuen G, Heaugwane D, Souply L, Giry C, Paty MC, Collet L, Gérardin P, Thouillot F, De Lamballerie X, Jaffar-Bandjee MC. Dynamics of emergence and genetic diversity of dengue virus in Reunion Island from 2012 to 2022. PLoS Negl Trop Dis 2024; 18:e0012184. [PMID: 38768248 DOI: 10.1371/journal.pntd.0012184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Dengue is a major public health concern in Reunion Island, marked by recurrent epidemics, including successive outbreaks of dengue virus serotypes 1 and 2 (DENV1 and DENV2) with over 70,000 cases confirmed since 2017. METHODOLOGY/PRINCIPAL FINDINGS In this study, we used Oxford Nanopore NGS technology for sequencing virologically-confirmed samples and clinical isolates collected between 2012 and 2022 to investigate the molecular epidemiology and evolution of DENV in Reunion Island. Here, we generated and analyzed a total of 499 DENV1, 360 DENV2, and 18 DENV3 sequences. By phylogenetic analysis, we show that different genotypes and variants of DENV have circulated in the past decade that likely originated from Seychelles, Mayotte and Southeast Asia and highly affected areas in Asia and Africa. CONCLUSIONS/SIGNIFICANCE DENV sequences from Reunion Island exhibit a high genetic diversity which suggests regular introductions of new viral lineages from various Indian Ocean islands. The insights from our phylogenetic analysis may inform local health authorities about the endemicity of DENV variants circulating in Reunion Island and may improve dengue management and surveillance. This work emphasizes the importance of strong local coordination and collaboration to inform public health stakeholders in Reunion Island, neighboring areas, and mainland France.
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Affiliation(s)
- Etienne Frumence
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - David A Wilkinson
- UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Plateforme technologique CYROI, Sainte-Clotilde, Réunion, France
| | - Raphaelle Klitting
- Unité des Virus Émergents (UVE), Aix-Marseille Univ, IRD 190, INSERM 1207, Marseille, France
- CNR des Arbovirus, Marseille, France
| | | | - Nicolas Mnemosyme
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | | | - Nicolas Traversier
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Ghislaine Li-Pat-Yuen
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Diana Heaugwane
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Laurent Souply
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Claude Giry
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | | | | | - Patrick Gérardin
- INSERM CIC 1410, CHU de la Réunion, Saint-Pierre, Réunion, France
| | | | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE), Aix-Marseille Univ, IRD 190, INSERM 1207, Marseille, France
- CNR des Arbovirus, Marseille, France
| | - Marie-Christine Jaffar-Bandjee
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
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Wilkinson DA, Edwards M, Shum C, Moinet M, Anderson NE, Benschop J, Nisa S. Molecular typing of Leptospira spp. in farmed and wild mammals reveals new host-serovar associations in New Zealand. N Z Vet J 2024; 72:1-9. [PMID: 37589061 DOI: 10.1080/00480169.2023.2248930] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
AIMS To apply molecular typing to DNA isolated from historical samples to determine Leptospira spp. infecting farmed and wild mammals in New Zealand. MATERIALS AND METHODS DNA samples used in this study were extracted from urine, serum or kidney samples (or Leptospira spp. cultures isolated from them) collected between 2007 and 2017 from a range of domestic and wildlife mammalian species as part of different research projects at Massey University. Samples were included in the study if they met one of three criteria: samples that tested positive with a lipL32 PCR for pathogenic Leptospira; samples that tested negative by lipL32 PCR but were recorded as positive to PCR for pathogenic Leptospira in the previous studies; or samples that were PCR-negative in all studies but were from animals with positive agglutination titres against serogroup Tarassovi. DNA samples were typed using PCR that targeted either the glmU or gyrB genetic loci. The resulting amplicons were sequenced and typed relative to reference sequences. RESULTS We identified several associations between mammalian hosts and Leptospira strains/serovars that had not been previously reported in New Zealand. Leptospira borgpetersenii strain Pacifica was found in farmed red deer (Cervus elaphus) samples, L. borgpetersenii serovars Balcanica and Ballum were found in wild red deer samples, Leptospira interrogans serovar Copenhageni was found in stoats (Mustela erminea) and brushtail possums (Trichosurus vulpecula), and L. borgpetersenii was found in a ferret (Mustela putorius furo). Furthermore, we reconfirmed previously described associations including dairy cattle with L. interrogans serovars Copenhageni and Pomona and L. borgpetersenii serovars Ballum, Hardjo type bovis and strain Pacifica, sheep with L. interrogans serovar Pomona and L. borgpetersenii serovar Hardjo type bovis, brushtail possum with L. borgpetersenii serovar Balcanica, farmed deer with L. borgpetersenii serovar Hardjo type bovis and hedgehogs (Erinaceus europaeus) with L. borgpetersenii serovar Ballum. CONCLUSIONS This study provides an updated summary of host-Leptospira associations in New Zealand and highlights the importance of molecular typing. Furthermore, strain Pacifica, which was first identified as Tarassovi using serological methods in dairy cattle in 2016, has circulated in animal communities since at least 2007 but remained undetected as serology is unable to distinguish the different genotypes. CLINICAL RELEVANCE To date, leptospirosis in New Zealand has been diagnosed with serological typing, which is deficient in typing all strains in circulation. Molecular methods are necessary to accurately type strains of Leptospira spp. infecting mammals in New Zealand.
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Affiliation(s)
- D A Wilkinson
- Molecular Epidemiology and Public Health Laboratory, Tāwharau Ora - School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - M Edwards
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Roslin, UK
| | - C Shum
- Molecular Epidemiology and Public Health Laboratory, Tāwharau Ora - School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - M Moinet
- Molecular Epidemiology and Public Health Laboratory, Tāwharau Ora - School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - N E Anderson
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Roslin, UK
| | - J Benschop
- Molecular Epidemiology and Public Health Laboratory, Tāwharau Ora - School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - S Nisa
- Molecular Epidemiology and Public Health Laboratory, Tāwharau Ora - School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
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Muylaert RL, Wilkinson DA, Kingston T, D'Odorico P, Rulli MC, Galli N, John RS, Alviola P, Hayman DTS. Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots. Nat Commun 2023; 14:6854. [PMID: 37891177 PMCID: PMC10611769 DOI: 10.1038/s41467-023-42627-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/31/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multiple drivers-landscape change, host distribution, and human exposure-associated with the risk of spillover of zoonotic SARS-like coronaviruses to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs before examining how access to healthcare varies within clusters and scenarios. We found 19 clusters with differing risk factor contributions within a single country (N = 9) or transboundary (N = 10). High-risk areas were mainly closer (11-20%) rather than far ( < 1%) from healthcare. Areas far from healthcare reveal healthcare access inequalities, especially Scenario 3, which includes wild mammals and not livestock as secondary hosts. China (N = 2) and Indonesia (N = 1) had clusters with the highest risk. Our findings can help stakeholders in land use planning, integrating healthcare implementation and One Health actions.
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Affiliation(s)
- Renata L Muylaert
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - David A Wilkinson
- UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Plateforme Technologique CYROI, Sainte-Clotilde, La Réunion, France
| | - Tigga Kingston
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Paolo D'Odorico
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Cristina Rulli
- Department of Civil and Environmental Engineering, Politecnico di Milano, Milan, Italy
| | - Nikolas Galli
- Department of Civil and Environmental Engineering, Politecnico di Milano, Milan, Italy
| | - Reju Sam John
- Department of Physics, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Phillip Alviola
- Institute of Biological Sciences, University of the Philippines- Los Banos, Laguna, Philippines
| | - David T S Hayman
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Padmanaban V, Grzyb C, Velasco C, Richardson A, Cekovich E, Reichwein R, Church EW, Wilkinson DA, Simon SD, Cockroft KM. Conscious sedation by sedation-trained interventionalists versus anesthesia providers in patients with acute ischemic stroke undergoing endovascular thrombectomy: A propensity score-matched analysis. Interv Neuroradiol 2023:15910199231207409. [PMID: 37828762 DOI: 10.1177/15910199231207409] [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] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The appropriate choice of perioperative sedation during endovascular thrombectomy for ischemic stroke is unknown. Few studies have evaluated the role of nursing-administered conscious sedation supervised by a trained interventionalist. OBJECTIVE To compare the safety and efficacy of endovascular thrombectomy for ischemic stroke performed with nursing-administered conscious sedation supervised by a trained interventionalist with monitored anesthesia care supervised by an anesthesiologist. METHODS A retrospective review of a prospectively collected stroke registry was performed. The primary outcome was functional independence at 90 days, defined as a modified Rankin score of 0-2. Propensity score matching was performed to control for known confounders including patient comorbidities, access type, and direct-to-suite transfers. RESULTS A total of 355 patients underwent endovascular thrombectomy for large vessel occlusion between 2018 and 2022. Thirty five patients were excluded as they arrived at the endovascular suite intubated. Three hundred and twenty patients were included in our study, 155 who underwent endovascular thrombectomy with nursing-administered conscious sedation and 165 who underwent endovascular thrombectomy with monitored anesthesia care. After propensity score matching, there were 111 patients in each group. There was no difference in modified Rankin score 0-2 at 90 days (26.1% vs 35.1%, p = 0.190). Patients undergoing monitored anesthesia care received significantly more vasoactive medications (23.4% vs 49.5%, p < 0.001) and had a lower intraoperative minimum systolic blood pressure (134 vs 123 mmHg, p < 0.046). There was no difference in procedural efficacy, safety, intubation rates, and postoperative complications. CONCLUSION Perioperative sedation with nursing-administered conscious sedation may be safe and effective in patients undergoing endovascular thrombectomy for ischemic stroke.
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Affiliation(s)
- Varun Padmanaban
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Chloe Grzyb
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Cesar Velasco
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Alicia Richardson
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Erin Cekovich
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Raymond Reichwein
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Department of Neurology, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Ephraim W Church
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - David A Wilkinson
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Scott D Simon
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Kevin M Cockroft
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Penn State Comprehensive Stroke Center, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Department of Radiology, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA
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5
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Moinet M, Oosterhof H, Nisa S, Haack N, Wilkinson DA, Aberdein D, Russell JC, Vallée E, Collins-Emerson J, Heuer C, Benschop J. A cross-sectional investigation of Leptospira at the wildlife-livestock interface in New Zealand. PLoS Negl Trop Dis 2023; 17:e0011624. [PMID: 37672535 PMCID: PMC10506710 DOI: 10.1371/journal.pntd.0011624] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/18/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
There has been a recent upsurge in human cases of leptospirosis in New Zealand, with wildlife a suspected emerging source, but up-to-date knowledge on this topic is lacking. We conducted a cross-sectional study in two farm environments to estimate Leptospira seroprevalence in wildlife and sympatric livestock, PCR/culture prevalence in wildlife, and compare seroprevalence and prevalence between species, sex, and age groups. Traps targeting house mice (Mus musculus), black rats (Rattus rattus), hedgehogs (Erinaceus europaeus) and brushtail possums (Trichosurus vulpecula) were set for 10 trap-nights in March-April 2017 on a dairy (A) and a beef and sheep (B) farm. Trapped wild animals and an age-stratified random sample of domestic animals, namely cattle, sheep and working dogs were blood sampled. Sera were tested by microagglutination test for five serogroups and titres compared using a Proportional Similarity Index (PSI). Wildlife kidneys were sampled for culture and qPCR targeting the lipL32 gene. True prevalence in mice was assessed using occupancy modelling by collating different laboratory results. Infection profiles varied by species, age group and farm. At the MAT cut-point of ≥ 48, up to 78% of wildlife species, and 16-99% of domestic animals were seropositive. Five of nine hedgehogs, 23/105 mice and 1/14 black rats reacted to L. borgpetersenii sv Ballum. The sera of 4/18 possums and 4/9 hedgehogs reacted to L. borgpetersenii sv Hardjobovis whilst 1/18 possums and 1/9 hedgehogs reacted to Tarassovi. In ruminants, seroprevalence for Hardjobovis and Pomona ranged 0-90% and 0-71% depending on the species and age group. Titres against Ballum, Tarassovi and Copenhageni were also observed in 4-20%, 0-25% and 0-21% of domestic species, respectively. The PSI indicated rodents and livestock had the most dissimilar serological responses. Three of nine hedgehogs, 31/105 mice and 2/14 rats were carrying leptospires (PCR and/or culture positive). True prevalence estimated by occupancy modelling in mice was 38% [95% Credible Interval 26, 51%] on Farm A and 22% [11, 40%] on Farm B. In the same environment, exposure to serovars found in wildlife species was commonly detected in livestock. Transmission pathways between and within species should be assessed to help in the development of efficient mitigation strategies against Leptospira.
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Affiliation(s)
- Marie Moinet
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Hedwich Oosterhof
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Shahista Nisa
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Neville Haack
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A. Wilkinson
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science & Research Centre, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Danielle Aberdein
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - James C. Russell
- School of Biological Sciences and Department of Statistics, University of Auckland, New Zealand
| | - Emilie Vallée
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Julie Collins-Emerson
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Cord Heuer
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- Tāwharau Ora School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Nisa S, Vallee E, Marshall J, Collins-Emerson J, Yeung P, Prinsen G, Douwes J, Baker MG, Wright J, Quin T, Holdaway M, Wilkinson DA, Fayaz A, Littlejohn S, Benschop J. Leptospirosis in Aotearoa New Zealand: Protocol for a Nationwide Case-Control Study. JMIR Res Protoc 2023; 12:e47900. [PMID: 37289491 DOI: 10.2196/47900] [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: 04/04/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND In Aotearoa New Zealand, 90% of patients with notified leptospirosis (a zoonotic bacterial disease) have been men working in agricultural industries. However, since 2008, the epidemiology of notified cases has been gradually changing, that is, more women are affected; there are more cases associated with occupations traditionally not considered high risk in New Zealand; infecting serovars have changed; and many patients experience symptoms long after infection. We hypothesized that there is a shift in leptospirosis transmission patterns with substantial burden on affected patients and their families. OBJECTIVE In this paper, we aimed to describe the protocols used to conduct a nationwide case-control study to update leptospirosis risk factors and follow-up studies to assess the burden and sources of leptospirosis in New Zealand. METHODS This study used a mixed methods approach, comprising a case-control study and 4 substudies that involved cases only. Cases were recruited nationwide, and controls were frequency matched by sex and rurality. All participants were administered a case-control questionnaire (study 1), with cases being interviewed again at least 6 months after the initial survey (study 2). A subset of cases from two high-risk populations, that is, farmers and abattoir workers, were further engaged in a semistructured interview (study 3). Some cases with regular animal exposure had their in-contact animals (livestock for blood and urine and wildlife for kidney) and environment (soil, mud, and water) sampled (study 4). Patients from selected health clinics suspected of leptospirosis also had blood and urine samples collected (study 5). In studies 4 and 5, blood samples were tested using the microscopic agglutination test to test for antibody titers against Leptospira serovars Hardjo type bovis, Ballum, Tarassovi, Pomona, and Copenhageni. Blood, urine, and environmental samples were also tested for pathogenic Leptospira DNA using polymerase chain reaction. RESULTS Participants were recruited between July 22, 2019, and January 31, 2022, and data collection for the study has concluded. In total, 95 cases (July 25, 2019, to April 13, 2022) and 300 controls (October 19, 2019, to January 26, 2022) were interviewed for the case-control study; 91 cases participated in the follow-up interviews (July 9, 2020, to October 25, 2022); 13 cases participated in the semistructured interviews (January 26, 2021, to January 19, 2022); and 4 cases had their in-contact animals and environments sampled (October 28, 2020, and July 29, 2021). Data analysis for study 3 has concluded and 2 manuscripts have been drafted for review. Results of the other studies are being analyzed and the specific results of each study will be published as individual manuscripts.. CONCLUSIONS The methods used in this study may provide a basis for future epidemiological studies of infectious diseases. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/47900.
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Affiliation(s)
- Shahista Nisa
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Emilie Vallee
- EpiCentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jonathan Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | - Julie Collins-Emerson
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Polly Yeung
- School of Social Work, Massey University, Palmerston North, New Zealand
| | - Gerard Prinsen
- School of People, Environment and Planning, Massey University, Palmerston North, New Zealand
| | - Jeroen Douwes
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Michael G Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Jackie Wright
- Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Tanya Quin
- Goodfellow Unit, University of Auckland, Auckland, New Zealand
| | - Maureen Holdaway
- College of Health, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- Unité Mixte de Recherche, Animal, Santé, Territoires, Risques et Ecosystèmes, Centre de coopération internationale en recherche agronomique pour le développement, Institut national de la recherche agronomique, University of Montpellier, Plateforme Technologique Cyclotron Réunion Océan Indien, Sainte-Clotilde, La Réunion, France
| | - Ahmed Fayaz
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Stuart Littlejohn
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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7
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Hafsia S, Barbar T, Wilkinson DA, Atyame C, Biscornet L, Bibi J, Louange M, Gedeon J, De Santis O, Flahault A, Cabie A, Bertolotti A, Mavingui P. Genetic characterization of dengue virus serotype 1 circulating in Reunion Island, 2019-2021, and the Seychelles, 2015-2016. BMC Infect Dis 2023; 23:294. [PMID: 37147570 PMCID: PMC10161969 DOI: 10.1186/s12879-023-08125-y] [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: 06/19/2022] [Accepted: 02/28/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND An unprecedent increase in the number of cases and deaths reported from dengue virus (DENV) infection has occurred in the southwestern Indian ocean in recent years. From 2017 to mid-2021 more than 70,000 confirmed dengue cases were reported in Reunion Island, and 1967 cases were recorded in the Seychelles from 2015 to 2016. Both these outbreaks displayed similar trends, with the initial circulation of DENV-2 which was replaced by DENV-1. Here, we aim to determine the origin of the DENV-1 epidemic strains and to explore their genetic characteristics along the uninterrupted circulation, particularly in Reunion. METHODS Nucleic acids were extracted from blood samples collected from dengue positive patients; DENV-1 was identified by RT-qPCR. Positive samples were used to infect VERO cells. Genome sequences were obtained from either blood samples or infected-cell supernatants through a combination of both Illumina or MinION technologies. RESULTS Phylogenetic analyses of partial or whole genome sequences revealed that all DENV-1 sequences from Reunion formed a monophyletic cluster that belonged to genotype I and were closely related to one isolate from Sri Lanka (OL752439.1, 2020). Sequences from the Seychelles belonged to the same major phylogenetic branch of genotype V, but fell into two paraphyletic clusters, with greatest similarity for one cluster to 2016-2017 isolate from Bangladesh, Singapore and China, and for the other cluster to ancestral isolates from Singapore, dating back to 2012. Compared to publicly available DENV-1 genotype I sequences, fifteen non-synonymous mutations were identified in the Reunion strains, including one in the capsid and the others in nonstructural proteins (NS) (three in NS1, two in NS2B, one in NS3, one in NS4B, and seven in NS5). CONCLUSION In contrast to what was seen in previous outbreaks, recent DENV-1 outbreaks in Reunion and the Seychelles were caused by distinct genotypes, all likely originating from Asia where dengue is (hyper)endemic in many countries. Epidemic DENV-1 strains from Reunion harbored specific non-synonymous mutations whose biological significance needs to be further investigated.
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Affiliation(s)
- Sarah Hafsia
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, CNRS 9192, INSERM U1187, IRD 249, Plateforme CYROI, Sainte Clotilde, La Réunion, France
| | - Tatiana Barbar
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, CNRS 9192, INSERM U1187, IRD 249, Plateforme CYROI, Sainte Clotilde, La Réunion, France
| | - David A Wilkinson
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, CNRS 9192, INSERM U1187, IRD 249, Plateforme CYROI, Sainte Clotilde, La Réunion, France
| | - Célestine Atyame
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, CNRS 9192, INSERM U1187, IRD 249, Plateforme CYROI, Sainte Clotilde, La Réunion, France
| | - Leon Biscornet
- Public Health Authority, Ministry of Health, Victoria, Seychelles
| | - Jastin Bibi
- Disease Surveillance and Response Unit, Epidemiology and Statistics Section, Public Health Authority, Ministry of Health, Victoria, Seychelles
| | - Meggy Louange
- Public Health Authority, Ministry of Health, Victoria, Seychelles
| | - Jude Gedeon
- Public Health Authority, Ministry of Health, Victoria, Seychelles
| | - Olga De Santis
- Institute of global health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Antoine Flahault
- Institute of global health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - André Cabie
- CHU de Martinique, service de maladies infectieuses et tropicales, INSERM, CHU de Martinique, PCCEI, Univ Montpellier, Univ Antilles, INSERM, EFS, CIC1424, Fort-de-France, Montpellier, France
| | - Antoine Bertolotti
- Service des Maladies Infectieuses - Dermatologie, CHU Réunion, INSERM CIC1410, Saint Pierre, Saint Pierre, La Réunion, France
| | - Patrick Mavingui
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion, CNRS 9192, INSERM U1187, IRD 249, Plateforme CYROI, Sainte Clotilde, La Réunion, France.
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8
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Wilkinson DA, Mercier A, Turpin M, Simbi MA, Turpin J, Lebarbenchon C, Cesari M, Jaffar-Bandjee MC, Josset L, Yemadje-Menudier L, Lina B, Mavingui P. Genomic evolution of SARS-CoV-2 in Reunion Island. Infect Genet Evol 2022; 106:105381. [PMID: 36309317 PMCID: PMC9598258 DOI: 10.1016/j.meegid.2022.105381] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 01/12/2023]
Abstract
Island communities are interesting study sites for microbial evolution during epidemics, as their insular nature reduces the complexity of the population's connectivity. This was particularly true on Reunion Island during the first half of 2021, when international travel was restricted in order to mitigate the risk for SARS-CoV-2 introductions. Concurrently, the SARS-CoV-2 Beta variant became dominant and started to circulate at high levels for several months before being completely replaced by the Delta variant as of October 2021. Here, we explore some of the particularities of SARS-CoV-2 genomic evolution within the insular context of Reunion Island. We show that island isolation allowed the amplification and expansion of unique genetic lineages that remained uncommon across the globe. Islands are therefore potential hotspots for the emergence of new genetic variants, meaning that they will play a key role in the continued evolution and propagation of COVID-19 as the pandemic persists.
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Affiliation(s)
- David A. Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France,GIP CYROI, Saint-Denis, La Réunion, France,Corresponding author at: Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Alizé Mercier
- Santé Publique France, Saint-Denis, La Réunion, France
| | - Magali Turpin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Marie-Alice Simbi
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France,GIP CYROI, Saint-Denis, La Réunion, France
| | - Jonathan Turpin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France,GIP CYROI, Saint-Denis, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | | | - Laurence Josset
- CNR des Virus des Infections Respiratoires, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France,Virpath, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, UCBL, Lyon, France
| | | | - Bruno Lina
- CNR des Virus des Infections Respiratoires, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France,Virpath, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, UCBL, Lyon, France
| | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) CNRS 9192, INSERM 1187, IRD 249, Sainte-Clotilde, La Réunion, France,Corresponding author
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9
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Wilkinson DA, Rogers LE, Bell A, Benschop J, Midwinter AC. Carriage of Staphylococcus pseudintermedius by clinically normal dogs in Canterbury, New Zealand. N Z Vet J 2022; 71:33-36. [PMID: 36165167 DOI: 10.1080/00480169.2022.2129855] [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] [Indexed: 10/24/2022]
Abstract
AIMS To investigate the frequency of carriage of methicillin-susceptible and methicillin-resistant Staphylococcus pseudintermedius (MRSP) in a population of clinically normal dogs within the Christchurch and wider Canterbury region, an area in which MRSP has been detected. METHODS Buccal and perianal swabs were collected from 126 clinically normal dogs presenting at veterinary clinics in the Christchurch/Canterbury region for de-sexing or routine vaccination. S. pseudintermedius was isolated by selective culture. Isolates were tested for susceptibility to 12 antimicrobials by disc diffusion. RESULTS S. pseudintermedius was isolated from 92/126 (73.0 (95% CI = 64.4-80.5)%) dogs, with 38/126 (30.2 (95% CI = 22.3-39.0)%) positive dogs carrying S. pseudintermedius at both sampled sites. More animals (78/126; 61.9; (95% CI: 52.8-70.4)%) had positive mouth cultures than positive perianal region cultures (52/126; 41.3 (95% CI: 32.6-50.4)%). No MRSP was isolated from clinically normal dogs. However, resistance to penicillin (106/130 (85.1%) swabs) and tetracycline (33/130 (25.4%) swabs) was seen. CONCLUSIONS The majority of the dogs in this sample were carriers of S. pseudintermedius. However none of these isolates were MRSP. CLINICAL RELEVANCE While most clinically normal dogs in the studied region are likely to be carriers of S. pseudintermedius, only a small proportion, if any, are likely to be carriers of MRSP. Antibiotic stewardship practices may be important to maintain low-level circulation of drug-resistant bacterial lineages.
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Affiliation(s)
- D A Wilkinson
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.,New Zealand Food Safety Science & Research Centre, Massey University, Palmerston North, New Zealand
| | - L E Rogers
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A Bell
- Dermvetonline, Auckland, New Zealand
| | - J Benschop
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A C Midwinter
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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10
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Abstract
In January 2021, after detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, genomic surveillance was established on Réunion Island to track the introduction and spread of SARS-CoV-2 lineages and variants of concern. This system identified 22 SARS-CoV-2 lineages, 71% of which were attributed to the Beta variant
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11
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Greening SS, Zhang J, Midwinter AC, Wilkinson DA, Fayaz A, Williamson DA, Anderson MJ, Gates MC, French NP. Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand's commercial poultry network. Epidemics 2021; 37:100521. [PMID: 34775297 DOI: 10.1016/j.epidem.2021.100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/05/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.
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Affiliation(s)
- Sabrina S Greening
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - Ji Zhang
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Ahmed Fayaz
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Deborah A Williamson
- Microbiological Diagnostic Unit and Public Health Laboratory, University of Melbourne, Parkville, Victoria, Australia
| | - Marti J Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - M Carolyn Gates
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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12
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Miltgen G, Garrigos T, Cholley P, Deleume M, Allou N, Allyn J, Wilkinson DA, Lugagne N, Belmonte O, Bertrand X, Hocquet D, Mavingui P. Nosocomial cluster of carbapenemase-producing Enterobacter cloacae in an intensive care unit dedicated COVID-19. Antimicrob Resist Infect Control 2021; 10:151. [PMID: 34674756 PMCID: PMC8529563 DOI: 10.1186/s13756-021-01022-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/21/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Concomitant prevention of SARS-CoV-2 and extensively drug-resistant bacteria transmission is a difficult challenge in intensive care units dedicated to COVID-19 patients. We report a nosocomial cluster of four patients carrying NDM-1 plasmid-encoded carbapenemase-producing Enterobacter cloacae. Two main factors may have contributed to cross-transmission: misuse of gloves and absence of change of personal protective equipment, in the context of COVID-19-associated shortage. This work highlights the importance of maintaining infection control measures to prevent CPE cross-transmission despite the difficult context and that this type of outbreak can potentially involve several species of Enterobacterales.
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Affiliation(s)
- Guillaume Miltgen
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France. .,UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.
| | - Thomas Garrigos
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Pascal Cholley
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Marine Deleume
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Nicolas Allou
- Service de Réanimation Polyvalente, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Jérôme Allyn
- Service de Réanimation Polyvalente, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - David A Wilkinson
- UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Nathalie Lugagne
- Service d'hygiène hospitalière, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Olivier Belmonte
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Xavier Bertrand
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Patrick Mavingui
- UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
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13
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Moinet M, Wilkinson DA, Aberdein D, Russell JC, Vallée E, Collins-Emerson JM, Heuer C, Benschop J. Of Mice, Cattle, and Men: A Review of the Eco-Epidemiology of Leptospira borgpetersenii Serovar Ballum. Trop Med Infect Dis 2021; 6:tropicalmed6040189. [PMID: 34698305 PMCID: PMC8544700 DOI: 10.3390/tropicalmed6040189] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
In New Zealand (NZ), leptospirosis is a mostly occupational zoonosis, with >66% of the recently notified cases being farm or abattoir workers. Livestock species independently maintain Leptospira borgpetersenii serovar Hardjo and L. interrogans serovar Pomona, and both are included in livestock vaccines. The increasing importance in human cases of Ballum, a serovar associated with wildlife, suggests that wildlife may be an overlooked source of infection. Livestock could also act as bridge hosts for humans. Drawing from disease ecology frameworks, we chose five barriers to include in this review based on the hypothesis that cattle act as bridge hosts for Ballum. Using a narrative methodology, we collated published studies pertaining to (a) the distribution and abundance of potential wild maintenance hosts of Ballum, (b) the infection dynamics (prevalence and pathogenesis) in those same hosts, (c) Ballum shedding and survival in the environment, (d) the exposure and competency of cattle as a potential bridge host, and (e) exposure for humans as a target host of Ballum. Mice (Mus musculus), rats (Rattus rattus, R. norvegicus) and hedgehogs (Erinaceus europaeus) were suspected as maintenance hosts of Ballum in NZ in studies conducted in the 1970s–1980s. These introduced species are distributed throughout NZ, and are present on pastures. The role of other wildlife in Ballum (and more broadly Leptospira) transmission remains poorly defined, and has not been thoroughly investigated in NZ. The experimental and natural Ballum infection of cattle suggest a low pathogenicity and the possibility of shedding. The seroprevalence in cattle appears higher in recent serosurveys (3 to 14%) compared with studies from the 1970s (0 to 3%). This review identifies gaps in the knowledge of Ballum, and highlights cattle as a potential spillover host. Further studies are required to ascertain the role that wild and domestic species may play in the eco-epidemiology of Ballum in order to understand its survival in the environment, and to inform control strategies.
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Affiliation(s)
- Marie Moinet
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
- Correspondence:
| | - David A. Wilkinson
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
- New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Danielle Aberdein
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
| | - James C. Russell
- Department of Statistics, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand;
| | - Emilie Vallée
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
| | - Julie M. Collins-Emerson
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
| | - Cord Heuer
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
| | - Jackie Benschop
- School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand; (D.A.W.); (D.A.); (E.V.); (J.M.C.-E.); (C.H.); (J.B.)
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14
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Wilkinson DA, Edwards M, Benschop J, Nisa S. Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding. PLoS One 2021; 16:e0257971. [PMID: 34587213 PMCID: PMC8480790 DOI: 10.1371/journal.pone.0257971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Leptospirosis is a zoonotic disease of global importance. The breadth of Leptospira diversity associated with both human and animal disease poses major logistical challenges to the use of classical diagnostic techniques, and increasingly molecular diagnostic tools are used for their detection. In New Zealand, this has resulted in an increase in positive cases reported nationally that have not been attributed to the infecting serovar or genomospecies. In this study, we used data from all pathogenic Leptospira genomes to identify a partial region of the glmU gene as a suitable locus for the discrimination of the infecting species and serovars of New Zealand-endemic Leptospira. This method can be used in culture and culture-independent scenarios making it flexible for diagnostics in humans, animals, and environmental samples. We explored the use of this locus as a molecular barcoding tool via the Oxford Nanopore Technology (ONT) sequencing platform MinION. Sequences obtained by this method allowed specific identification of Leptospira species in mixed and enriched environmental cultures, however read error inherent in the MinION sequencing system reduced the accuracy of strain/variant identification. Using this approach to characterise Leptospira in enriched environmental cultures, we detected the likely presence of Leptospira genomospecies that have not been reported in New Zealand to date. This included a strain of L. borgpetersenii that has recently been identified in dairy cattle and sequences similar to those of L. mayottensis. L. tipperaryensis, L. dzianensis and L. alstonii.
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Affiliation(s)
- David A. Wilkinson
- New Zealand Food Safety, Science & Research Centre, Massey University, Palmerston North, New Zealand
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
- * E-mail:
| | - Matthew Edwards
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Shahista Nisa
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
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15
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Wilkinson DA, Joffrin L, Lebarbenchon C, Mavingui P. Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses. J Gen Virol 2020; 101:1261-1269. [PMID: 32902374 PMCID: PMC7819353 DOI: 10.1099/jgv.0.001494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/06/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.
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Affiliation(s)
- David A. Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Present address: Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT) INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
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16
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Daou BJ, Palmateer G, Wilkinson DA, Thompson BG, Maher CO, Chaudhary N, Gemmete JJ, Hayman JA, Lam K, Wahl DR, Kim M, Pandey AS. Radiation-Induced Imaging Changes and Cerebral Edema following Stereotactic Radiosurgery for Brain AVMs. AJNR Am J Neuroradiol 2020; 42:82-87. [PMID: 33214183 DOI: 10.3174/ajnr.a6880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/17/2020] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE T2 signal and FLAIR changes in patients undergoing stereotactic radiosurgery for brain AVMs may occur posttreatment and could result in adverse radiation effects. We aimed to evaluate outcomes in patients with these imaging changes, the frequency and degree of this response, and factors associated with it. MATERIALS AND METHODS Through this retrospective cohort study, consecutive patients treated with stereotactic radiosurgery for brain AVMs who had at least 1 year of follow-up MR imaging were identified. Logistic regression analysis was used to evaluate predictors of outcomes. RESULTS One-hundred-sixty AVMs were treated in 148 patients (mean, 35.6 years of age), including 42 (26.2%) pediatric AVMs. The mean MR imaging follow-up was 56.5 months. The median Spetzler-Martin grade was III. The mean maximal AVM diameter was 2.8 cm, and the mean AVM target volume was 7.4 mL. The median radiation dose was 16.5 Gy. New T2 signal and FLAIR hyperintensity were noted in 40% of AVMs. T2 FLAIR volumes at 3, 6, 12, 18, and 24 months were, respectively, 4.04, 55.47, 56.42, 48.06, and 29.38 mL Radiation-induced neurologic symptoms were encountered in 34.4%. In patients with radiation-induced imaging changes, 69.2% had new neurologic symptoms versus 9.5% of patients with no imaging changes (P = .0001). Imaging changes were significantly associated with new neurologic findings (P < .001). Larger AVM maximal diameter (P = .04) and the presence of multiple feeding arteries (P = .01) were associated with radiation-induced imaging changes. CONCLUSIONS Radiation-induced imaging changes are common following linear particle accelerator-based stereotactic radiosurgery for brain AVMs, appear to peak at 12 months, and are significantly associated with new neurologic findings.
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Affiliation(s)
- B J Daou
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
| | - G Palmateer
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
| | - D A Wilkinson
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
| | - B G Thompson
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
| | - C O Maher
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
| | - N Chaudhary
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.).,Radiology (N.C., J.J.G.)
| | - J J Gemmete
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.).,Radiology (N.C., J.J.G.)
| | - J A Hayman
- From the Departments of Radiation Oncology (J.A.H., K.L., D.R.W., M.K.).,Radiation Oncology (J.A.H., K.L., D.R.W., M.K.), University of Michigan, Ann Arbor, Michigan
| | - K Lam
- From the Departments of Radiation Oncology (J.A.H., K.L., D.R.W., M.K.).,Radiation Oncology (J.A.H., K.L., D.R.W., M.K.), University of Michigan, Ann Arbor, Michigan
| | - D R Wahl
- From the Departments of Radiation Oncology (J.A.H., K.L., D.R.W., M.K.).,Radiation Oncology (J.A.H., K.L., D.R.W., M.K.), University of Michigan, Ann Arbor, Michigan
| | - M Kim
- From the Departments of Radiation Oncology (J.A.H., K.L., D.R.W., M.K.).,Radiation Oncology (J.A.H., K.L., D.R.W., M.K.), University of Michigan, Ann Arbor, Michigan
| | - A S Pandey
- Neurosurgery (B.J.D., G.P., D.A.W., B.G.T., C.O.M., N.C., J.J.G., A.S.P.)
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17
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Lake RJ, Campbell DM, Hathaway SC, Ashmore E, Cressey PJ, Horn BJ, Pirikahu S, Sherwood JM, Baker MG, Shoemack P, Benschop J, Marshall JC, Midwinter AC, Wilkinson DA, French NP. Source attributed case-control study of campylobacteriosis in New Zealand. Int J Infect Dis 2020; 103:268-277. [PMID: 33221520 DOI: 10.1016/j.ijid.2020.11.167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/01/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Following an initial reduction in human campylobacteriosis in New Zealand after the implementation of poultry food chain-focused interventions during 2006-2008, further decline has been relatively small. We report a year-long study of notified campylobacteriosis cases, incorporating a case control study combined with a source attribution study. The purpose was to generate up-to-date evidence on the relative contributions of different sources of campylobacteriosis in New Zealand. METHODS The study approach included: • A case-control study of notified cases (aged six months or more) sampled in a major urban centre (Auckland, every second case) and a mixed urban/rural area (Manawatū/Whanganui, every case), between 12 March 2018 and 11 March 2019. • Source attribution of human campylobacteriosis cases sampled from these two regions over the study period by modelling of multilocus sequence typing data of Campylobacter jejuni and C. coli isolates from faecal samples of notified human cases and relevant sources (poultry, cattle, sheep). RESULTS Most cases (84%) were infected with strains attributed to a poultry source, while 14% were attributed to a cattle source. Approximately 90% of urban campylobacteriosis cases were attributed to poultry sources, compared to almost 75% of rural cases. Poultry consumption per se was not identified as a significant risk factor. However specific risk factors related to poultry meat preparation and consumption did result in statistically significantly elevated odds ratios. CONCLUSIONS The overall findings combining source attribution and analysis of specific risk factors indicate that poultry meat remains a dominant pathway for exposure and infection.
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Affiliation(s)
- R J Lake
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand; New Zealand Food Safety Science and Research Centre, School of Veterinary Science, Massey University, New Zealand.
| | - D M Campbell
- New Zealand Food Safety, Ministry of Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - S C Hathaway
- New Zealand Food Safety, Ministry of Primary Industries, PO Box 2526, Wellington 6140, New Zealand
| | - E Ashmore
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - P J Cressey
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - B J Horn
- Risk Assessment and Social Systems Group, Institute of Environmental Science and Research, Christchurch Science Centre, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - S Pirikahu
- School of Population and Global Health, The University of Western Australia, 35 Stirling Hwy, Crawley WA, Perth, Australia
| | - J M Sherwood
- Institute of Environmental Science and Research, Kenepuru Science Centre, PO Box 50348, Porirua 5240, New Zealand
| | - M G Baker
- University of Otago, Wellington, Box 7343, Wellington, 6242, New Zealand
| | - P Shoemack
- Bay of Plenty District Health Board, PO Box 2120, Tauranga, 3140, New Zealand
| | - J Benschop
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - J C Marshall
- School of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, 4474, New Zealand
| | - A C Midwinter
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - D A Wilkinson
- Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
| | - N P French
- New Zealand Food Safety Science and Research Centre, School of Veterinary Science, Massey University, New Zealand; Tāwharau Ora, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand
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18
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Nisa S, Wilkinson DA, Angelin-Bonnet O, Paine S, Cullen K, Wight J, Baker MG, Benschop J. Diverse Epidemiology of Leptospira serovars Notified in New Zealand, 1999-2017. Pathogens 2020; 9:pathogens9100841. [PMID: 33066613 PMCID: PMC7602385 DOI: 10.3390/pathogens9100841] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 09/13/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022] Open
Abstract
Leptospirosis in New Zealand has been strongly associated with animal-contact occupations and with serovars Hardjo and Pomona. However, recent data suggest changes in these patterns, hence, serovar-specific epidemiology of leptospirosis from 1999 to 2017 was investigated. The 19-year average annual incidence is 2.01/100,000. Early (1999-2007) and late (2008-2017) study period comparisons showed a significant increase in notifications with serovar Ballum (IRR: 1.59, 95% CI: 1.22-2.09) in all cases and serovar Tarassovi (IRR: 1.75, 95% CI: 1.13-2.78) in Europeans and a decrease in notifications with serovars Hardjo and Pomona in all cases. Incidences of Ballum peaked in winter, Hardjo peaked in spring and Tarassovi peaked in summer. Incidence was highest in Māori (2.24/100,000) with dominant serovars being Hardjo and Pomona. Stratification by occupation showed meat workers had the highest incidence of Hardjo (57.29/100,000) and Pomona (45.32/100,000), farmers had the highest incidence of Ballum (11.09/100,000) and dairy farmers had the highest incidence of Tarassovi (12.59/100,000). Spatial analysis showed predominance of Hardjo and Pomona in Hawke's Bay, Ballum in West Coast and Northland and Tarassovi in Waikato, Taranaki and Northland. This study highlights the serovar-specific heterogeneity of human leptospirosis in New Zealand that should be considered when developing control and prevention strategies.
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Affiliation(s)
- Shahista Nisa
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North 4474, New Zealand;
| | - David A. Wilkinson
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North 4474, New Zealand;
| | - Olivia Angelin-Bonnet
- School of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4474, New Zealand;
| | - Shevaun Paine
- Institute of Environmental Science and Research, Wellington 5022, New Zealand; (S.P.); (K.C.); (J.W.)
| | - Karen Cullen
- Institute of Environmental Science and Research, Wellington 5022, New Zealand; (S.P.); (K.C.); (J.W.)
| | - Jackie Wight
- Institute of Environmental Science and Research, Wellington 5022, New Zealand; (S.P.); (K.C.); (J.W.)
| | - Michael G. Baker
- Department of Public Health, University of Otago, Wellington 6021, New Zealand;
| | - Jackie Benschop
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North 4474, New Zealand;
- Global Leptospirosis Environmental Action Network, World Health Organization, Geneva, Switzerland
- Correspondence: ; Tel.: +64-6-359-9099 (ext. 83994)
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19
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Crawshaw TR, Hunter S, Wilkinson DA, Rogers LE, Christensen NH, Midwinter AC. Isolation of Campylobacter hepaticus from free-range poultry with spotty liver disease in New Zealand. N Z Vet J 2020; 69:58-64. [PMID: 32781921 DOI: 10.1080/00480169.2020.1801532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/23/2022]
Abstract
Case history: In October 2019, a free-range egg laying flock suffering an outbreak of spotty liver disease was investigated. Eight 32-week-old hens were examined post-mortem. Clinical and pathological findings: Five of the eight hens had sparse, focal, gross hepatic lesions typical of spotty liver disease. Histopathology of the liver showed random, focal hepatic necrosis, lymphoplasmacytic cholangitis/pericholangitis and, in one hen, severe lymphoplasmacytic cholecystitis. Campylobacter-like organisms were grown from all eight bile samples which were confirmed by PCR as Campylobacter hepaticus. The genome of C. hepaticus isolates from the outbreak were sequenced and compared to those of isolates from Australia and the United Kingdom. Phylogenetic analysis based on single nucleotide polymorphisms showed that the C. hepaticus isolates from this outbreak were most closely related to isolates from Australia. Diagnosis: Campylobacter hepaticus focal hepatic necrosis. Clinical relevance: This is the first report of an outbreak of spotty liver disease confirmed to be caused by C. hepaticus in poultry in New Zealand. Therefore infection with C. hepaticus should be considered as a differential diagnosis for mortality in laying hens around peak lay in New Zealand.
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Affiliation(s)
- T R Crawshaw
- Massey Farm Services, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - S Hunter
- Wildbase Pathology, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - D A Wilkinson
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - L E Rogers
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | | | - A C Midwinter
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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20
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Gilpin BJ, Walker T, Paine S, Sherwood J, Mackereth G, Wood T, Hambling T, Hewison C, Brounts A, Wilson M, Scholes P, Robson B, Lin S, Cornelius A, Rivas L, Hayman DT, French NP, Zhang J, Wilkinson DA, Midwinter AC, Biggs PJ, Jagroop A, Eyre R, Baker MG, Jones N. A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand. J Infect 2020; 81:390-395. [DOI: 10.1016/j.jinf.2020.06.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
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21
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Crump JA, Thomas KM, Benschop J, Knox MA, Wilkinson DA, Midwinter AC, Munyua P, Ochieng JB, Bigogo GM, Verani JR, Widdowson MA, Prinsen G, Cleaveland S, Karimuribo ED, Kazwala RR, Mmbaga BT, Swai ES, French NP, Zadoks RN. Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa. Clin Infect Dis 2020; 73:e1570-e1578. [PMID: 32777036 PMCID: PMC8492120 DOI: 10.1093/cid/ciaa1153] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 04/16/2020] [Accepted: 08/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. Methods We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity. Results We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources. Conclusions Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand.,Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Kate M Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jackie Benschop
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthew A Knox
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Peninah Munyua
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - John B Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey M Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Gerard Prinsen
- School of People, Environment and Planning, Massey University, Palmerston North, New Zealand
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Esron D Karimuribo
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Rudovick R Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Emanuel S Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, Tanzania
| | - Nigel P French
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.,Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
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22
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Collis RM, Biggs PJ, Midwinter AC, Browne AS, Wilkinson DA, Irshad H, French NP, Brightwell G, Cookson AL. Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies. PLoS One 2020; 15:e0235066. [PMID: 32584859 PMCID: PMC7316241 DOI: 10.1371/journal.pone.0235066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/08/2020] [Indexed: 11/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.
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Affiliation(s)
- Rose M. Collis
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J. Biggs
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A. Springer Browne
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A. Wilkinson
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Hamid Irshad
- Animal Health Programme, National Agricultural Research Centre, Islamabad, Pakistan
| | - Nigel P. French
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- * E-mail:
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23
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Joffrin L, Goodman SM, Wilkinson DA, Ramasindrazana B, Lagadec E, Gomard Y, Le Minter G, Dos Santos A, Corrie Schoeman M, Sookhareea R, Tortosa P, Julienne S, Gudo ES, Mavingui P, Lebarbenchon C. Bat coronavirus phylogeography in the Western Indian Ocean. Sci Rep 2020; 10:6873. [PMID: 32327721 PMCID: PMC7181612 DOI: 10.1038/s41598-020-63799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.
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Affiliation(s)
- Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, USA
| | - David A Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Association Vahatra, Antananarivo, Madagascar
- Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar
| | - Erwan Lagadec
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Pablo Tortosa
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Simon Julienne
- Seychelles Ministry of Health, Victoria, Mahe, Seychelles
| | | | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
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24
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French NP, Zhang J, Carter GP, Midwinter AC, Biggs PJ, Dyet K, Gilpin BJ, Ingle DJ, Mulqueen K, Rogers LE, Wilkinson DA, Greening SS, Muellner P, Fayaz A, Williamson DA. Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016. Emerg Infect Dis 2020; 25:2226-2234. [PMID: 31742539 PMCID: PMC6874264 DOI: 10.3201/eid2512.190267] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2014, antimicrobial drug–resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. We hypothesize that the tetO gene and a phage were inserted into the chromosome after conjugation, leaving a remnant plasmid that was lost from isolates from company C. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand, coupled with evolutionary change in the accessory genome, demonstrate the need for ongoing Campylobacter surveillance among poultry and humans.
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25
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Browne AS, Biggs PJ, Wilkinson DA, Cookson AL, Midwinter AC, Bloomfield SJ, Hranac CR, Rogers LE, Marshall JC, Benschop J, Withers H, Hathaway S, George T, Jaros P, Irshad H, Fong Y, Dufour M, Karki N, Winkleman T, French NP. Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand. Emerg Infect Dis 2019; 25:489-500. [PMID: 30789138 PMCID: PMC6390770 DOI: 10.3201/eid2503.180899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.
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26
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Muylaert RL, Bovendorp RS, Sabino-Santos G, Prist PR, Melo GL, Priante CDF, Wilkinson DA, Ribeiro MC, Hayman DTS. Hantavirus host assemblages and human disease in the Atlantic Forest. PLoS Negl Trop Dis 2019; 13:e0007655. [PMID: 31404077 PMCID: PMC6748440 DOI: 10.1371/journal.pntd.0007655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/17/2019] [Accepted: 07/24/2019] [Indexed: 11/18/2022] Open
Abstract
Several viruses from the genus Orthohantavirus are known to cause lethal disease in humans. Sigmodontinae rodents are the main hosts responsible for hantavirus transmission in the tropical forests, savannas, and wetlands of South America. These rodents can shed different hantaviruses, such as the lethal and emerging Araraquara orthohantavirus. Factors that drive variation in host populations may influence hantavirus transmission dynamics within and between populations. Landscape structure, and particularly areas with a predominance of agricultural land and forest remnants, is expected to influence the proportion of hantavirus rodent hosts in the Atlantic Forest rodent community. Here, we tested this using 283 Atlantic Forest rodent capture records and geographically weighted models that allow us to test if predictors vary spatially. We also assessed the correspondence between proportions of hantavirus hosts in rodent communities and a human vulnerability to hantavirus infection index across the entire Atlantic Forest biome. We found that hantavirus host proportions were more positively influenced by landscape diversity than by a particular habitat or agricultural matrix type. Local small mammal diversity also positively influenced known pathogenic hantavirus host proportions, indicating that a plasticity to habitat quality may be more important for these hosts than competition with native forest dwelling species. We found a consistent positive effect of sugarcane and tree plantation on the proportion of rodent hosts, whereas defaunation intensity did not correlate with the proportion of hosts of potentially pathogenic hantavirus genotypes in the community, indicating that non-defaunated areas can also be hotspots for hantavirus disease outbreaks. The spatial match between host hotspots and human disease vulnerability was 17%, while coldspots matched 20%. Overall, we discovered strong spatial and land use change influences on hantavirus hosts at the landscape level across the Atlantic Forest. Our findings suggest disease surveillance must be reinforced in the southern and southeastern regions of the biome where the highest predicted hantavirus host proportion and levels of vulnerability spatially match. Importantly, our analyses suggest there may be more complex rodent community dynamics and interactions with human disease than currently hypothesized.
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Affiliation(s)
- Renata L. Muylaert
- Departamento de Ecologia, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
- Molecular Epidemiology and Public Health Laboratory, Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Ricardo Siqueira Bovendorp
- Departamento de Ecologia, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
- PPG Ecologia e Conservação da Biodiversidade, LEAC, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Gilberto Sabino-Santos
- Center for Virology Research, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- Vitalant Research Institute, San Francisco, California, United States of America
| | - Paula R. Prist
- Instituto de Biociências, Departamento de Ecologia, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Geruza Leal Melo
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | | | - David A. Wilkinson
- Molecular Epidemiology and Public Health Laboratory, Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Milton Cezar Ribeiro
- Departamento de Ecologia, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - David T. S. Hayman
- Molecular Epidemiology and Public Health Laboratory, Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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27
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Tamminen LM, Söderlund R, Wilkinson DA, Torsein M, Eriksson E, Churakov M, Dicksved J, Keeling LJ, Emanuelson U. Risk factors and dynamics of verotoxigenic Escherichia coli O157:H7 on cattle farms: An observational study combining information from questionnaires, spatial data and molecular analyses. Prev Vet Med 2019; 170:104726. [PMID: 31421496 DOI: 10.1016/j.prevetmed.2019.104726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/13/2019] [Accepted: 07/02/2019] [Indexed: 01/29/2023]
Abstract
The increasing number of human cases infected with a highly virulent type of verotoxigenic Escherichia coli (VTEC) O157:H7 in Sweden is the result of domestic transmission originating in regional clusters of infected cattle farms. To control the spread of the bacteria a comprehensive picture of infection dynamics, routes of transmission between farms and risk factors for persistence is urgently needed. The aim of the study was to investigate different aspects of the epidemiology of VTEC O157:H7 on the Swedish island of Öland by combining information from environmental sampling of VTEC O157:H7 from 80 farms with information from farmer questionnaires, spatial and molecular analyses. The farms were sampled in the spring and fall of 2014 and on four of them additional samples were collected during summer and winter. The results show a high prevalence of VTEC O157:H7 and a high proportion of strains belonging to the virulent clade 8. Farms that became infected between samplings were all located in an area with high cattle density. The most important risk factors identified are generally associated with biosecurity and indicate that visitors travelling between farms may be important for transmission. In addition, whole genome sequencing of a subset of isolates from the four farms where additional sampling was performed revealed ongoing local transmission that cannot be observed with a lower resolution typing method. Our observations also show that VTEC O157:H7 may persist in the farm environment for extended periods of time, suggesting that specific on-farm measures to reduce environmental prevalence and spread between groups of animals may be required in these cases.
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Affiliation(s)
- Lena-Mari Tamminen
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden.
| | | | - David A Wilkinson
- Molecular Epidemiology and Public Health Laboratory (mEpilab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Maria Torsein
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 234, SE-53223, Skara, Sweden
| | - Erik Eriksson
- National Veterinary Institute (SVA), SE-75189, Uppsala, Sweden
| | - Mikhail Churakov
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-75007, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-75007, Uppsala, Sweden
| | - Linda J Keeling
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 7068, SE-75007, Uppsala, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden
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28
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Nisa S, Bercker C, Midwinter AC, Bruce I, Graham CF, Venter P, Bell A, French NP, Benschop J, Bailey KM, Wilkinson DA. Combining MALDI-TOF and genomics in the study of methicillin resistant and multidrug resistant Staphylococcus pseudintermedius in New Zealand. Sci Rep 2019; 9:1271. [PMID: 30718644 PMCID: PMC6361924 DOI: 10.1038/s41598-018-37503-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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] [Received: 07/03/2018] [Accepted: 11/28/2018] [Indexed: 02/05/2023] Open
Abstract
Staphylococcus pseudintermedius is an opportunistic and emerging zoonotic pathogen that primarily colonises the skin of dogs. Many common variants are methicillin resistant (MRSP) or multidrug resistant (MDR), and drug resistance is increasingly reported across the globe. In New Zealand, MRSP isolation remains rare in clinics. To pre-emptively inform diagnostic and antimicrobial stewardship practices, we examine isolates of S. pseudintermedius, MRSP and MDR-MRSP from New Zealand dogs using a combination of methodologies. Genetic and genomic data combined with antimicrobial susceptibility screening identify common drug-resistance profiles and their genetic determinants. We demonstrate that sensitive and specific species-level identification of S. pseudintermedius can be achieved using Bruker MALDI-TOF MS and, further, that this technique can be used to identify some common subtype variants, providing a level of categorical precision that falls somewhere between single-locus and multi-locus sequence typing. Comparative genomics analysis of global S. pseudintermedius data shows that MRSP moves frequently across the globe, but that horizontal gene transfer events resulting in the acquisition of the SCCmec cassette (responsible for beta-lactam antibiotic resistance) are infrequent. This suggests that biosecurity and surveillance in addition to antibiotic stewardship should play important roles in mitigating the risk of MRSP, especially in countries such as New Zealand where MRSP is still rare.
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Affiliation(s)
- Shahista Nisa
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Clément Bercker
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.,Ecole Nationale Veterinaire de Toulouse, Toulouse, France
| | - Anne C Midwinter
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Ian Bruce
- NZVP (IDEXX), Palmerston North, New Zealand
| | | | - Pierre Venter
- Fonterra Research & Development Centre, Palmerston North, New Zealand
| | | | - Nigel P French
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | | | - David A Wilkinson
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand. .,New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand.
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29
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El Kalamouni C, Frumence E, Bos S, Turpin J, Nativel B, Harrabi W, Wilkinson DA, Meilhac O, Gadea G, Desprès P, Krejbich-Trotot P, Viranaïcken W. Subversion of the Heme Oxygenase-1 Antiviral Activity by Zika Virus. Viruses 2018; 11:v11010002. [PMID: 30577437 PMCID: PMC6356520 DOI: 10.3390/v11010002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 10/15/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022] Open
Abstract
Heme oxygenase-1 (HO-1), a rate-limiting enzyme involved in the degradation of heme, is induced in response to a wide range of stress conditions. HO-1 exerts antiviral activity against a broad range of viruses, including the Hepatitis C virus, the human immunodeficiency virus, and the dengue virus by inhibiting viral growth. It has been reported that HO-1 displays antiviral activity against the Zika virus (ZIKV) but the mechanisms of viral inhibition remain largely unknown. Using a ZIKV RNA replicon with the Green Fluorescent Protein (GFP) as a reporter protein, we were able to show that HO-1 expression resulted in the inhibition of viral RNA replication. Conversely, we observed a decrease in HO-1 expression in cells replicating the ZIKV RNA replicon. The study of human cells infected with ZIKV showed that the HO-1 expression level was significantly lower once viral replication was established, thereby limiting the antiviral effect of HO-1. Our work highlights the capacity of ZIKV to thwart the anti-replicative activity of HO-1 in human cells. Therefore, the modulation of HO-1 as a novel therapeutic strategy against ZIKV infection may display limited effect.
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Affiliation(s)
- Chaker El Kalamouni
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Etienne Frumence
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Sandra Bos
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Jonathan Turpin
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Brice Nativel
- Université de la Réunion, Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), F-97490 Sainte-Clotilde, France.
| | - Wissal Harrabi
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - David A Wilkinson
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Olivier Meilhac
- Université de la Réunion, Inserm, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), F-97490 Sainte-Clotilde, France.
- CHU de La Réunion, Saint-Denis de La Réunion, F-97400 Bellepierre, France.
| | - Gilles Gadea
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Philippe Desprès
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Pascale Krejbich-Trotot
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
| | - Wildriss Viranaïcken
- Université de La Réunion, INSERM UMR 1187, CNRS 9192, IRD 249 UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, Plateforme CYROI, 2, rue Maxime Rivière, F-97490 Sainte-Clotilde, France.
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30
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Wilkinson DA, Marshall JC, French NP, Hayman DTS. Habitat fragmentation, biodiversity loss and the risk of novel infectious disease emergence. J R Soc Interface 2018; 15:rsif.2018.0403. [PMID: 30518565 DOI: 10.1098/rsif.2018.0403] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [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: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 01/02/2023] Open
Abstract
The number of microbes on Earth may be 1030, exceeding all other diversity. A small number of these can infect people and cause disease. The diversity of parasitic organisms likely correlates with the hosts they live in and the number mammal hosts for zoonotic infections increases with species richness among mammalian orders. Thus, while habitat loss and fragmentation may reduce species diversity, the habitat encroachment by people into species-rich areas may increase the exposure of people to novel infectious agents from wildlife. Here, we present a theoretical framework that exploits the species-area relationship to link the exposure of people to novel infections with habitat biodiversity. We model changes in human exposure to microbes through defined classes of habitat fragmentation and predict that increased habitat division intrinsically increases the hazard from microbes for all modelled biological systems. We apply our model to African tropical forests as an example. Our results suggest that it is possible to identify high-risk areas for the mitigation and surveillance of novel disease emergence and that mitigation measures may reduce this risk while conserving biodiversity.
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Affiliation(s)
- David A Wilkinson
- Molecular Epidemiology and Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North, New Zealand .,New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- Molecular Epidemiology and Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Nigel P French
- Molecular Epidemiology and Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North, New Zealand.,New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - David T S Hayman
- Molecular Epidemiology and Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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31
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Lebon C, Soupapoule K, Wilkinson DA, Le Goff G, Damiens D, Gouagna LC. Laboratory evaluation of the effects of sterilizing doses of γ-rays from Caesium-137 source on the daily flight activity and flight performance of Aedes albopictus males. PLoS One 2018; 13:e0202236. [PMID: 30107004 PMCID: PMC6091941 DOI: 10.1371/journal.pone.0202236] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/30/2018] [Indexed: 12/17/2022] Open
Abstract
The control of Aedes albopictus through Sterile Male Releases requires that the most competitive males be mass-reared and sterilized usually with gamma- or X-ray radiation prior to release. Developing an understanding of the impact of irradiation treatment on flight performance in sterile males is very important because any fitness cost may reduce the efficacy of SIT intervention in the field. Here, we examined the role of irradiation exposure and sugar-feeding on daily flight activity and performance of Ae. albopictus males sterilized during pupal stage with gamma-radiation at 35Gray from a Caesium 137 source. We used a previously developed automated video tracking system to monitor the flight activity of different groups of sterile and control non-sterile males over 24 hours in a flight arena. This monitoring took place under controlled laboratory conditions and we wished to quantify the daily flight activity and to highlight any changes due to radiation treatment and nutritional conditions (starved versus sugar fed). Our experimental evidence demonstrated a characteristic diurnal flight activity with a bimodal pattern regardless of the treatment. Precisely, both irradiated and non-irradiated males exhibited two distinct peaks in flight activity in the morning (6-8 a.m.) and late afternoon (4-6 p.m.). Under changing physiological conditions, irradiated males were generally more active over time and flew longer overall distances than control male populations. These results suggest some internal circadian control of the phase relation to the light-dark cycle, with evidence for modification of flight performance by nutritional status. The fact that daily activity patterns are alike in irradiated and control Ae. albopictus males, and that sterile males could display higher flight performance, is in contrast with the hypothesis that irradiation treatment appears to reduce the fitness of male mosquitoes. We discuss the implications of the present study in sterile-male release programs against Ae. albopictus.
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Affiliation(s)
- Cyrille Lebon
- Institut de Recherche pour le Développement (IRD, Unité Mixte de Recherche « Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle » MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion / GIP CYROI (Recherche Santé Bio-innovation), Sainte-Clotilde, La Réunion Island, France
| | - Kevin Soupapoule
- Université de La Rochelle–UFR Sciences—Département de Biotechnologies, La Rochelle, France
| | - David A. Wilkinson
- Université de La Réunion, Unité Mixte de Recherche « Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT)», INSERM U1187-CNRS9192-IRD249. Plateforme de Recherche CYROI, Ste Clotilde, La Réunion Island, France
| | - Gilbert Le Goff
- Institut de Recherche pour le Développement (IRD, Unité Mixte de Recherche « Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle » MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion / GIP CYROI (Recherche Santé Bio-innovation), Sainte-Clotilde, La Réunion Island, France
| | - David Damiens
- Institut de Recherche pour le Développement (IRD, Unité Mixte de Recherche « Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle » MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion / GIP CYROI (Recherche Santé Bio-innovation), Sainte-Clotilde, La Réunion Island, France
| | - Louis Clément Gouagna
- Institut de Recherche pour le Développement (IRD, Unité Mixte de Recherche « Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle » MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion / GIP CYROI (Recherche Santé Bio-innovation), Sainte-Clotilde, La Réunion Island, France
- * E-mail:
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32
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Abstract
This year marks the 20th anniversary of the Primary Trauma Care Foundation (PTC), which provides a course aimed at providing a systematic approach to trauma and the unwell patient in low- and middle-income countries. The course is based on the original 36-page PTC manual and a key ethos of being appropriate to the target audience, affordable to those who need it, adaptable to the needs of each local area and sustainable to perpetuate itself. The concept is simple: a two-day course for candidates, followed by a one-day instructor course, and finally a first course delivered to local healthcare staff by the first cohort. Now in its 20th year, its reach spans 76 countries, is ingrained in the syllabus of many healthcare systems and continues to reach new territories with a programme shown to produce a measurable improvement in the care delivered.
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Affiliation(s)
- RA Ley Greaves
- Principle House Officer, Bundaberg Hospital Emergency Department, Queensland, Australia
| | - LF Wilkinson
- Principle House Officer, Bundaberg Hospital Emergency Department, Queensland, Australia
| | - DA Wilkinson
- Consultant Anaesthetist and intensivist, Nuffield Department of Anaesthetics, Founder of Primary Trauma Care Foundation, Oxford, UK
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33
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Wilkinson DA, Hayman DTS. Bat and virus ecology in a dynamic world. Microbiol Aust 2017. [DOI: 10.1071/ma17011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The emergence of infectious diseases caused by bat-associated viruses has had a devastating and wide-reaching effect on human populations. These viruses include lyssaviruses such as rabies virus, the filoviruses, Ebola (EBOV) and Marburg virus, Severe Acute Respiratory Syndrome (SARS) coronavirus, and the paramyxoviruses, Hendra virus (HeV) and Nipah virus (NiV)1. As a result bats have been the focus of substantial research (Fig. 1) and certain cellular and physiological traits of bats are hypothesised to lead to ‘special’ bat-virus associations2,3 (but see Han et al.4). The anthropogenic changes in the world we live will influence human health5, including through their impact on bat ecology and the viruses within bat populations. Australian people and livestock have been infected by novel bat viruses, such as HeV, Menangle viruses (MenV) and Australian bat lyssavirus (ABLV), and are at the forefront of both epidemiological and virological research efforts into cross-species transmission events (spillover): here we put some of those efforts and the potential impacts of anthropogenic changes on bat-virus ecology under the microscope.
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34
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Damiens D, Lebon C, Wilkinson DA, Dijoux-Millet D, Le Goff G, Bheecarry A, Gouagna LC. Cross-Mating Compatibility and Competitiveness among Aedes albopictus Strains from Distinct Geographic Origins - Implications for Future Application of SIT Programs in the South West Indian Ocean Islands. PLoS One 2016; 11:e0163788. [PMID: 27806056 PMCID: PMC5091895 DOI: 10.1371/journal.pone.0163788] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/14/2016] [Indexed: 11/24/2022] Open
Abstract
The production of large numbers of males needed for a sustainable sterile insect technique (SIT) control program requires significant developmental and operational costs. This may constitute a significant economic barrier to the installation of large scale rearing facilities in countries that are undergoing a transition from being largely dependent on insecticide use to be in a position to integrate the SIT against Aedes albopictus. Alternative options available for those countries could be to rely on outsourcing of sterile males from a foreign supplier, or for one centralised facility to produce mosquitoes for several countries, thus increasing the efficiency of the mass-rearing effort. However, demonstration of strain compatibility is a prerequisite for the export of mosquitoes for transborder SIT applications. Here, we compared mating compatibility among Ae. albopictus populations originating from three islands of the South Western Indian Ocean, and assessed both insemination rates and egg fertility in all possible cross-mating combinations. Furthermore, competitiveness between irradiated and non-irradiated males from the three studied strains, and the subsequent effect on female fertility were also examined. Although morphometric analysis of wing shapes suggested phenoptypic differences between Ae. albopictus strains, perfect reproductive compatibility between them was observed. Furthermore, irradiated males from the different islands demonstrated similar levels of competitiveness and induced sterility when confronted with fertile males from any of the other island populations tested. In conclusion, despite the evidence of inter-strain differences based on male wing morphology, collectively, our results provide a new set of expectations for the use of a single candidate strain of mass-reared sterile males for area-wide scale application of SIT against Ae. albopictus populations in different islands across the South Western Indian Ocean. Cross-mating competitiveness tests such as those applied here are necessary to assess the quality of mass reared strains for the trans-border application of sterile male release programs.
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Affiliation(s)
- David Damiens
- Institut de Recherche pour le Développement (IRD), Unité Mixte de Recherche MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion - Plateforme de Recherche CYROI, Sainte-Clotilde, Reunion Island, France
| | - Cyrille Lebon
- IRD La Réunion - Plateforme de Recherche CYROI, Sainte-Clotilde, Reunion Island, France
| | - David A. Wilkinson
- Université de La Réunion, Unité Mixte de Recherche « Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT) », INSERM U1187-CNRS9192-IRD249. Plateforme de Recherche CYROI. Ste Clotilde, Saint-Denis, La Réunion, France
| | - Damien Dijoux-Millet
- Université de La Réunion, Institut Universitaire de Technologie, Département Génie Biologique, Saint Pierre, La Réunion, France
| | - Gilbert Le Goff
- Institut de Recherche pour le Développement (IRD), Unité Mixte de Recherche MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion - Plateforme de Recherche CYROI, Sainte-Clotilde, Reunion Island, France
| | - Ambicadutt Bheecarry
- Vector Biology and Control Division, Ministry of Health and Quality of Life, SSR Botanical Garden Rd, Curepipe, Mauritius
| | - Louis Clément Gouagna
- Institut de Recherche pour le Développement (IRD), Unité Mixte de Recherche MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
- IRD La Réunion - Plateforme de Recherche CYROI, Sainte-Clotilde, Reunion Island, France
- * E-mail:
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Séré M, Wilkinson DA, Schleyer MH, Chabanet P, Quod JP, Tortosa P. Characterisation of an atypical manifestation of black band disease on Porites lutea in the Western Indian Ocean. PeerJ 2016; 4:e2073. [PMID: 27441106 PMCID: PMC4941741 DOI: 10.7717/peerj.2073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 01/28/2016] [Accepted: 05/03/2016] [Indexed: 11/20/2022] Open
Abstract
Recent surveys conducted on Reunion Island coral reefs revealed an atypical manifestation of black band disease on the main framework building coral, Porites lutea. This BBD manifestation (PorBBD) presented a thick lighter-colored band, which preceded the typical BBD lesion. Whilst BBD aetiology has been intensively described worldwide, it remains unclear if corals with apparently similar lesions across coral reefs are affected by the same pathogens. Therefore, a multidisciplinary approach involving field surveys, gross lesion monitoring, histopathology and 454-pyrosequencing was employed to provide the first comprehensive characterization of this particular manifestation. Surveys conducted within two geomorphological zones over two consecutive summers and winters showed spatial and seasonal patterns consistent with those found for typical BBD. Genetic analyses suggested an uncharacteristically high level of Vibrio spp. bacterial infection within PorBBD. However, microscopic analysis revealed high densities of cyanobacteria, penetrating the compromised tissue as well as the presence of basophilic bodies resembling bacterial aggregates in the living tissue, adjacent to the bacterial mat. Additionally, classical BBD-associated cyanobacterial strains, genetically related to Pseudoscillatoria coralii and Roseofilum reptotaenium were identified and isolated and the presence of sulfate-reducers or sulfide-oxidizers such as Desulfovibrio and Arcobacter, previously shown to be associated with anoxic microenvironment within typical BBD was also observed, confirming that PorBBD is a manifestation of classical BBD.
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Affiliation(s)
- Mathieu Séré
- Agence pour la Recherche et la VAlorisation Marines (ARVAM), Saint-Denis, Réunion, France; Oceanographic Research Institute (ORI), Durban, KwaZulu-Natal, South Africa; UMR ENTROPIE, Labex CORAIL, Research Institute for the Development (IRD), Saint-Denis, Réunion, France
| | - David A Wilkinson
- Unité Mixte de Recherche "Processus Infectieux en Milieu Insulaire Tropical" (UMR PIMIT), Université de La Réunion, Inserm1187, CNRS9192, IRD249, Plateforme de Recherche CYROI , Saint Denis , Réunion , France
| | - Michael H Schleyer
- Oceanographic Research Institute (ORI) , Durban , KwaZulu-Natal , South Africa
| | - Pascale Chabanet
- UMR ENTROPIE, Labex CORAIL, Research Institute for the Development (IRD) , Saint-Denis , Réunion , France
| | - Jean-Pascal Quod
- Agence pour la Recherche et la VAlorisation Marines (ARVAM) , Saint-Denis , Réunion , France
| | - Pablo Tortosa
- Unité Mixte de Recherche "Processus Infectieux en Milieu Insulaire Tropical" (UMR PIMIT), Université de La Réunion, Inserm1187, CNRS9192, IRD249, Plateforme de Recherche CYROI , Saint Denis , Réunion , France
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McCoy KD, Dietrich M, Jaeger A, Wilkinson DA, Bastien M, Lagadec E, Boulinier T, Pascalis H, Tortosa P, Le Corre M, Dellagi K, Lebarbenchon C. The role of seabirds of the Iles Eparses as reservoirs and disseminators of parasites and pathogens. Acta Oecol (Montrouge) 2016; 72:98-109. [PMID: 32288503 PMCID: PMC7128210 DOI: 10.1016/j.actao.2015.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/30/2022]
Abstract
The role of birds as reservoirs and disseminators of parasites and pathogens has received much attention over the past several years due to their high vagility. Seabirds are particularly interesting hosts in this respect. In addition to incredible long-distance movements during migration, foraging and prospecting, these birds are long-lived, site faithful and breed in dense aggregations in specific colony locations. These different characteristics can favor both the local maintenance and large-scale dissemination of parasites and pathogens. The Iles Eparses provide breeding and feeding grounds for more than 3 million breeding pairs of seabirds including at least 13 species. Breeding colonies on these islands are relatively undisturbed by human activities and represent natural metapopulations in which seabird population dynamics, movement and dispersal can be studied in relation to that of circulating parasites and pathogens. In this review, we summarize previous knowledge and recently-acquired data on the parasites and pathogens found in association with seabirds of the Iles Eparses. These studies have revealed the presence of a rich diversity of infectious agents (viruses, bacteria and parasites) carried by the birds and/or their local ectoparasites (ticks and louse flies). Many of these agents are widespread and found in other ecosystems confirming a role for seabirds in their large scale dissemination and maintenance. The heterogeneous distribution of parasites and infectious agents among islands and seabird species suggests that relatively independent metacommunities of interacting species may exist within the western Indian Ocean. In this context, we discuss how the patterns and determinants of seabird movements may alter parasite and pathogen circulation. We conclude by outlining key aspects for future research given the baseline data now available and current concerns in eco-epidemiology and biodiversity conservation.
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Affiliation(s)
- Karen D. McCoy
- MIVEGEC (Maladies Infectieuses et Vecteurs: Evolution, Génétique, Ecologie, Contrôle) UMR 5290 CNRS-IRD-Université de Montpellier, Centre IRD, 34393 Montpellier, France
| | - Muriel Dietrich
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
| | - Audrey Jaeger
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR ENTROPIE, Université de la Réunion-IRD-CNRS, CS92003, 97744 Saint Denis, Reunion Island, France
| | - David A. Wilkinson
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Matthieu Bastien
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Erwan Lagadec
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Thierry Boulinier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-Université de Montpellier UMR 5175, 34293 Montpellier, France
| | - Hervé Pascalis
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Pablo Tortosa
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Matthieu Le Corre
- UMR ENTROPIE, Université de la Réunion-IRD-CNRS, CS92003, 97744 Saint Denis, Reunion Island, France
| | - Koussay Dellagi
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
| | - Camille Lebarbenchon
- CRVOI (Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien), 97490 Sainte Clotilde, Reunion Island, France
- UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, 97490 Sainte Clotilde, Reunion Island, France
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Razanajatovo NH, Nomenjanahary LA, Wilkinson DA, Razafimanahaka JH, Goodman SM, Jenkins RK, Jones JPG, Heraud JM. Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar. Virol J 2015; 12:42. [PMID: 25888853 PMCID: PMC4404003 DOI: 10.1186/s12985-015-0271-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 09/04/2014] [Accepted: 02/24/2015] [Indexed: 04/21/2023] Open
Abstract
Background Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island’s chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. Methods Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. Results From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. Conclusions Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.
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Affiliation(s)
- Norosoa H Razanajatovo
- Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only.
| | - Lalaina A Nomenjanahary
- Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only.
| | - David A Wilkinson
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l'Ocean Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Riviere, 97490, Sainte Clotilde, La Reunion, France.
| | - Julie H Razafimanahaka
- Madagasikara Voakajy, BP 5181, Antananarivo, Madagascar. .,Department of Animal Biology, Faculty of Sciences, University of Antananarivo, BP 906, Antananarivo, Madagascar.
| | | | - Richard K Jenkins
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom.
| | - Julia P G Jones
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom.
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only.
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Dietrich M, Wilkinson DA, Benlali A, Lagadec E, Ramasindrazana B, Dellagi K, Tortosa P. Leptospira and paramyxovirus infection dynamics in a bat maternity enlightens pathogen maintenance in wildlife. Environ Microbiol 2015; 17:4280-9. [PMID: 25580582 DOI: 10.1111/1462-2920.12766] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/26/2023]
Abstract
Bats are reservoirs for several zoonotic pathogens of medical importance; however, infection dynamics of pathogens in wild bat populations remain poorly understood. Here, we examine the influence of host crowding and population age structure on pathogen transmission and diversity in bat populations. Focusing on two pathogen taxa of medical importance, Leptospira bacteria and paramyxoviruses, we monitored host population and pathogen shedding dynamics within a maternity colony of the tropical bat species Mormopterus francoismoutoui, endemic to Réunion Island. Our data reveal astonishingly similar infection dynamics for Leptospira and paramyxoviruses, with infection peaks during late pregnancy and 2 months after the initial birth pulse. Furthermore, although co-infection occurs frequently during the peaks of transmission, the patterns do not suggest any interaction between the two pathogens. Partial sequencing reveals a unique bat-specific Leptospira strain contrasting with the co-circulation of four separate paramyxovirus lineages along the whole breeding period. Patterns of infection highlight the importance of host crowding in pathogen transmission and suggest that most bats developed immune response and stop excreting pathogens. Our results support that bat maternity colonies may represent hot spots of transmission for bacterial and viral infectious agents, and highlight how seasonality can be an important determinant of host-parasite interactions and disease emergence.
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Affiliation(s)
- Muriel Dietrich
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Université de La Réunion, France
| | - David A Wilkinson
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Université de La Réunion, France
| | - Aude Benlali
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Université de La Réunion, France
| | - Erwan Lagadec
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Institut de Recherche pour le Développement, Sainte Clotilde, France
| | - Beza Ramasindrazana
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Institut de Recherche pour le Développement, Sainte Clotilde, France
| | - Koussay Dellagi
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Institut de Recherche pour le Développement, Sainte Clotilde, France
| | - Pablo Tortosa
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien, France.,Université de La Réunion, France.,Joint Chair Centre National de la Recherche Scientifique-Université de La Réunion, Sainte Clotilde, France
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Wilkinson DA, Lebon C, Wood T, Rosser G, Gouagna LC. Straightforward multi-object video tracking for quantification of mosquito flight activity. J Insect Physiol 2014; 71:114-121. [PMID: 25450566 DOI: 10.1016/j.jinsphys.2014.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/07/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
Mosquito flight activity has been studied using a variety of different methodologies, and largely concentrates on female mosquito activity as vectors of disease. Video recording using standard commercially available hardware has limited accuracy for the measurement of flight activity due to the lack of depth-perception in two-dimensional images, but multi-camera observation for three dimensional trajectory reconstructions remain challenging and inaccessible to the majority of researchers. Here, in silico simulations were used to quantify the limitations of two-dimensional flight observation. We observed that, under the simulated conditions, two dimensional observation of flight was more than 90% accurate for the determination of population flight speeds and thus that two dimensional imaging can be used to provide accurate estimates of mosquito population flight speeds, and to measure flight activity over long periods of time. We optimized single camera video imaging to study male Aedes albopictus mosquitoes over a 30 h time period, and tested two different multi-object tracking algorithms for their efficiency in flight tracking. A. Albopictus males were observed to be most active at the start of the day period (06h00-08h00) with the longest period of activity in the evening (15h00-18h00) and that a single mosquito will fly more than 600 m over the course of 24 h. No activity was observed during the night period (18h00-06h00). Simplistic tracking methodologies, executable on standard computational hardware, are sufficient to produce reliable data when video imaging is optimized under laboratory conditions. As this methodology does not require overly-expensive equipment, complex calibration of equipment or extensive knowledge of computer programming, the technology should be accessible to the majority of computer-literate researchers.
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Affiliation(s)
- David A Wilkinson
- Centre de Recherche et de Veille sur les maladies Emergentes dans l'Océan Indien (CRVOI), 97490 Sainte-Clotilde, La Réunion, France.
| | - Cyrille Lebon
- Centre de Recherche et de Veille sur les maladies Emergentes dans l'Océan Indien (CRVOI), 97490 Sainte-Clotilde, La Réunion, France.
| | - Trevor Wood
- Oxford Centre for Industrial Applied Mathematics, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.
| | - Gabriel Rosser
- UCL Civil, Environmental & Geomatic Engineering, University College London, Chadwick Building, Gower Street, London, WC1E 6BT, UK.
| | - Louis Clément Gouagna
- Centre de Recherche et de Veille sur les maladies Emergentes dans l'Océan Indien (CRVOI), 97490 Sainte-Clotilde, La Réunion, France; Institut de Recherche pour le Développement (IRD), UM1-CNRS 5290-IRD 224: Maladies Infectieuses et Vecteurs - Ecologie-Génétique, Evolution et Contrôle (MIVEGEC), Montpellier, France.
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40
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Wilkinson DA, Dietrich M, Lebarbenchon C, Jaeger A, Le Rouzic C, Bastien M, Lagadec E, McCoy KD, Pascalis H, Le Corre M, Dellagi K, Tortosa P. Massive infection of seabird ticks with bacterial species related to Coxiella burnetii. Appl Environ Microbiol 2014; 80:3327-33. [PMID: 24657860 PMCID: PMC4018846 DOI: 10.1128/aem.00477-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 02/11/2014] [Accepted: 03/12/2014] [Indexed: 11/20/2022] Open
Abstract
Seabird ticks are known reservoirs of bacterial pathogens of medical importance; however, ticks parasitizing tropical seabirds have received less attention than their counterparts from temperate and subpolar regions. Recently, Rickettsia africae was described to infect seabird ticks of the western Indian Ocean and New Caledonia, constituting the only available data on bacterial pathogens associated with tropical seabird tick species. Here, we combined a pyrosequencing-based approach with a classical molecular analysis targeting bacteria of potential medical importance in order to describe the bacterial community in two tropical seabird ticks, Amblyomma loculosum and Carios (Ornithodoros) capensis. We also investigated the patterns of prevalence and host specificity within the biogeographical context of the western Indian Ocean islands. The bacterial community of the two tick species was characterized by a strong dominance of Coxiella and Rickettsia. Our data support a strict Coxiella-host tick specificity, a pattern resembling the one found for Rickettsia spp. in the same two seabird tick species. Both the high prevalence and stringent host tick specificity suggest that these bacteria may be tick symbionts with probable vertical transmission. Detailed studies of the pathogenicity of these bacteria will now be required to determine whether horizontal transmission can occur and to clarify their status as potential human pathogens. More generally, our results show that the combination of next generation sequencing with targeted detection/genotyping approaches proves to be efficient in poorly investigated fields where research can be considered to be starting from scratch.
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Affiliation(s)
- David A. Wilkinson
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Muriel Dietrich
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Audrey Jaeger
- Laboratoire ECOMAR, FRE3560 INEE-CNRS, Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Céline Le Rouzic
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Laboratoire ECOMAR, FRE3560 INEE-CNRS, Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Matthieu Bastien
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Laboratoire ECOMAR, FRE3560 INEE-CNRS, Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Erwan Lagadec
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Institut de Recherche pour le Développement, Ste Clotilde, La Réunion, France
| | - Karen D. McCoy
- Unité Mixte de Recherche 5290 CNRS IRD UM1 UM2, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Montpellier, France
| | - Hervé Pascalis
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Institut de Recherche pour le Développement, Ste Clotilde, La Réunion, France
| | - Matthieu Le Corre
- Laboratoire ECOMAR, FRE3560 INEE-CNRS, Université de La Réunion, Ste Clotilde, La Réunion, France
| | - Koussay Dellagi
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Institut de Recherche pour le Développement, Ste Clotilde, La Réunion, France
| | - Pablo Tortosa
- Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), GIP CYROI, Ste Clotilde, La Réunion, France
- Université de La Réunion, Ste Clotilde, La Réunion, France
- Institut Écologie et Environnement, CNRS, Paris, France
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Dietrich M, Wilkinson DA, Soarimalala V, Goodman SM, Dellagi K, Tortosa P. Diversification of an emerging pathogen in a biodiversity hotspot: Leptospira in endemic small mammals of Madagascar. Mol Ecol 2014; 23:2783-96. [PMID: 24784171 DOI: 10.1111/mec.12777] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [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: 02/26/2014] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/14/2023]
Abstract
Biodiversity hotspots and associated endemism are ideal systems for the study of parasite diversity within host communities. Here, we investigated the ecological and evolutionary forces acting on the diversification of an emerging bacterial pathogen, Leptospira spp., in communities of endemic Malagasy small mammals. We determined the infection rate with pathogenic Leptospira in 20 species of sympatric rodents (subfamily Nesomyinae) and tenrecids (family Tenrecidae) at two eastern humid forest localities. A multilocus genotyping analysis allowed the characterization of bacterial diversity within small mammals and gave insights into their genetic relationships with Leptospira infecting endemic Malagasy bats (family Miniopteridae and Vespertilionidae). We report for the first time the presence of pathogenic Leptospira in Malagasy endemic small mammals, with an overall prevalence of 13%. In addition, these hosts harbour species of Leptospira (L. kirschneri, L. borgpetersenii and L. borgpetersenii group B) which are different from those reported in introduced rats (L. interrogans) on Madagascar. The diversification of Leptospira on Madagascar can be traced millions of years into evolutionary history, resulting in the divergence of endemic lineages and strong host specificity. These observations are discussed in relation to the relative roles of endemic vs. introduced mammal species in the evolution and epidemiology of Leptospira on Madagascar, specifically how biodiversity and biogeographical processes can shape community ecology of an emerging pathogen and lead to its diversification within native animal communities.
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Affiliation(s)
- Muriel Dietrich
- Centre de Recherche et de Veille sur les maladies émergentes dans l'Océan Indien (CRVOI), 97490, Sainte Clotilde, Réunion, France; Université de La Réunion, 97400, Saint Denis, Réunion, France
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Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, de Lamballerie X, Dellagi K. Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. PLoS One 2012; 7:e43742. [PMID: 22952752 PMCID: PMC3428279 DOI: 10.1371/journal.pone.0043742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/23/2012] [Indexed: 01/08/2023] Open
Abstract
Background/Objectives Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. Methodology We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. Principal Findings We found that i) Reunion pH1N1 sequences stemmed from global “clade 7” but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. Conclusions Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.
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Affiliation(s)
- Hervé Pascalis
- GIS CRVOI, Centre de Recherche et de Veille sur maladies émergentes dans l'Océan Indien, Plateforme technologique CYROI, Saint-Denis, La Réunion, France.
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Scott KA, Porter SL, Bagg EAL, Hamer R, Hill JL, Wilkinson DA, Armitage JP. Specificity of localization and phosphotransfer in the CheA proteins of Rhodobacter sphaeroides. Mol Microbiol 2010; 76:318-30. [PMID: 20525091 DOI: 10.1111/j.1365-2958.2010.07095.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Specificity of protein-protein interactions plays a vital role in signal transduction. The chemosensory pathway of Rhodobacter sphaeroides comprises multiple homologues of chemotaxis proteins characterized in organisms such as Escherichia coli. Three CheA homologues are essential for chemotaxis in R. sphaeroides under laboratory conditions. These CheAs are differentially localized to two chemosensory clusters, one at the cell pole and one in the cytoplasm. The polar CheA, CheA(2), has the same domain structure as E. coli CheA and can phosphorylate all R. sphaeroides chemotaxis response regulators. CheA(3) and CheA(4) independently localize to the cytoplasmic cluster; each protein has a subset of the CheA domains, with CheA(3) phosphorylating CheA(4) together making a functional CheA protein. Interestingly, CheA(3)-P can only phosphorylate two response regulators, CheY(6) and CheB(2). R. sphaeroides CheAs exhibit two interesting differences in specificity: (i) the response regulators that they phosphorylate and (ii) the chemosensory cluster to which they localize. Using a domain-swapping approach we investigated the role of the P1 and P5 CheA domains in determining these specificities. We show that the P1 domain is sufficient to determine which response regulators will be phosphorylated in vitro while the P5 domain is sufficient to localize the CheAs to a specific chemosensory cluster.
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Affiliation(s)
- Kathryn A Scott
- Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
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Abstract
Chronic alcoholics who maintain abstinence often demonstrate remarkable improvement of neurological and mental dysfunction. This paper presents an overview of the clinical and laboratory work of our group. Reversible clinical manifestations include psychometric scores, ataxia, tremor, Parkinsonism, dyskinesia, cerebral atrophy, EEG parameters, and a CSF acidosis. Electrophysiological investigations showed that in the in vitro hippocampus of rats fed ethanol for several months there was evidence for diminished long-term potentiation, impaired neuronal inhibitory mechanisms (diminished inhibitory post-synaptic potentials and post-spike after hyperpolarisations), decreased neuronal specific membrane capacitance and increased specific membrane resistance. Golgi stains showed attenuation of hippocampal CA1 neuronal dendrites in rats fed ethanol for five months, which reverted to control size in rats permitted two months of alcohol withdrawal.
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Affiliation(s)
- P L Carlen
- Neurology Program, Addiction Research Foundation, Toronto, Ontario
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Wilkinson DA, Kolar M, Fleming PA, Singh AD. Dosimetric comparison of 106Ru and 125I plaques for treatment of shallow (<or=5 mm) choroidal melanoma lesions. Br J Radiol 2008; 81:784-9. [PMID: 18628320 DOI: 10.1259/bjr/76813976] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The aim of this study was to compare dosimetric parameters between iodine-125 ((125)I) and ruthenium-106 ((106)Ru) plaques of similar sizes in the treatment of choroidal melanomas. The study design included retrospective double planning of each case. 26 consecutive patients with choroidal melanomas measuring 5 mm or less in thickness were included. Dose distributions were calculated using Plaque Simulator treatment-planning software for a prescription of 85 Gy to the tumour apex. Doses to the outer sclera, lens, fovea and optic disc were obtained for each case using appropriately sized plaques of each isotope. Statistical inferences were made using the non-parametric Wilcoxon signed rank test. The mean dose to the macula, disc and lens was 18%, 53% and 89% less, respectively, with (106)Ru than with (125)I. Scleral doses were greater for (106)Ru. The use of collaborative ocular melanoma study dosimetry results in even higher mean doses to the macula, disc, lens and sclera. Two-dimensional dose distributions and dose volume histograms demonstrated the increase in dose outside the tumour volume using (125)I. This comparison shows that, for tumours not exceeding 5 mm in thickness, the use of (106)Ru plaques has the potential to reduce the radiation dose to nearby normal structures and possibly lower the risk of radiation-induced visual loss.
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Affiliation(s)
- D A Wilkinson
- Department of Radiation Oncology, Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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Wilkinson DA, Popham PA. Seizures and the pituitary gland during pregnancy. Anaesth Intensive Care 2005; 32:835-7. [PMID: 15648999 DOI: 10.1177/0310057x0403200620] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We present the anaesthetic management of a woman who, at 10 days post partum, suffered a series of convulsions in the context of two episodes of post partum haemorrhage. The probable aetiology of the convulsions is discussed.
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Affiliation(s)
- D A Wilkinson
- Department of Anaesthesia, Royal Women's Hospital, Melbourne, Victoria
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Wilkinson DA, Popham P, Morgan D. Pacemaker interference from cardiac monitors revisited. Anaesth Intensive Care 2004; 32:842-3. [PMID: 15649001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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Kushner DM, Fleming PA, Kennedy AW, Wilkinson DA, Lee E, Saffle PA. High dose rate192Ir afterloading brachytherapy for cancer of the vagina. Br J Radiol 2003; 76:719-25. [PMID: 14512332 DOI: 10.1259/bjr/15634046] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [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: 01/03/2023] Open
Abstract
We report results of brachytherapy for carcinoma of the vagina, utilizing a Nucletron high dose rate system for Delclos Vaginal Applicators (cylinder) and Syed Template Applicators (interstitial). The linear quadratic (LQ) model was used to determine the optimum time-dose-fractionation schedules. Interstitial doses were determined at the isodose line that included gross tumour. Cylinder doses were determined either at the vaginal surface (5 cases), at 0.5 cm depth (5 cases), or at 1.0 cm depth (1 case). For the first treatment (n=19), interstitial templates were utilized in 8 patients and vaginal cylinders in 11. 11 patients received second treatments: 6 templates and 5 cylinders. The median dose of external beam radiation (n=15) was 40.0 Gy followed, after a median 23 day interval, by high dose rate brachytherapy (HDRB) of 4 fractions in 30-42 h; then a median interval gap of 25 days, followed by repeat HDRB. The median total fractionated HDRB dose per patient was 23.0 Gy (range: 6.9 Gy to 40.4 Gy; calculated low dose rate equivalent of 29.8 Gy). Tumour histologies included 14 squamous cell carcinomas, 2 adenocarcinomas, 2 melanomas, and 1 small cell tumour. Three patients experienced early brachytherapy-related complications (diarrhoea, dysuria and labial dermatitis). Three patients (15.8%) developed serious/late complications including ureteral stenosis, painful vaginal necrosis and small bowel obstruction. The first of these patients received 2 templates, the second a cylinder followed by a template and a cylinder, and the third a single cylinder. The 2 year progression-free survival was 39.3% (median 15.7 months), while the 2 year overall survival was 66.1% (median 29.9 months). (192)Ir afterloading HDRB is a feasible approach to women with vaginal cancer with acceptable toxicity and tumour response. Potential advantages include patient preference, outpatient cost-effectiveness in the case of cylinder technique, and no radiation exposure to hospital personnel. Long-term follow-up is needed to further assess late complications, and larger studies are needed to confirm our results.
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Affiliation(s)
- D M Kushner
- Department of Obstertrics and Gynecology, University of Wisconsin Hospital and Clinics, H4/636 CSC, 600 Highland Avenue, Madison, WI 53792-3236, USA
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Wilkinson DA, Lee EJ, Ciezki JP, Mohan DS, Zippe C, Angermeier K, Ulchaker J, Klein EA, Mohan D. Dosimetric comparison of pre-planned and or-planned prostate seed brachytherapy. Int J Radiat Oncol Biol Phys 2000; 48:1241-4. [PMID: 11072184 DOI: 10.1016/s0360-3016(00)00734-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PURPOSE To compare the dosimetry of the traditional two step procedure (volume study + treatment planning several weeks later) with that of an OR-based single procedure in which these two steps follow one another immediately. Computer generated treatment plans were used in both procedures. METHODS AND MATERIALS Several dosimetric parameters relating to target coverage were obtained from dose volume histograms of CT-based evaluation plans developed either 1 or 3 days following seed implantation. A total of 113 patients with early stage (T1C, T2A) prostate cancer were used for this retrospective study. RESULTS The fraction of target (prostate) covered by the prescription dose (144 Gy), 90% of the prescription dose (115 Gy), and the dose encompassing 90% of the target in the evaluation plan were all statistically significantly improved for OR-based plans compared to pre-planned cases. CONCLUSION In our hands, there is a small but significant improvement in dose coverage of the prostate when the ultrasound volume study and treatment planning are combined into a single procedure.
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Affiliation(s)
- D A Wilkinson
- Department of Radiation Oncology, The Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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Wilkinson DA, Scicutella CJ, Wu A, Kalnicki S. Conformal prostate treatment planning using a low-energy (6-MV) beam. Med Dosim 2000; 25:37-40. [PMID: 10751718 DOI: 10.1016/s0958-3947(99)00040-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A 4-field noncoplanar technique for treatment of prostate cancer developed at the University of Michigan was modified for use with low-energy (6 MV) beams. These modifications include the use of wedges on the 2 anterior inferior-superior oblique fields and adjusting the weights of the oblique and lateral fields appropriately. A margin of 1.5 cm around the physician-defined target region was used to define the blocks on each beam's-eye view. Dose distributions produced using this technique with 6-MV and 24-MV beams were compared visually on several dose planes (transverse and sagittal) and quantitatively by dose volume histograms (target, rectum, and bladder). These comparisons showed insignificant differences between the high-energy and low-energy treatment plans. Much larger differences were observed in comparisons of 2 types of coplanar plans with the noncoplanar setup for the 6-MV photon machine. Rectal doses measured in situ were used to help validate the dose distribution predicted by the treatment planning system for the 6-MV noncoplanar technique.
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Affiliation(s)
- D A Wilkinson
- Department of Radiation Oncology, Cleveland Clinic Foundation, OH 44195, USA
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