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Dao TL, Hoang VT, Ly TDA, Magmoun A, Canard N, Drali T, Fenollar F, Ninove L, Raoult D, Parola P, Courjon J, Gautret P. Infectious disease symptoms and microbial carriage among French medical students travelling abroad: A prospective study. Travel Med Infect Dis 2019; 34:101548. [PMID: 31870880 PMCID: PMC7102604 DOI: 10.1016/j.tmaid.2019.101548] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022]
Abstract
Background In France, no previous studies have focused specifically on health problems among medical students during internships abroad including the clinical symptoms suggestive of infectious diseases and the acquisition of pathogen carriage. Methods Clinical follow up and qPCR based respiratory, gastrointestinal and vaginal pathogen carriage before and after travel were prospectively assessed in a cohort of medical students departing from Marseille, France. Results 134 students were included. 73.9%, 38.8% and 5.0% of students reported gastrointestinal, respiratory and vaginal symptoms, respectively. The acquisition rate of Enteroaggregative Escherichia coli (EAEC) and Enteropathogenic E. coli (EPEC) was 53% and 41%, respectively. The acquisition of respiratory viruses was low but associated with persisting symptoms, while bacterial acquisition ranged from 3.3% for Streptococcus pyogenes to 15.0% for Haemophilus influenzae. Gardnerella vaginalis and Atopobium vaginae acquisition rates were 7.7% and 14.3% respectively. Five students (5.1%) had molecular quantification criteria for bacterial vaginosis on return. Conclusion This preliminary study demonstrates that besides the known risk of gastrointestinal and respiratory infections and associated changes in intestinal and respiratory microbiota, medical students abroad may also experience changes in vaginal microbiota leading, in some cases, to clinical symptoms or the acquisition of bacterial vaginosis, which may be asymptomatic.
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Affiliation(s)
- Thi Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Van Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Amal Magmoun
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Naomie Canard
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Tassadit Drali
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Laetitia Ninove
- IHU-Méditerranée Infection, Marseille, France; Unité des Virus Émergents (UVE: Aix - Marseille Univ - IRD 190 - Inserm 1207), Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Johan Courjon
- Infectiologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; Université Côte d'Azur, Nice, France; U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Virulence Microbienne et Signalisation Inflammatoire, INSERM, Nice, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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Hoang VT, Dao TL, Ly TDA, Belhouchat K, Chaht KL, Gaudart J, Mrenda BM, Drali T, Yezli S, Alotaibi B, Fournier PE, Raoult D, Parola P, de Santi VP, Gautret P. The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj. Emerg Microbes Infect 2019; 8:1701-1710. [PMID: 31749410 PMCID: PMC6882464 DOI: 10.1080/22221751.2019.1693247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. Each participant underwent four successive systematic nasopharyngeal swabs before and during their stay in Saudi Arabia. Carriage of the main respiratory pathogens was assessed by PCR. 121 pilgrims were included and 93.4% reported respiratory symptoms during the study period. The acquisition of rhinovirus, coronaviruses and Staphylococcus aureus occurred soon after arrival in Saudi Arabia and rates decreased gradually after days 5 and 6. In contrast, Streptococcus pneumoniae and Klebsiella pneumoniae carriage increased progressively until the end of the stay in Saudi Arabia. Haemophilus influenzae and Moraxella catarrhalis carriage increased starting around days 12 and 13, following an initial clearance. Influenza viruses were rarely isolated. We observed an independent positive mutual association between S. aureus and rhinovirus carriage and between H. influenzae and M. catarrhalis carriage. Dual carriage of H. influenzae and M. catarrhalis was strongly associated with S. pneumoniae carriage (OR = 6.22). Finally, our model showed that M. catarrhalis carriage was negatively associated with K. pneumoniae carriage. Chronic respiratory disease was associated with symptoms of LRTI. K. pneumoniae, M. catarrhalis-S. aureus and H. influenzae-rhinovirus dual carriage was associated with LRTI symptoms. Our data suggest that RTIs at the Hajj are a result of complex interactions between a number of respiratory viruses and bacteria.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Thi-Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Khadidja Belhouchat
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Kamel Larbi Chaht
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean Gaudart
- Aix Marseille Univ, INSERM, IRD, SESSTIM UMR1252, Faculty of Medicine Marseille, France.,APHM, La Timone Hospital, Biostatistics & ICT Marseille, France
| | | | - Tassadit Drali
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Badriah Alotaibi
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Vincent Pommier de Santi
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,French Military Centre for Epidemiology and Public Health, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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53
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Respiratory tract infections among French Hajj pilgrims from 2014 to 2017. Sci Rep 2019; 9:17771. [PMID: 31780750 PMCID: PMC6883043 DOI: 10.1038/s41598-019-54370-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/11/2019] [Indexed: 01/03/2023] Open
Abstract
Respiratory tract infections (RTIs) are common among Hajj pilgrims, but risk factors for RTIs and respiratory pathogen acquisition during the Hajj are not clearly identified. Based on previous studies, most frequent pathogens acquired by Hajj pilgrims were investigated: rhinovirus, human coronaviruses, influenza viruses, Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Haemophilus influenzae. 485 pilgrims were included. 82.1% presented with RTIs. Respiratory chronic diseases were associated with cough, Influenza-like illness (ILI) and the acquisition of H. influenzae. Vaccination against invasive pneumococcal diseases (IPD) and influenza was associated with a decrease in the acquisition of S. pneumoniae and prevalence of ILI (aRR = 0.53, 95%CI [0.39-0.73] and aRR = 0.69, 95%CI [0.52-0.92] respectively). Individuals carrying rhinovirus and H. influenzae-S. pneumoniae together were respectively twice and five times more likely to have respiratory symptoms. Individual with H. influenzae-K. pneumoniae carriage were twice (p = 0.04) as likely to develop a cough. The use of disposable handkerchiefs was associated with a decrease in the acquisition of S. aureus (aRR = 0.75, 95%CI [0.57-0.97]). Results could be used to identify pilgrims at increased risk of RTIs and acquisition of respiratory pathogens. Results also confirm the effectiveness of influenza and IPD vaccinations in reducing ILI symptoms and acquisition of S. pneumoniae carriage respectively.
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54
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Environmental investigation of respiratory pathogens during the Hajj 2016 and 2018. Travel Med Infect Dis 2019; 33:101500. [PMID: 31600567 PMCID: PMC7110696 DOI: 10.1016/j.tmaid.2019.101500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Respiratory tract infections are common in the context of the Hajj pilgrimage and respiratory pathogens can be transmitted via contact with contaminated surfaces. We sampled surfaces during the Hajj to detect the presence of respiratory bacteria and viruses. METHODS Frequently touched surfaces at Mecca, Mina, Arafat and Medina were sampled. The common respiratory pathogens were tested by qPCR. RESULTS 70/142 (49.3%) environmental samples collected were positive for at least one respiratory pathogen. Among the positive samples, Klebsiella pneumoniae was the bacterium most frequently tested positive (57.1%), followed by Streptococcus pneumoniae (12.9%), Staphylococcus aureus (10.0%) and Haemophilus influenzae (7.1%). 32.9% positive samples tested positive for rhinovirus and 1.4% for coronavirus. Surfaces with the highest rates of positive samples were kitchen tables (100%), water fountain faucet (73.3%) and edge of water coolers lid (84.6%). Samples collected in Mina were the most frequently contaminated with 68.8% being positive for at least one pathogen and 18.8% positive for a combination of multiple pathogens. CONCLUSION These preliminary results indicate that respiratory pathogens are common in environmental surfaces from areas frequented by Hajj pilgrims. Further larger-scale studies are needed to better assess the possible role of environmental respiratory pathogens in respiratory infections in Hajj pilgrims.
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55
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Capai L, Maestrini O, Casabianca F, Villechenaud N, Masse S, Bosseur F, Lamballerie X, Charrel RN, Falchi A. Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France. Transbound Emerg Dis 2019; 66:2462-2473. [DOI: 10.1111/tbed.13304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/08/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Lisandru Capai
- EA 7310, Laboratoire de Virologie Université de Corse Corte France
| | - Oscar Maestrini
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE) Institut National de la Recherche Agronomique (INRA) Corte France
| | - François Casabianca
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE) Institut National de la Recherche Agronomique (INRA) Corte France
| | | | - Shirley Masse
- EA 7310, Laboratoire de Virologie Université de Corse Corte France
| | - Frédéric Bosseur
- Sciences Pour l’Environnement – UMR CNRS 6134 niversité de Corse Corte France
| | - Xavier Lamballerie
- IRD 190, INSERM 1207 IHU Méditerranée Infection, Unité des Virus Émergents (UVE): Aix Marseille Univ Marseille France
| | - Rémi N. Charrel
- IRD 190, INSERM 1207 IHU Méditerranée Infection, Unité des Virus Émergents (UVE): Aix Marseille Univ Marseille France
- Emerging Pathogens Institute University of Florida Gainesville Florida
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56
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Nguyen VH, Russell FM, Dance DA, Vilivong K, Phommachan S, Syladeth C, Lai J, Lim R, Morpeth M, Mayxay M, Newton PN, De Lamballerie X, Dubot-Pérès A. Nasal or throat sampling is adequate for the detection of the human respiratory syncytial virus in children with acute respiratory infections. J Med Virol 2019; 91:1602-1607. [PMID: 31050005 PMCID: PMC6772119 DOI: 10.1002/jmv.25496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 11/30/2022]
Abstract
Human respiratory syncytial virus (HRSV) is one of the most important causes of acute respiratory infections (ARI) in young children. HRSV diagnosis is based on the detection of the virus in respiratory specimens. Nasopharyngeal swabbing is considered the preferred method of sampling, although there is limited evidence of the superiority of nasopharyngeal swabs (NPS) over the less invasive nasal (NS) and throat (TS) swabs for virus detection by real‐time reverse transcription quantitative polymerase chain reaction (RT‐qPCR). In the current study, we compared the three swabbing methods for the detection of HRSV by RT‐qPCR in children hospitalized with ARI at Mahosot Hospital, Vientiane, Laos. In 2014, NS, NPS, and TS were collected from 288 children. All three samples were tested for HRSV by RT‐qPCR; 141 patients were found positive for at least one sample. Almost perfect agreements (κ > 0.8) between the swabs, compared two by two, were observed. Detection rates for the three swabs (between 93% and 95%) were not significantly different, regardless of the clinical presentation. Our findings suggest that the uncomfortable and technically more demanding NPS method is not mandatory for HRSV detection by RT‐qPCR.
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Affiliation(s)
- Van Hoan Nguyen
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Fiona M Russell
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - David Ab Dance
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Keoudomphone Vilivong
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Souphatsone Phommachan
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Chanthaphone Syladeth
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR
| | - Jana Lai
- Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Ruth Lim
- Pneumococcal Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Melinda Morpeth
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Mayfong Mayxay
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Institute of Research and Education Development, University of Health Sciences, Vientiane, Lao PDR
| | - Paul N Newton
- Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France.,Microbiology Laboratory, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane Capital, Lao PDR.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Minodier L, Masse S, Capai L, Blanchon T, Ceccaldi PE, van der Werf S, Hanslik T, Charrel R, Falchi A. Risk factors for seasonal influenza virus detection in stools of patients consulting in general practice for acute respiratory infections in France, 2014-2016. Influenza Other Respir Viruses 2019; 13:398-406. [PMID: 29144593 PMCID: PMC6586184 DOI: 10.1111/irv.12523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2017] [Indexed: 11/29/2022] Open
Abstract
Background Previous studies reported detection of influenza RNA in stools of patients with seasonal influenza infection. While this detection may have a clinical significance, other factors may influence the stool positivity for influenza viruses. Objectives The objective of this study was to investigate demographical, clinical, and microbiological factors which could favor the presence of influenza viral RNA in the stools of patients with laboratory‐confirmed influenza infection. Methods Acute respiratory infection (ARI) patients were enrolled by general practitioners (GP) during two winter seasons (2014‐2016). Nasopharyngeal swabs, stool specimens, and clinical data were collected. Samples were tested for 12 respiratory pathogen groups (nasopharyngeal and stool specimens) and for 12 enteric pathogens (stool specimens). Results Among the 331 patients with ARI enrolled by GP, 114 (34.4%) presented influenza infection. Influenza RNA was detected in stool samples of 21% (24/114) of the 114 stool specimens analyzed. Hospitalization (adjusted odds ratio (aOR) = 7.8 (95% confidence interval (CI)) [1.7‐33.7], P = .02), age between 45 and 64 years (aOR = 4.8 [1.7‐14.5], P = .01), consumption of raw shellfish and/or mollusks (aOR = 16.7 [3.6‐90.9], P = .00), and use of antibiotics (aOR = 6.4 [2.1‐19.8], P = .006) or antiviral treatment (aOR = 7.4 [1.9‐29], P = .01) were significantly associated with an increased odds of the detection of influenza RNA in stools. Among the 24 stool samples subjected to viral isolation, no one showed virus growth. Conclusions These findings will be useful to studies investigating the dissemination route of influenza viruses to gastrointestinal tract.
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Affiliation(s)
- Laëtitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Shirley Masse
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Lisandru Capai
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
| | - Thierry Blanchon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Pierre-Emmanuel Ceccaldi
- Pasteur Institute, Virology Department, Epidemiology and Physiopathology of Oncogenic Viruses Unit, Paris, France.,UMR CNRS 3569, Paris, France.,Sorbonne Paris Cité, Institut Pasteur, Cellule Pasteur, Université Paris Diderot, Paris, France
| | - Sylvie van der Werf
- UMR CNRS 3569, Paris, France.,Pasteur Institute, Virology Department, Molecular Genetics of RNA Viruses Unit, Paris, France.,Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Thomas Hanslik
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Université Versailles Saint Quentin en Yvelines, UFR de Médecine, Versailles, France.,Hôpital universitaire Ambroise Paré APHP, Service de médecine interne, Boulogne-Billancourt, France
| | - Remi Charrel
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille Univ - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, Corte, France
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58
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Hoang VT, Goumballa N, Dao TL, Ly TDA, Ninove L, Ranque S, Raoult D, Parola P, Sokhna C, Pommier de Santi V, Gautret P. Respiratory and gastrointestinal infections at the 2017 Grand Magal de Touba, Senegal: A prospective cohort survey. Travel Med Infect Dis 2019; 32:101410. [PMID: 31048009 PMCID: PMC7110953 DOI: 10.1016/j.tmaid.2019.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 11/07/2022]
Abstract
Background The Grand Magal of Touba is the largest Muslim pilgrimage in Senegal with a potential for infectious disease transmission. Methods Clinical follow-up, adherence to preventive measures and qPCR-based respiratory and gastrointestinal pathogens carriage pre- and post-Magal, were assessed. Results 110 pilgrims from South Senegal were included. The duration of stay in Touba was 3 days. 41.8% and 14.5% pilgrims reported respiratory and gastrointestinal symptoms. Most individuals having the onset of symptoms during their stay in Touba, or soon after returning. The acquisition of rhinoviruses, coronaviruses and adenovirus was 13.0, 16.7 and 4.6% respectively and that of Streptococcus pneumoniae and Haemophilus influenzae was 3.7% and 26.9%. Acquisition of gastrointestinal viruses and parasites was low, while bacterial acquisition ranged from 2.2% for Campylobacter jejuni to 33.0% for enteropathogenic Escherichia coli. Conclusion This preliminary study confirms that Grand Magal pilgrims are likely to be exposed to communicable disease risk as observed in other pilgrimage settings. Further study including larger numbers of pilgrims are needed to investigate potential risk factors for respiratory and gastrointestinal infections at the Grand Magal.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Viet Nam
| | - Ndiaw Goumballa
- VITROME, Campus International IRD/UCAD de Hann, Dakar, Senegal
| | - Thi-Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Stéphane Ranque
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Vincent Pommier de Santi
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France; French Military Center for Epidemiology and Public Health Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
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59
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Bharucha T, Sengvilaipaseuth O, Seephonelee M, Vongsouvath M, Vongsouvath M, Rattanavong S, Piorkowski G, Lecuit M, Gorman C, Pommier JD, Garson JA, Newton PN, de Lamballerie X, Dubot-Pérès A. Viral RNA Degradation Makes Urine a Challenging Specimen for Detection of Japanese Encephalitis Virus in Patients With Suspected CNS Infection. Open Forum Infect Dis 2019; 6:ofz048. [PMID: 30882014 PMCID: PMC6411208 DOI: 10.1093/ofid/ofz048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/14/2022] Open
Abstract
Background Japanese encephalitis virus (JEV) is a leading cause of central nervous system (CNS) infections in Asia and results in significant morbidity and mortality. JEV RNA is rarely detected in serum or cerebrospinal fluid (CSF), and diagnosis of JEV infection is usually based on serological tests that are frequently difficult to interpret. Unlike serum or CSF, urine is relatively easy to obtain, but, to date, there has been minimal work on the feasibility of testing urine for JEV RNA. Methods We investigated the use of lysis buffer and a Microsep device to optimize urine storage for detection of JEV RNA by reverse transcription real-time polymerase chain reaction (RT-qPCR). The best of the studied methods was then evaluated in consecutive patients admitted to the hospital with suspected CNS infections in Laos. Results We demonstrated degradation of JEV RNA in urine after even short storage periods at 4°C or –80°C. Although there was no advantage in using a Microsep concentration device alone, immediate addition of lysis buffer to fresh urine improved the detection of JEV RNA at the limit of detection. Conclusions In 2 studies of 41 patients with acute encephalitis syndrome, 11 (27%) were positive for JEV IgM in CSF and/or serum, and 2 (4.9%) were JEV RT-qPCR positive from throat swabs. JEV RNA was not detected in any of these patients’ urine samples. However, lysis buffer was only used during a prospective study, that is, for only 17/41 (41%) patient urine samples. Our findings suggest a need for larger studies testing urine for JEV RNA, with urine collected at different times from symptom onset, and using lysis buffer, which stabilizes RNA, for storage.
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Affiliation(s)
- Tehmina Bharucha
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Division of Infection and Immunity, University College London, London, UK
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Malee Seephonelee
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Malavanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Marc Lecuit
- Biology of Infection Unit, Inserm U1117, Institut Pasteur, Paris, France.,Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris Descartes University, Paris, France
| | - Christopher Gorman
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jean-David Pommier
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jeremy A Garson
- Division of Infection and Immunity, University College London, London, UK.,Transfusion Microbiology, NHS Blood and Transplant, London, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK.,Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
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Krumbholz A, Schäfer M, Lorentz T, Sauerbrei A. Quadruplex real-time PCR for rapid detection of human alphaherpesviruses. Med Microbiol Immunol 2019; 208:197-204. [PMID: 30680459 DOI: 10.1007/s00430-019-00580-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/14/2019] [Indexed: 01/12/2023]
Abstract
Infections with the herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) as well as with the varicella-zoster virus (VZV) may take a serious course. Thus, rapid and reliable detection of these alphaherpesviruses is urgently needed. For this, we established a qualitative quadruplex real-time polymerase chain reaction (PCR) covering HSV-1, HSV-2, VZV and endogenous human glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The PCR was validated with quality assessment samples and pre-characterized clinical samples including swabs, blood and cerebrospinal as well as respiratory fluids. For comparison, nucleic acids (NA) of selected samples were extracted manually and automatically. The protocol takes approx. 90 min, starting with the preparation of NA until the report of results. The oligonucleotide and hydrolysis probe sequences specifically detect and distinguish HSV-1 (530 nm), HSV-2 (705 nm) and VZV (560 nm) DNA. The detection limit was estimated with 100-500 copies/ml HSV-1 and HSV-2/VZV, respectively. All quality assessment samples as well as all the patient samples were classified correctly. Parallel detection of GAPDH (670 nm) DNA was implemented to demonstrate correct sampling, but was uncertain in case of swabs. To this end, alphaherpesvirus-free human DNA was also added directly into the mastermix to exclude PCR inhibition. The established protocol for parallel detection and differentiation of alphaherpesviruses is fast, highly specific as well as rather sensitive. It will facilitate HSV-1/2 and VZV diagnostics and may be further improved by opening the 670 nm channel for a combined extraction and PCR inhibition control.
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Affiliation(s)
- Andi Krumbholz
- Labor Dr. Krause und Kollegen MVZ GmbH Kiel, Steenbeker Weg 23, 24106, Kiel, Germany. .,Institut für Infektionsmedizin, Christian-Albrechts-Universität zu Kiel und Universitätsklinikum Schleswig-Holstein, Campus Kiel, Brunswiker Strasse 4, 24105, Kiel, Germany.
| | - Miriam Schäfer
- Labor Dr. Krause und Kollegen MVZ GmbH Kiel, Steenbeker Weg 23, 24106, Kiel, Germany
| | - Thomas Lorentz
- Labor Dr. Krause und Kollegen MVZ GmbH Kiel, Steenbeker Weg 23, 24106, Kiel, Germany
| | - Andreas Sauerbrei
- Sektion Experimentelle Virologie, Institut für Medizinische Mikrobiologie, Universitätsklinikum Jena, Hans-Knöll-Strasse 2, 07745, Jena, Germany
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Balkema-Buschmann A, Rissmann M, Kley N, Ulrich R, Eiden M, Groschup MH. Productive Propagation of Rift Valley Fever Phlebovirus Vaccine Strain MP-12 in Rousettus aegyptiacus Fruit Bats. Viruses 2018; 10:v10120681. [PMID: 30513679 PMCID: PMC6315703 DOI: 10.3390/v10120681] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/25/2022] Open
Abstract
Rift Valley fever phlebovirus (RVFV), the causative agent of an emerging zoonotic disease in Africa and Arabia, can infect a variety of species, predominantly ruminants, camelids, and humans. While clinical symptoms are mostly absent in adult ruminants and camelids, RVFV infection may lead to a serious, sometimes fatal disease in humans. Virus transmissions between individuals and between species mainly occur through mosquito bites, but direct or even indirect contact with infectious materials may also result in infection. Although the main reservoir of the virus is not yet identified, small mammals such as rodents and bats may act as amplifying hosts. We therefore inoculated Rousettus aegyptiacus fruit bats that are abundant in northern Africa with the vaccine strain MP-12, in order to elucidate the general competence of this species for virus propagation and transmission. We were able to detect the RVFV genome in the spleen of each of these animals, and re-isolated the virus from the spleen and liver of some animals. Moreover, we were able to identify the Gc RVFV surface antigen in mild subacute multifocal necrotizing hepatic lesions of one bat which was sacrificed 7 days post exposure. These findings demonstrate that Rousettus aegyptiacus fruit bats can propagate RVFV.
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Affiliation(s)
- Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
| | - Melanie Rissmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
| | - Nils Kley
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
| | - Reiner Ulrich
- ²Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
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Neduvat AC, Murthy PM, Sundarrajan S, Padmanabhan S. Use of coagulation factor XIII (F13) gene as an internal control for normalization of genomic DNA's for HLA typing. MethodsX 2018; 5:881-889. [PMID: 30151348 PMCID: PMC6107889 DOI: 10.1016/j.mex.2018.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 07/27/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic DNA (gDNA) obtained from whole blood samples is a critical element for genomic research and clinical diagnosis. PCR efficiencies of the targeted genes like HLA-A, -B, -C, DPB1 and DRB1 using such isolated gDNAs were variable in spite of having similar amounts of gDNA taken for PCR. We addressed such PCR variabilities by normalizing the gDNA’s using an internal control of human coagulation factor XIII that was found to be variable with all samples and did not correlate with the observed A260 nm readings. The PCR and Q-PCR methodologies for the human coagulation factor XIII have been optimized, and the advantages of normalizing gDNA preparations based on F13 copy numbers have been discussed. This method will serve as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples for the next-generation sequencing purposes, and in forensic labs with limited sample availability.
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Affiliation(s)
- Anupama Cheleri Neduvat
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Prerana Madhusudhana Murthy
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Sudarson Sundarrajan
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd, Rangadore Memorial Hospital, 1st Cross, Shankarapuram, Bangalore 560004, India
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Frequency of Instrument, Environment, and Laboratory Technologist Contamination during Routine Diagnostic Testing of Infectious Specimens. J Clin Microbiol 2018; 56:JCM.00225-18. [PMID: 29563204 DOI: 10.1128/jcm.00225-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/14/2018] [Indexed: 02/03/2023] Open
Abstract
Laboratory testing to support the care of patients with highly infectious diseases may pose a risk for laboratory workers. However, data on the risk of virus transmission during routine laboratory testing conducted using standard personal protective equipment (PPE) are sparse. Our objective was to measure laboratory contamination during routine analysis of patient specimens. Remnant specimens were spiked with the nonpathogenic bacteriophage MS2 at 1.0 × 107 PFU/ml, and contamination was assessed using reverse transcriptase PCR (RT-PCR) for MS2. Specimen containers were exteriorly coated with a fluorescent powder to enable the visualization of gross contamination using UV light. Testing was performed by two experienced laboratory technologists using standard laboratory PPE and sample-to-answer instrumentation. Fluorescence was noted on the gloves, bare hands, and laboratory coat cuffs of the laboratory technologist in 36/36 (100%), 13/36 (36%), and 4/36 (11%) tests performed, respectively. Fluorescence was observed in the biosafety cabinet (BSC) in 8/36 (22%) tests, on test cartridges/devices in 14/32 (44%) tests, and on testing accessory items in 29/32 (91%) tests. Fluorescence was not observed on or in laboratory instrumentation or adjacent surfaces. In contrast to fluorescence detection, MS2 detection was infrequent (3/286 instances [1%]) and occurred during test setup for the FilmArray instrument and on FilmArray accessory equipment. The information from this study may provide opportunities for the improvement of clinical laboratory safety practices so as to reduce the risk of pathogen transmission to laboratory workers.
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64
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Bharucha T, Sengvilaipaseuth O, Seephonelee M, Vongsouvath M, Vongsouvath M, Rattanavong S, Piorkowski G, Lecuit M, Gorman C, Pommier JD, Newton PN, de Lamballerie X, Dubot-Pérès A. Detection of Japanese Encephalitis Virus RNA in Human Throat Samples in Laos - A Pilot study. Sci Rep 2018; 8:8018. [PMID: 29789537 PMCID: PMC5964078 DOI: 10.1038/s41598-018-26333-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/10/2018] [Indexed: 11/09/2022] Open
Abstract
Japanese encephalitis virus (JEV) is the most commonly identified cause of acute encephalitis syndrome (AES) in Asia. The WHO recommended test is anti-JEV IgM-antibody-capture-enzyme-linked-immunosorbent-assay (JEV MAC-ELISA). However, data suggest this has low positive predictive value, with false positives related to other Flavivirus infections and vaccination. JEV RT-PCR in cerebrospinal fluid (CSF) and/or serum is highly specific, but is rarely positive; 0-25% of patients that fulfil the WHO definition of JE (clinical Acute Encephalitis Syndrome (AES) and JEV MAC-ELISA positive). Testing other body fluids by JEV RT-qPCR may improve the diagnosis. As a pilot study thirty patients admitted to Mahosot Hospital 2014-2017, recruited to the South-East-Asia-Encephalitis study, were tested by JEV MAC-ELISA and two JEV real-time RT-PCR (RT-qPCR) assays (NS2A and NS3). Eleven (36.7%) were JEV MAC-ELISA positive. Available CSF and serum samples of these patients were JEV RT-qPCR negative but 2 (7%) had JEV RNA detected in their throat swabs. JEV RNA was confirmed by re-testing, and sequencing of RT-qPCR products. As the first apparent report of JEV RNA detection in human throat samples, the provides new perspectives on human JEV infection, potentially informing improving JEV detection. We suggest that testing patients' throat swabs for JEV RNA is performed, in combination with molecular and serological CSF and serum investigations, on a larger scale to investigate the epidemiology of the presence of JEV in human throats. Throat swabs are an easy and non-invasive tool that could be rolled out to a wider population to improve knowledge of JEV molecular epidemiology.
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Affiliation(s)
- Tehmina Bharucha
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR. .,Division of Infection and Immunity, University College London, London, UK.
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Malee Seephonelee
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Malavanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Géraldine Piorkowski
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm, U1117, Paris, France.,Paris Descartes University, Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, Paris, France
| | - Christopher Gorman
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Jean-David Pommier
- Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, UK.,UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
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Ly TDA, Edouard S, Badiaga S, Tissot-Dupont H, Hoang VT, Pommier de Santi V, Brouqui P, Raoult D, Gautret P. Epidemiology of respiratory pathogen carriage in the homeless population within two shelters in Marseille, France, 2015-2017: cross sectional 1-day surveys. Clin Microbiol Infect 2018; 25:249.e1-249.e6. [PMID: 29777925 PMCID: PMC7128312 DOI: 10.1016/j.cmi.2018.04.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 12/31/2022]
Abstract
Objectives To assess risk factors for respiratory tract infection symptoms and signs in sheltered homeless people in Marseille during the winter season, including pathogen carriage. Methods Data on 479 male participants within two shelters who completed questionnaires and a total of 950 nasal and pharyngeal samples were collected during the winters of 2015–2017. Respiratory pathogen carriage including seven viruses and four bacteria was assessed by quantitative PCR. Results The homeless population was characterized by a majority of individuals of North African origin (300/479, 62.6%) with a relatively high prevalence of chronic homelessness (175/465, 37.6%). We found a high prevalence of respiratory symptoms and signs (168/476, 35.3%), a very high prevalence of bacterial carriage (313/477, 65.6%), especially Haemophilus influenzae (280/477, 58.7%), and a lower prevalence of virus carriage (51/473, 10.8%) with human rhinovirus being the most frequent (25/473, 5.3%). Differences were observed between the microbial communities of the nose and throat. Duration of homelessness (odds ratio (OR) 1.77, p 0.017), chronic respiratory diseases (OR 5.27, p <0.0001) and visiting countries of origin for migrants (OR 1.68, p 0.035) were identified as independent risk factors for respiratory symptoms and signs. A strong association between virus (OR 2.40, p 0.012) or Streptococcus pneumoniae (OR 2.32, p 0.014) carriage and respiratory symptoms and signs was also found. Conclusions These findings allowed identification of the individuals at higher risk for contracting respiratory tract infections to better target preventive measures aimed at limiting the transmission of these diseases in this setting.
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Affiliation(s)
- T D A Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - S Edouard
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - S Badiaga
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - H Tissot-Dupont
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - V T Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - V Pommier de Santi
- French Military Centre for Epidemiology and Public Health Marseille, France
| | - P Brouqui
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - P Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.
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A protocol for culturing environmental strains of the Buruli ulcer agent, Mycobacterium ulcerans. Sci Rep 2018; 8:6778. [PMID: 29712992 PMCID: PMC5928104 DOI: 10.1038/s41598-018-25278-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/13/2018] [Indexed: 11/08/2022] Open
Abstract
Contaminations and fastidiousness of M. ulcerans may have both hamper isolation of strains from environmental sources. We aimed to optimize decontamination and culture of environmental samples to circumvent both limitations. Three strains of M. ulcerans cultured onto Middlebrook 7H10 at 30 °C for 20 days yielded a significantly higher number of colonies in micro-aerophilic atmosphere compared to ambient atmosphere, 5% CO2 and anaerobic atmosphere. In a second step, we observed that M. ulcerans genome uniquely encoded chitinase, fucosidase and A-D-GlcNAc-diphosphoryl polyprenol A-3-L-rhamnosyl transferase giving M. ulcerans the potential to metabolize chitine, fucose and N-acetyl galactosamine (NAG), respectively. A significant growth-promoting effect of 0.2 mg/mL chitin (p < 0.05), 0.01 mg/mL N-acetyl galactosamine (p < 0.05), 0.01 mg/mL fucose (p < 0.05) was observed with M. ulcerans indicating that NAG alone or combined with fucose and chitin could complement Middlebrook 7H10. Finally, the protocol combining 1% chlorhexidine decontamination with micro-aerophilic incubation on Middlebrook 7H10 medium containing chitin (0.2%), NAG (0.01%) and fucose (0.01%) medium and auto-fluorescence detection of colonies allowed for the isolation of one mycolactone-encoding strain from Thryonomys swinderianus (aulacode) feces specimens collected near the Kossou Dam, Côte d'Ivoire. We propose that incubation of chlorhexidine-decontaminated environmental specimens on Middlebrook 7H10-enriched medium under micro-aerophilic atmosphere at 30 °C may be used for the tentative isolation of M. ulcerans strains from potential environmental sources.
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Development of an improved RT-qPCR Assay for detection of Japanese encephalitis virus (JEV) RNA including a systematic review and comprehensive comparison with published methods. PLoS One 2018; 13:e0194412. [PMID: 29570739 PMCID: PMC5865736 DOI: 10.1371/journal.pone.0194412] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/02/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Japanese encephalitis virus (JEV) is a major cause of encephalitis in Asia, and the commonest cause of mosquito-borne encephalitis worldwide. Detection of JEV RNA remains challenging due to the characteristic brief and low viraemia, with 0-25% of patients positive, and the mainstay of diagnosis remains detection of anti-JEV IgM antibody. METHODS We performed a systematic review of published RT-PCR protocols, and evaluated them in silico and in vitro alongside new primers and probes designed using a multiple genome alignment of all JEV strains >9,000nt from GenBank, downloaded from the NCBI website (November 2016). The new assays included pan-genotype and genotype specific assays targeting genotypes 1 and 3. RESULTS Ten RT-qPCR assays were compared, a pre-existing in-house assay, three published assays and six newly designed assays, using serial RNA dilutions. We selected three assays, one published and two novel assays, with the lowest limit of detection (LOD) for further optimisation and validation. One of the novel assays, detecting NS2A, showed the best results, with LOD approximately 4 copies/ reaction, and no cross-reaction on testing closely related viruses in the JEV serocomplex, West Nile Virus and St. Louis Virus. The optimised assays were validated in consecutive patients with central nervous system infections admitted to hospitals in Laos, testing paired CSF and serum samples. CONCLUSIONS We succeeded in developing a JEV specific RT-qPCR assay with at least 1 log10 improved sensitivity as compared to existing assays. Further evaluation is required, field-testing the assay in a larger group of patients.
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Castonguay-Vanier J, Klitting R, Sengvilaipaseuth O, Piorkowski G, Baronti C, Sibounheuang B, Vongsouvath M, Chanthongthip A, Thongpaseuth S, Mayxay M, Phommasone K, Douangdala P, Inthalath S, Souvannasing P, Newton PN, de Lamballerie X, Dubot-Pérès A. Molecular epidemiology of dengue viruses in three provinces of Lao PDR, 2006-2010. PLoS Negl Trop Dis 2018; 12:e0006203. [PMID: 29377886 PMCID: PMC5805359 DOI: 10.1371/journal.pntd.0006203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 02/08/2018] [Accepted: 01/02/2018] [Indexed: 01/12/2023] Open
Abstract
Few data on dengue epidemiology are available for Lao PDR. Here, we provide information on the complexity of dengue epidemiology in the country, demonstrating dynamic circulation that varies over space and time, according to serotype. We recruited 1,912 consenting patients presenting with WHO dengue criteria at Mahosot Hospital, Vientiane (central Laos), between 2006 and 2010. Between 2008 and 2010, 1,413 patients with undifferentiated fever were also recruited at Luang Namtha (LNT) Provincial Hospital (northern Laos) and 555 at Salavan (SV) Provincial Hospital (southern Laos). We report significant variations in Dengue virus (DENV) circulation between the three sites. Peaks of DENV infection were observed in the rainy seasons, although 11% of confirmed cases in the provinces and 4.6% in the capital were detected during the dry and cool seasons (between December and February). Four DENV serotypes were detected among the 867 RT-PCR positive patients: 76.9% DENV-1, 9.6% DENV-2, 7.7% DENV-4 and 5.3% DENV-3. DENV-1 was the predominant serotype throughout the study except in LNT in 2008 and 2009 when it was DENV-2. Before July 2009, DENV-2 was not detected in SV and only rarely detected in Vientiane. DENV-3 and DENV-4 were commonly detected in Vientiane, before 2008 for DENV-4 and after 2009 for DENV-3. The phylogenetic analyses of DENV envelope sequences suggest concurrent multiple introductions of new strains as well as active DENV circulation throughout Laos and with neighboring countries. It is therefore of great importance to develop and strengthen a year-round nation-wide surveillance network in order to collect data that would allow anticipation of public health issues caused by the occurrence of large dengue outbreaks. Dengue is a mosquito-borne disease that can be caused by 4 viruses. It is a flu-like disease but can sometime be more severe and cause hemorrhage or death. An estimated 390 million people are infected every year, mainly in the Western Pacific and in South-East Asia. In Laos, where our study was conducted from 2006 to 2010, little was known on the circulation of the different dengue viruses. A total of 1,912 patients were recruited at Mahosot Hospital, Vientiane (central Laos), 1,413 patients at Luang Namtha Provincial Hospital (northern Laos) and 555 at Salavan Provincial Hospital (southern Laos). Although most Dengue virus infections were detected during rainy seasons (where mosquitoes are the most active) in all three provinces, some patients were also infected during the dryer months. All 4 dengue viruses were detected with different distributions: mostly type 1 in the capital and in the South, and type 1 and 2 in equal proportion in the north. Type 3 and 4 were not detected in Luang Namtha and rarely in Salavan. Comparison of Dengue virus sequences from Laos with sequences collected worldwide showed an active year-round circulation of dengue within Laos and with neighboring countries. It is hence of great importance to develop and strengthen a year-round nation-wide surveillance network in order to collect data that would allow anticipation of public health issues caused by the occurrence of large dengue outbreaks.
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Affiliation(s)
- Josée Castonguay-Vanier
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Raphaëlle Klitting
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Géraldine Piorkowski
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Cécile Baronti
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Bountoy Sibounheuang
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Soulignasack Thongpaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | - Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | | | - Saythong Inthalath
- Luang Namtha Provincial Hospital, Luang Namtha, Luang Namtha Province, Lao PDR
| | | | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- UMR "Unité des Virus Emergents" (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
- * E-mail:
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Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013-2017. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1423718. [PMID: 29392127 PMCID: PMC5748090 DOI: 10.1155/2017/1423718] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/25/2017] [Accepted: 11/16/2017] [Indexed: 12/02/2022]
Abstract
Background The current study aims to describe the demographical and clinical characteristics of elderly nursing home (NH) residents with acute respiratory infections (ARIs) during four winter seasons (2013/2014–2016/2017), as well as the microbiological etiology of these infections. Methods Seventeen NHs with at least one ARI resident in Corsica, France, were included. An ARI resident was defined as a resident developing a sudden onset of any constitutional symptoms in addition to any respiratory signs. Nasopharyngeal swabs from ARI residents were screened for the presence of 21 respiratory agents, including seasonal influenza viruses. Results Of the 107 ARI residents enrolled from NHs, 61 (57%) were positive for at least one of the 21 respiratory pathogens. Forty-one (38.3%) of the 107 ARI residents had influenza: 38 (92%) were positive for influenza A (100% A(H3N2)) and three (8%) for influenza B/Victoria. Axillary fever (≥38°C) was significantly more common among patients infected with influenza A(H3N2). Conclusion The circulation of seasonal respiratory viruses other than influenza A(H3N2) seems to be sporadic among elderly NH residents. Investigating the circulation of respiratory viruses in nonwinter seasons seems to be important in order to understand better the dynamic of their year-round circulation in NHs.
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Minodier L, Masse S, Capai L, Blanchon T, Ceccaldi PE, van der Werf S, Hanslik T, Charrel R, Falchi A. Clinical and virological factors associated with gastrointestinal symptoms in patients with acute respiratory infection: a two-year prospective study in general practice medicine. BMC Infect Dis 2017; 17:729. [PMID: 29166867 PMCID: PMC5700681 DOI: 10.1186/s12879-017-2823-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023] Open
Abstract
Background Gastrointestinal (GI) symptoms, such as diarrhea, vomiting, abdominal pain and nausea are not an uncommon manifestation of an acute respiratory infection (ARI). We therefore evaluated clinical and microbiological factors associated with the presence of GI symptoms in patients consulting a general practitioner (GP) for ARI. Methods Nasopharyngeal swabs, stool specimens and clinical data from patients presenting to GPs with an ARI were prospectively collected during two winter seasons (2014-2016). Samples were tested by quantitative real-time PCR for 12 respiratory pathogen groups and for 12 enteric pathogens. Results Two hundred and four of 331 included patients (61.6%) were positive for at least one respiratory pathogen. Sixty-nine stools (20.8%) were positive for at least one pathogen (respiratory and/or enteric). GI symptoms were more likely declared in case of laboratory confirmed-enteric infection (adjusted odds ratio (aOR) = 3.2; 95% confidence interval [CI] [1.2–9.9]; p = 0.02) or human coronavirus (HCoV) infection (aOR = 2.7; [1.2–6.8]; p = 0.02). Consumption of antipyretic medication before the consultation seemed to reduce the risk of developing GI symptoms for patients with laboratory-confirmed influenza (aOR = 0.3; [0.1–0.6]; p = 0.002). Conclusions The presence of GI symptoms in ARI patients could not be explained by the detection of respiratory pathogens in stools. However, the detection of enteric pathogens in stool samples could explained by the presence of GI symptoms in some of ARI cases. The biological mechanisms explaining the association between the presence of HCoVs in nasopharynx and GI symptoms need to be explored. Electronic supplementary material The online version of this article (10.1186/s12879-017-2823-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Shirley Masse
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Lisandru Capai
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France
| | - Thierry Blanchon
- Institut Pierre Louis d'Epidémiologie et de Santé Publique, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, 56, Boulevard Vincent Auriol, 81393-75646, Paris, France.,INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, 56, Boulevard Vincent Auriol, 81393-75646, Paris, France
| | - Pierre-Emmanuel Ceccaldi
- Pasteur Institute, Virology Department, Epidemiology and Physiopathology of Oncogenic Viruses Unit, F-75015, Paris, France.,UMR CNRS 3569, 75015, Paris, France.,Sorbonne Paris Cité, Cellule Pasteur, Université Paris Diderot, Institut Pasteur, 75015, Paris, France
| | - Sylvie van der Werf
- UMR CNRS 3569, 75015, Paris, France.,Pasteur Institute, Virology Department, Molecular Genetics of RNA Viruses Unit, F-75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, EA302, F-75015, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, UPMC Université Paris 06, Institut Pierre-Louis d'Épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Hôpital Ambroise Paré, service de médecine interne, Boulogne-Billancourt, France.,UFR des Sciences de la Santé Simone-Veil, Université Versailles Saint Quentin en Yvelines, Versailles, France
| | - Remi Charrel
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille Univ - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250, Corte, France.
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Woods K, Nic-Fhogartaigh C, Arnold C, Boutthasavong L, Phuklia W, Lim C, Chanthongthip A, Tulsiani SM, Craig SB, Burns MA, Weier SL, Davong V, Sihalath S, Limmathurotsakul D, Dance DAB, Shetty N, Zambon M, Newton PN, Dittrich S. A comparison of two molecular methods for diagnosing leptospirosis from three different sample types in patients presenting with fever in Laos. Clin Microbiol Infect 2017; 24:1017.e1-1017.e7. [PMID: 29092789 PMCID: PMC6125144 DOI: 10.1016/j.cmi.2017.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 02/01/2023]
Abstract
OBJECTIVES To compare two molecular assays (rrs quantitative PCR (qPCR) versus a combined 16SrRNA and LipL32 qPCR) on different sample types for diagnosing leptospirosis in febrile patients presenting to Mahosot Hospital, Vientiane, Laos. METHODS Serum, buffy coat and urine samples were collected on admission, and follow-up serum ∼10 days later. Leptospira spp. culture and microscopic agglutination tests (MAT) were performed as reference standards. Bayesian latent class modelling was performed to estimate sensitivity and specificity of each diagnostic test. RESULTS In all, 787 patients were included in the analysis: 4/787 (0.5%) were Leptospira culture positive, 30/787 (3.8%) were MAT positive, 76/787 (9.7%) were rrs qPCR positive and 20/787 (2.5%) were 16SrRNA/LipL32 qPCR positive for pathogenic Leptospira spp. in at least one sample. Estimated sensitivity and specificity (with 95% CI) of 16SrRNA/LipL32 qPCR on serum (53.9% (33.3%-81.8%); 99.6% (99.2%-100%)), buffy coat (58.8% (34.4%-90.9%); 99.9% (99.6%-100%)) and urine samples (45.0% (27.0%-66.7%); 99.6% (99.3%-100%)) were comparable with those of rrs qPCR, except specificity of 16SrRNA/LipL32 qPCR on urine samples was significantly higher (99.6% (99.3%-100%) vs. 92.5% (92.3%-92.8%), p <0.001). Sensitivities of MAT (16% (95% CI 6.3%-29.4%)) and culture (25% (95% CI 13.3%-44.4%)) were low. Mean positive Cq values showed that buffy coat samples were more frequently inhibitory to qPCR than either serum or urine (p <0.001). CONCLUSIONS Serum and urine are better samples for qPCR than buffy coat, and 16SrRNA/LipL32 qPCR performs better than rrs qPCR on urine. Quantitative PCR on admission is a reliable rapid diagnostic tool, performing better than MAT or culture, with significant implications for clinical and epidemiological investigations of this global neglected disease.
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Affiliation(s)
- K Woods
- National Infection Service, Public Health England, London, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
| | - C Nic-Fhogartaigh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Bart's Health Division of Infection, Pathology and Pharmacy Department, Royal London Hospital, London, UK
| | - C Arnold
- National Infection Service, Public Health England, London, UK
| | - L Boutthasavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - W Phuklia
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - C Lim
- Mahidol-Oxford-Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - A Chanthongthip
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - S M Tulsiani
- Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Qld, Australia
| | - S B Craig
- Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Qld, Australia; University of the Sunshine Coast, Faculty of Science Health, Education and Engineering, Sippy Downs, Qld, Australia; Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - M-A Burns
- Queensland Health Forensic and Scientific Service, WHO Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Qld, Australia
| | - S L Weier
- Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - V Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - S Sihalath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - D Limmathurotsakul
- Mahidol-Oxford-Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - D A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - N Shetty
- National Infection Service, Public Health England, London, UK
| | - M Zambon
- National Infection Service, Public Health England, London, UK
| | - P N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
| | - S Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK; Foundation for Innovative New Diagnostics, Geneva, Switzerland
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Kwon JH, Burnham CAD, Reske KA, Liang SY, Hink T, Wallace MA, Shupe A, Seiler S, Cass C, Fraser VJ, Dubberke ER. Assessment of Healthcare Worker Protocol Deviations and Self-Contamination During Personal Protective Equipment Donning and Doffing. Infect Control Hosp Epidemiol 2017; 38:1077-1083. [PMID: 28606192 PMCID: PMC6263164 DOI: 10.1017/ice.2017.121] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To evaluate healthcare worker (HCW) risk of self-contamination when donning and doffing personal protective equipment (PPE) using fluorescence and MS2 bacteriophage. DESIGN Prospective pilot study. SETTING Tertiary-care hospital. PARTICIPANTS A total of 36 HCWs were included in this study: 18 donned/doffed contact precaution (CP) PPE and 18 donned/doffed Ebola virus disease (EVD) PPE. INTERVENTIONS HCWs donned PPE according to standard protocols. Fluorescent liquid and MS2 bacteriophage were applied to HCWs. HCWs then doffed their PPE. After doffing, HCWs were scanned for fluorescence and swabbed for MS2. MS2 detection was performed using reverse transcriptase PCR. The donning and doffing processes were videotaped, and protocol deviations were recorded. RESULTS Overall, 27% of EVD PPE HCWs and 50% of CP PPE HCWs made ≥1 protocol deviation while donning, and 100% of EVD PPE HCWs and 67% of CP PPE HCWs made ≥1 protocol deviation while doffing (P=.02). The median number of doffing protocol deviations among EVD PPE HCWs was 4, versus 1 among CP PPE HCWs. Also, 15 EVD PPE protocol deviations were committed by doffing assistants and/or trained observers. Fluorescence was detected on 8 EVD PPE HCWs (44%) and 5 CP PPE HCWs (28%), most commonly on hands. MS2 was recovered from 2 EVD PPE HCWs (11%) and 3 CP PPE HCWs (17%). CONCLUSIONS Protocol deviations were common during both EVD and CP PPE doffing, and some deviations during EVD PPE doffing were committed by the HCW doffing assistant and/or the trained observer. Self-contamination was common. PPE donning/doffing are complex and deserve additional study. Infect Control Hosp Epidemiol 2017;38:1077-1083.
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Affiliation(s)
- Jennie H. Kwon
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stephen Y. Liang
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Angela Shupe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sondra Seiler
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Victoria J. Fraser
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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Kunkel SA, Azimi P, Zhao H, Stark BC, Stephens B. Quantifying the size-resolved dynamics of indoor bioaerosol transport and control. INDOOR AIR 2017; 27:977-987. [PMID: 28190263 DOI: 10.1111/ina.12374] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
Understanding the bioaerosol dynamics of droplets and droplet nuclei emitted during respiratory activities is important for understanding how infectious diseases are transmitted and potentially controlled. To this end, we conducted experiments to quantify the size-resolved dynamics of indoor bioaerosol transport and control in an unoccupied apartment unit operating under four different HVAC particle filtration conditions. Two model organisms (Escherichia coli K12 and bacteriophage T4) were aerosolized under alternating low and high flow rates to roughly represent constant breathing and periodic coughing. Size-resolved aerosol sampling and settle plate swabbing were conducted in multiple locations. Samples were analyzed by DNA extraction and quantitative polymerase chain reaction (qPCR). DNA from both organisms was detected during all test conditions in all air samples up to 7 m away from the source, but decreased in magnitude with the distance from the source. A greater fraction of T4 DNA was recovered from the aerosol size fractions smaller than 1 μm than E. coli K12 at all air sampling locations. Higher efficiency HVAC filtration also reduced the amount of DNA recovered in air samples and on settle plates located 3-7 m from the source.
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Affiliation(s)
- S A Kunkel
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - P Azimi
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - H Zhao
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - B C Stark
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - B Stephens
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
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Biscornet L, Dellagi K, Pagès F, Bibi J, de Comarmond J, Mélade J, Govinden G, Tirant M, Gomard Y, Guernier V, Lagadec E, Mélanie J, Rocamora G, Le Minter G, Jaubert J, Mavingui P, Tortosa P. Human leptospirosis in Seychelles: A prospective study confirms the heavy burden of the disease but suggests that rats are not the main reservoir. PLoS Negl Trop Dis 2017; 11:e0005831. [PMID: 28846678 PMCID: PMC5591009 DOI: 10.1371/journal.pntd.0005831] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 09/08/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Background Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira for which rats are considered as the main reservoir. Disease incidence is higher in tropical countries, especially in insular ecosystems. Our objectives were to determine the current burden of leptospirosis in Seychelles, a country ranking first worldwide according to historical data, to establish epidemiological links between animal reservoirs and human disease, and to identify drivers of transmission. Methods A total of 223 patients with acute febrile symptoms of unknown origin were enrolled in a 12-months prospective study and tested for leptospirosis through real-time PCR, IgM ELISA and MAT. In addition, 739 rats trapped throughout the main island were investigated for Leptospira renal carriage. All molecularly confirmed positive samples were further genotyped. Results A total of 51 patients fulfilled the biological criteria of acute leptospirosis, corresponding to an annual incidence of 54.6 (95% CI 40.7–71.8) per 100,000 inhabitants. Leptospira carriage in Rattus spp. was overall low (7.7%) but dramatically higher in Rattus norvegicus (52.9%) than in Rattus rattus (4.4%). Leptospira interrogans was the only detected species in both humans and rats, and was represented by three distinct Sequence Types (STs). Two were novel STs identified in two thirds of acute human cases while noteworthily absent from rats. Conclusions This study shows that human leptospirosis still represents a heavy disease burden in Seychelles. Genotype data suggests that rats are actually not the main reservoir for human disease. We highlight a rather limited efficacy of preventive measures so far implemented in Seychelles. This could result from ineffective control measures of excreting animal populations, possibly due to a misidentification of the main contaminating reservoir(s). Altogether, presented data stimulate the exploration of alternative reservoir animal hosts. Leptospirosis is an emerging environmental infectious disease caused by corkscrew shaped bacteria called Leptospira. Humans usually get infected during recreational or work-related outdoor activities through contact with urine excreted by animal reservoirs. As a zoonotic disease, leptospirosis is a good example of the One Health concept for it links humans, animals and ecosystems in a web of pathogen maintenance and transmission. This zoonosis is highly prevalent in the tropics and especially in tropical islands. Seychelles archipelago has been reported as the country with highest human incidence worldwide, although figures are based on dated studies and/or poorly specific tests. The presented investigation aimed at providing an updated information on human leptospirosis burden in Seychelles and exploring the transmission chains in their environmental aspects. Presented data confirms that the disease still heavily impacts the country. Genotyping of pathogenic Leptospira in human acute cases reveals that three distinct Sequence Types (STs) are involved in the disease. However, rats typically considered as the main reservoir in Seychelles, harbor only one of these STs, found only in a minority of human cases. Hence, it appears that rats are likely not the main reservoir of leptospirosis in Seychelles, which has important consequences in terms of preventive measures to be implemented for a better control of human leptospirosis.
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Affiliation(s)
- Leon Biscornet
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- Infectious Disease Surveillance Unit, Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Mont Fleuri, Seychelles
| | - Koussay Dellagi
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Frédéric Pagès
- Regional Office of the French Institute for Public Health Surveillance (Santé Publique France), Saint-Denis, La Réunion, France
| | - Jastin Bibi
- Disease Surveillance and Response Unit, Epidemiology and Statistics Section, Public Health Authority, Ministry of Health, Mont Fleuri, Seychelles
| | - Jeanine de Comarmond
- Disease Surveillance and Response Unit, Epidemiology and Statistics Section, Public Health Authority, Ministry of Health, Mont Fleuri, Seychelles
| | - Julien Mélade
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Graham Govinden
- Infectious Disease Surveillance Unit, Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health, Mont Fleuri, Seychelles
| | - Maria Tirant
- Regional Office of the French Institute for Public Health Surveillance (Santé Publique France), Saint-Denis, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Vanina Guernier
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Erwan Lagadec
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- CRVOI, Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien, Ste Clotilde, Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Jimmy Mélanie
- Veterinary Services Section, Seychelles Agricultural Agency, Ministry of Agriculture and Fisheries, Victoria, Seychelles
| | - Gérard Rocamora
- Island Biodiversity and Conservation Centre, University of Seychelles, Victoria, Seychelles
| | - Gildas Le Minter
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Julien Jaubert
- Service de Bactériologie, Parasitologie, Virologie et Hygiène, Groupe Hospitalier Sud Réunion-Centre Hospitalier Universitaire (GHSR-CHU), Saint Pierre, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
| | - Pablo Tortosa
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), CNRS 9192, INSERM U 1187, IRD 249. Plateforme de Recherche CYROI, Sainte Clotilde, La Réunion, France
- * E-mail:
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Pavlovic M, Koehler N, Anton M, Dinkelmeier A, Haase M, Stellberger T, Busch U, Baiker AE. Reverse Transcription Quantitative Polymerase Chain Reaction for Detection of and Differentiation Between RNA and DNA of HIV-1-Based Lentiviral Vectors. Hum Gene Ther Methods 2017. [PMID: 28817345 DOI: 10.1089/hgtb.2017.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The purpose of the described method is the detection of and differentiation between RNA and DNA of human immunodeficiency virus (HIV)-derived lentiviral vectors (LV) in cell culture supernatants and swab samples. For the analytical surveillance of genetic engineering, operations methods for the detection of the HIV-1-based LV generations are required. Furthermore, for research issues, it is important to prove the absence of LV particles for downgrading experimental settings in terms of the biosafety level. Here, a quantitative polymerase chain reaction method targeting the long terminal repeat U5 subunit and the start sequence of the packaging signal ψ is described. Numerous controls are included in order to monitor the technical procedure.
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Affiliation(s)
- Melanie Pavlovic
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Nina Koehler
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Martina Anton
- 2 Institute of Experimental Oncology and Therapy Research and Institute of Molecular Immunology , Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Anna Dinkelmeier
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Maren Haase
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | | | - Ulrich Busch
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Armin E Baiker
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
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76
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Pavlovic M, Koehler N, Anton M, Dinkelmeier A, Haase M, Stellberger T, Busch U, Baiker AE. Reverse Transcription Quantitative Polymerase Chain Reaction for Detection of and Differentiation Between RNA and DNA of HIV-1-Based Lentiviral Vectors. Hum Gene Ther Methods 2017; 28:215-221. [PMID: 28817345 DOI: 10.1089/hgtb.2017-081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The purpose of the described method is the detection of and differentiation between RNA and DNA of human immunodeficiency virus (HIV)-derived lentiviral vectors (LV) in cell culture supernatants and swab samples. For the analytical surveillance of genetic engineering, operations methods for the detection of the HIV-1-based LV generations are required. Furthermore, for research issues, it is important to prove the absence of LV particles for downgrading experimental settings in terms of the biosafety level. Here, a quantitative polymerase chain reaction method targeting the long terminal repeat U5 subunit and the start sequence of the packaging signal ψ is described. Numerous controls are included in order to monitor the technical procedure.
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Affiliation(s)
- Melanie Pavlovic
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Nina Koehler
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Martina Anton
- 2 Institute of Experimental Oncology and Therapy Research and Institute of Molecular Immunology , Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Anna Dinkelmeier
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Maren Haase
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | | | - Ulrich Busch
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Armin E Baiker
- 1 Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
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77
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Rissmann M, Eiden M, Wade A, Poueme R, Abdoulkadiri S, Unger H, Ziegler U, Homeier T, Groschup M. Evidence for enzootic circulation of Rift Valley fever virus among livestock in Cameroon. Acta Trop 2017; 172:7-13. [PMID: 28427961 DOI: 10.1016/j.actatropica.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/22/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Rift Valley fever virus (RVFV) is an arthropod-borne pathogen, causing serious epidemics in Africa and the Arabian Peninsula. In Cameroon serological data indicate the presence of RVFV, but active circulation of RVFV, causing clinical infections has not been proven yet. For this purpose we carried out a serological and molecular study on a total of 1953 randomly selected serum samples of small ruminants and cattle, which were collected in years 2013 and 2014 in Cameroon. In a first step, sera were screened serologically using a variety of assay formats to reveal RVFV specific antibodies. At the second stage, seropositive specimen were assessed for acute RVFV infections via IgM-specific ELISA and quantitative real-time RT-PCR. Our data show a significant difference in the antibody prevalence in cattle (13.5% [95% confidence interval: 11.4-15.7]) and small ruminants (3.4% [95% confidence interval: 2.3-4.7]), with indications for annual fluctuations and significant regional differences of seropositivity. One small ruminant and three bovines were eventually found to be positive in IgM ELISA and indications for viremia were found in one bovine by RVFV genome detection using quantitative real-time RT-PCR. The results of this study therefore corroborate the presence of acute RVFV-infection and its circulation in Cameroon.
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78
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Huemer H, Prudhomme J, Amaro F, Baklouti A, Walder G, Alten B, Moutailler S, Ergunay K, Charrel RN, Ayhan N. Practical Guidelines for Studies on Sandfly-Borne Phleboviruses: Part II: Important Points to Consider for Fieldwork and Subsequent Virological Screening. Vector Borne Zoonotic Dis 2017; 17:81-90. [PMID: 28055572 DOI: 10.1089/vbz.2016.1965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this series of review articles entitled "Practical guidelines for studies on sandfly-borne phleboviruses," the important points to be considered at the prefieldwork stage were addressed in part I, including parameters to be taken into account to define the geographic area for sand fly trapping and how to organize field collections. Here in part II, the following points have been addressed: (1) factors influencing the efficacy of trapping and the different types of traps with their respective advantages and drawbacks, (2) how to process the trapped sand flies in the field, and (3) how to process the sand flies in the virology laboratory. These chapters provide the necessary information for adopting the most appropriate procedures depending on the requirements of the study. In addition, practical information gathered through years of experience of translational projects is included to help newcomers to fieldwork studies.
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Affiliation(s)
- Hartwig Huemer
- 1 Division for Human Medicine, Austrian Agency for Health and Food Safety (AGES) , Vienna, Austria
| | - Jorian Prudhomme
- 2 Centre IRD, UMR MIVEGEC (IRD 224-CNRS 5290-Universite Montpellier) , Montpellier, France
| | - Fatima Amaro
- 3 Centre for Vectors and Infectious Diseases Research, National Institute of Health Ricardo Jorge , Aguas de Moura, Portugal
| | - Amal Baklouti
- 4 UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University-IRD 190-INSERM 1207-EHESP) , Marseille, France .,5 Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille, France
| | | | - Bulent Alten
- 7 EBAL-VERG Laboratories, Ecology Division, Department of Biology, Faculty of Science, Science and Engineering Institute, Hacettepe University , Ankara, Turkey
| | - Sara Moutailler
- 8 UMR BIPAR, Animal Health Laboratory , ANSES, Maisons-Alfort, France
| | - Koray Ergunay
- 9 Department of Medical Microbiology, Faculty of Medicine, Hacettepe University , Ankara, Turkey
| | - Remi N Charrel
- 4 UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University-IRD 190-INSERM 1207-EHESP) , Marseille, France .,5 Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille, France .,10 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Nazli Ayhan
- 4 UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University-IRD 190-INSERM 1207-EHESP) , Marseille, France .,5 Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille, France
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79
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Zambenedetti MR, Pavoni DP, Dallabona AC, Dominguez AC, Poersch CDO, Fragoso SP, Krieger MA. Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics. Mem Inst Oswaldo Cruz 2017; 112:339-347. [PMID: 28403327 PMCID: PMC5398160 DOI: 10.1590/0074-02760160380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.
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Affiliation(s)
- Miriam Ribas Zambenedetti
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Departamento de Bioprocessos e Biotecnologia, Curitiba, PR, Brasil
| | - Daniela Parada Pavoni
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | | | | | | | - Stenio Perdigão Fragoso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | - Marco Aurélio Krieger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Fundação Oswaldo Cruz-Fiocruz, Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil
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80
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Tian RBD, Asmar S, Napez C, Lépidi H, Drancourt M. Effectiveness of purified methylene blue in an experimental model of Mycobacterium ulcerans infection. Int J Antimicrob Agents 2017; 49:290-295. [PMID: 28131607 DOI: 10.1016/j.ijantimicag.2016.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 10/20/2022]
Abstract
Mycobacterium ulcerans is responsible for Buruli ulcer, characterised by extensive, disabling ulcers. Standard treatment combining rifampicin and streptomycin exposes patients to toxicity and daily painful injections. In this study, the in vitro susceptibilities of 3 M. ulcerans strains, 1 Mycobacterium marinum strain and 18 strains representative of eleven other Mycobacterium species and subspecies to methylene blue were determined. Whilst growth of M. ulcerans was inhibited by 0.0125 g/L methylene blue, growth of all other tested strains was not inhibited by 1 g/L methylene blue. The effectiveness of methylene blue in a murine model of M. ulcerans infection was then tested. Topical treatment by brushing a methylene blue solution on the skin lesion, systemic treatment by intraperitoneal injection of methylene blue, and a combined treatment (topical and systemic) were tested. The three treatment groups exhibited a significantly lower clinical score compared with the non-treated control group (P <0.05). Moreover, subcutaneous nodules were significantly smaller in the systemic treatment group (excluding males) (3 ± 0.7 mm) compared with the other groups (P <0.05). The M. ulcerans insertion sequence IS2404 and the KR-B gene were detected in all challenged mice, but not in negative controls. The density of M. ulcerans (mycobacteria/cell) was significantly lower in the combined treatment group compared with the other groups. These data provide evidence for the effectiveness of purified methylene blue against the initial stage of Buruli ulcer.
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Affiliation(s)
- Roger B D Tian
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Shady Asmar
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Claude Napez
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Hubert Lépidi
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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81
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Rissmann M, Ulrich R, Schröder C, Hammerschmidt B, Hanke D, Mroz C, Groschup MH, Eiden M. Vaccination of alpacas against Rift Valley fever virus: Safety, immunogenicity and pathogenicity of MP-12 vaccine. Vaccine 2016; 35:655-662. [PMID: 28012779 DOI: 10.1016/j.vaccine.2016.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/25/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023]
Abstract
Rift Valley fever (RVF) is an emerging zoonosis of major public health concern in Africa and Arabia. Previous outbreaks attributed camelids a significant role in the epidemiology of Rift Valley fever virus (RVFV), making them an important target species for vaccination. Using three alpacas as model-organisms for dromedary camels, the safety, immunogenicity and pathogenicity of the MP-12 vaccine were evaluated in this study. To compare both acute and subacute effects, animals were euthanized at 3 and 31days post infection (dpi). Clinical monitoring, analysis of liver enzymes and hematological parameters demonstrated the tolerability of the vaccine, as no significant adverse effects were observed. Comprehensive analysis of serological parameters illustrated the immunogenicity of the vaccine, eliciting high neutralizing antibody titers and antibodies targeting different viral antigens. RVFV was detected in serum and liver of the alpaca euthanized 3dpi, whereas no virus was detectable at 31dpi. Viral replication was confirmed by detection of various RVFV-antigens in hepatocytes by immunohistochemistry and the presence of mild multifocal necrotizing hepatitis. In conclusion, results indicate that MP-12 is a promising vaccine candidate but still has a residual pathogenicity, which requires further investigation.
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Affiliation(s)
- M Rissmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - R Ulrich
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - C Schröder
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - B Hammerschmidt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - D Hanke
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - C Mroz
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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82
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Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days. PLoS One 2016; 11:e0159564. [PMID: 27548676 PMCID: PMC4993482 DOI: 10.1371/journal.pone.0159564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/05/2016] [Indexed: 11/19/2022] Open
Abstract
Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines.
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83
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Paleomicrobiology Data: Authentification and Interpretation. Microbiol Spectr 2016; 4. [PMID: 27337456 DOI: 10.1128/microbiolspec.poh-0017-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The authenticity of some of the very first works in the field of paleopathology has been questioned, and standards have been progressively established for the experiments and the interpretation of data. Whereas most problems initially arose from the contamination of ancient specimens with modern human DNA, the situation is different in the field of paleomicrobiology, in which the risk for contamination is well-known and adequately managed by any laboratory team with expertise in the routine diagnosis of modern-day infections. Indeed, the exploration of ancient microbiota and pathogens is best done by such laboratory teams, with research directed toward the discovery and implementation of new techniques and the interpretation of data.
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84
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Vongsouvath M, Phommasone K, Sengvilaipaseuth O, Kosoltanapiwat N, Chantratita N, Blacksell SD, Lee SJ, de Lamballerie X, Mayxay M, Keomany S, Newton PN, Dubot-Pérès A. Using Rapid Diagnostic Tests as a Source of Viral RNA for Dengue Serotyping by RT-PCR - A Novel Epidemiological Tool. PLoS Negl Trop Dis 2016; 10:e0004704. [PMID: 27159058 PMCID: PMC4861341 DOI: 10.1371/journal.pntd.0004704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/20/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Dengue virus infection causes major public health problems in tropical and subtropical areas. In many endemic areas, including the Lao PDR, inadequate access to laboratory facilities is a major obstacle to surveillance and study of dengue epidemiology. Filter paper is widely used for blood collection for subsequent laboratory testing for antibody and nucleic acid detection. For the first time, we demonstrate that dengue viral RNA can be extracted from dengue rapid diagnostic tests (RDT) and then submitted to real-time RT-PCR for serotyping. METHODOLOGY/PRINCIPAL FINDINGS We evaluated the Standard Diagnostics (SD) Bioline Dengue Duo RDT, a commonly used test in dengue endemic areas. First, using the QIAamp RNA kit, dengue RNA was purified from the sample pad of the NS1 RDT loaded with virus isolates of the four serotypes, then quantified by RT-PCR. We observed greater recovery of virus, with a mean of 27 times more RNA recovered from RDT, than from filter paper. Second, we evaluated dengue NS1 RDTs from patients at Mahosot Hospital, Vientiane, (99 patients) and from rural Salavan Provincial Hospital (362 patients). There was good agreement between dengue RT-PCR from NS1 RDT with RT-PCR performed on RNA extracted from patient sera, either using RDT loaded with blood (82.8% and 91.4%, in Vientiane and Salavan, respectively) or serum (91.9% and 93.9%). There was 100% concordance between RDT and serum RT-PCR of infecting dengue serotype. CONCLUSIONS/SIGNIFICANCE Therefore, the collection of NS1 positive RDTs, which do not require cold storage, may be a novel approach for dengue serotyping by RT-PCR and offers promising prospects for the collection of epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions.
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Affiliation(s)
- Manivanh Vongsouvath
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
| | - Stuart D. Blacksell
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Sue J. Lee
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Xavier de Lamballerie
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | - Sommay Keomany
- Salavan Provincial Hospital, Salavan Provincial Health Department, Salavan Province, Laos
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
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85
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Ball CS, Light YK, Koh CY, Wheeler SS, Coffey LL, Meagher RJ. Quenching of Unincorporated Amplification Signal Reporters in Reverse-Transcription Loop-Mediated Isothermal Amplification Enabling Bright, Single-Step, Closed-Tube, and Multiplexed Detection of RNA Viruses. Anal Chem 2016; 88:3562-8. [PMID: 26980448 DOI: 10.1021/acs.analchem.5b04054] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reverse-transcription-loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes postamplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of the reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for quenching of unincorporated amplification signal reporters, read "quasar"), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). Furthermore, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.
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Affiliation(s)
- Cameron S Ball
- Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States
| | - Yooli K Light
- Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States
| | - Chung-Yan Koh
- Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States
| | - Sarah S Wheeler
- University of California Davis , School of Veterinary Medicine, Department of Pathology, Microbiology and Immunology, One Shield Avenue, Davis, California 95616, United States
| | - Lark L Coffey
- University of California Davis , School of Veterinary Medicine, Department of Pathology, Microbiology and Immunology, One Shield Avenue, Davis, California 95616, United States
| | - Robert J Meagher
- Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States
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86
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Tian RBD, Niamké S, Tissot-Dupont H, Drancourt M. Detection of Mycobacterium ulcerans DNA in the Environment, Ivory Coast. PLoS One 2016; 11:e0151567. [PMID: 26982581 PMCID: PMC4794205 DOI: 10.1371/journal.pone.0151567] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/01/2016] [Indexed: 11/19/2022] Open
Abstract
Background Ivory Coast is a West African country with the highest reported cases of Buruli ulcer, a disabling subcutaneous infection due to Mycobacterium ulcerans. However, the prevalence of environmental M. ulcerans is poorly known in this country. Methods We collected 496 environmental specimens consisting of soil (n = 100), stagnant water (n = 200), plants (n = 100) and animal feces (n = 96) in Ivory Coast over five months in the dry and wet seasons in regions which are free of Buruli ulcer (control group A; 250 specimens) and in regions where the Buruli ulcer is endemic (group B; 246 specimens). After appropriate total DNA extraction incorporating an internal control, the M. ulcerans IS2404 and KR-B gene were amplified by real-time PCR in samples. In parallel, a calibration curve was done for M. ulcerans Agy99 IS2404 and KR-B gene. Results Of 460 samples free of PCR inhibition, a positive real-time PCR detection of insertion sequence IS2404 and KR-B gene was observed in 1/230 specimens in control group A versus 9/230 specimens in group B (P = 0.02; Fisher exact test). Positive specimens comprised seven stagnant water specimens, two feces specimens confirmed to be of Thryonomys swinderianus (agouti) origin by real-time PCR of the cytb gene; and one soil specimen. Extrapolation from the calibration curves indicated low inoculums ranging from 1 to 102 mycobacteria/mL. Conclusion This study confirms the presence of M. ulcerans in the watery environment surrounding patients with Buruli ulcer in Ivory Coast. It suggests that the agouti, which is in close contacts with populations, could play a role in the environmental cycle of M. ulcerans, as previously suggested for the closely related possums in Australia.
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Affiliation(s)
- Roger Bi Diangoné Tian
- Aix Marseille Université, URMITE, UMR, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France
- Laboratoire de biotechnologies, UFR Biosciences, Université Félix Houphouet Boigny Abidjan, Côte d’Ivoire
| | - Sébastian Niamké
- Laboratoire de biotechnologies, UFR Biosciences, Université Félix Houphouet Boigny Abidjan, Côte d’Ivoire
| | - Hervé Tissot-Dupont
- Aix Marseille Université, URMITE, UMR, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Marseille, France
- * E-mail:
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87
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Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes. PLoS One 2015; 10:e0139810. [PMID: 26431175 PMCID: PMC4592258 DOI: 10.1371/journal.pone.0139810] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/17/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Metagenomic analyses have been widely used in the last decade to describe viral communities in various environments or to identify the etiology of human, animal, and plant pathologies. Here, we present a simple and standardized protocol that allows for the purification and sequencing of RNA viromes from complex biological samples with an important reduction of host DNA and RNA contaminants, while preserving the infectivity of viral particles. PRINCIPAL FINDINGS We evaluated different viral purification steps, random reverse transcriptions and sequence-independent amplifications of a pool of representative RNA viruses. Viruses remained infectious after the purification process. We then validated the protocol by sequencing the RNA virome of human body lice engorged in vitro with artificially contaminated human blood. The full genomes of the most abundant viruses absorbed by the lice during the blood meal were successfully sequenced. Interestingly, random amplifications differed in the genome coverage of segmented RNA viruses. Moreover, the majority of reads were taxonomically identified, and only 7-15% of all reads were classified as "unknown", depending on the random amplification method. CONCLUSION The protocol reported here could easily be applied to generate RNA viral metagenomes from complex biological samples of different origins. Our protocol allows further virological characterizations of the described viral communities because it preserves the infectivity of viral particles and allows for the isolation of viruses.
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88
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Baronti C, Piorkowski G, Leparc-Goffart I, de Lamballerie X, Dubot-Pérès A. Rapid next-generation sequencing of dengue, EV-A71 and RSV-A viruses. J Virol Methods 2015; 226:7-14. [PMID: 26376168 DOI: 10.1016/j.jviromet.2015.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 11/16/2022]
Abstract
Accurate characterisation of viral strains constitutes a crucial objective for the management of modern virus collections. Next-generation sequencing (NGS) provides technical solution for fast and cost-effective full genome sequencing. Here, we report protocols for rapid full-genome characterisation of RNA viruses of medical importance: dengue virus, enterovirus A71 and respiratory syncytial virus A, based on a specific amplification step followed by NGS-sequencing. A subset of full-length genome sequences representing the genetic diversity of each virus type was selected in GenBank and used to design primer sets allowing the amplification of the complete genome in 3-8 overlapping PCR fragments. The technique was used for characterising 53 strains (33 DENV, 8 EV-A71, 12 RSV-A) from various genotypes and origins. In a single assay, and in just 4 days, it provided for all strains an excellent genomic coverage (∼ 99% including complete ORF for all strains) and accurate sequences with high number of reads per position (250-3500 on average). The elaboration of specific PCR-based full-genome sequencing protocols for diverse virus groups is likely to revolutionise the characterisation of viral isolates in modern collection, but also to contribute in the next future to the study of RNA viruses directly from biological samples.
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Affiliation(s)
- Cécile Baronti
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France.
| | - Géraldine Piorkowski
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France
| | - Isabelle Leparc-Goffart
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; French National Reference Centre for Arboviruses, IRBA, 13013 Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France
| | - Audrey Dubot-Pérès
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, PDR Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
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89
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de Fabritus L, Nougairède A, Aubry F, Gould EA, de Lamballerie X. Attenuation of tick-borne encephalitis virus using large-scale random codon re-encoding. PLoS Pathog 2015; 11:e1004738. [PMID: 25734338 PMCID: PMC4348424 DOI: 10.1371/journal.ppat.1004738] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 12/20/2022] Open
Abstract
Large-scale codon re-encoding (i.e. introduction of a large number of synonymous mutations) is a novel method of generating attenuated viruses. Here, it was applied to the pathogenic flavivirus, tick-borne encephalitis virus (TBEV) which causes febrile illness and encephalitis in humans in forested regions of Europe and Asia. Using an infectious clone of the Oshima 5–10 strain ("wild-type virus"), a cassette of 1.4kb located in the NS5 coding region, was modified by randomly introducing 273 synonymous mutations ("re-encoded virus"). Whilst the in cellulo replicative fitness of the re-encoded virus was only slightly reduced, the re-encoded virus displayed an attenuated phenotype in a laboratory mouse model of non-lethal encephalitis. Following intra-peritoneal inoculation of either 2.105 or 2.106 TCID50 of virus, the frequency of viraemia, neurovirulence (measured using weight loss and appearance of symptoms) and neuroinvasiveness (detection of virus in the brain) were significantly decreased when compared with the wild-type virus. Mice infected by wild-type or re-encoded viruses produced comparable amounts of neutralising antibodies and results of challenge experiments demonstrated that mice previously infected with the re-encoded virus were protected against subsequent infection by the wild-type virus. This constitutes evidence that a mammalian species can be protected against infection by a virulent wild-type positive-stranded RNA virus following immunisation with a derived randomly re-encoded strain. Our results demonstrate that random codon re-encoding is potentially a simple and effective method of generating live-attenuated vaccine candidates against pathogenic flaviviruses. The arbovirus Tick-borne encephalitis virus (TBEV; genus Flavivirus) is transmitted by ticks of the Ixodes genus. TBEV causes febrile illness and encephalitis in humans in forested regions of Europe and Asia. The incidence of TBE is increasing across Central and Eastern European countries despite the availability of several licensed inactivated vaccines and appropriate vaccination programmes. Large-scale codon re-encoding, a recently developed attenuation method that modifies viral RNA nucleotide composition of large coding regions without alteration of the encoded proteins, has been successfully applied to a variety of RNA viruses. In contrast with previous empirical methods of generating live attenuated vaccines, large-scale codon re-encoding facilitates rapid generation of vaccine candidates using reverse genetics methods, by direct control of the attenuation phenotype. Additional benefits include reduced costs and induction of long-term immunity. Here, we have applied the large-scale codon re-encoding method to the TBEV to demonstrate the principle of developing a live attenuated virus vaccine which protects mice against subsequent infection with the wild type virulent virus. This study therefore illustrates that codon re-encoding is potentially an easily derived and effective method of producing live attenuated vaccine candidates against positive-stranded RNA viruses.
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Affiliation(s)
- Lauriane de Fabritus
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
- * E-mail:
| | - Antoine Nougairède
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Fabien Aubry
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
| | - Ernest A Gould
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Memish ZA, Assiri A, Turkestani A, Yezli S, Al Masri M, Charrel R, Drali T, Gaudart J, Edouard S, Parola P, Gautret P. Mass gathering and globalization of respiratory pathogens during the 2013 Hajj. Clin Microbiol Infect 2015; 21:571.e1-8. [PMID: 25700892 PMCID: PMC7129181 DOI: 10.1016/j.cmi.2015.02.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/29/2015] [Accepted: 02/09/2015] [Indexed: 12/02/2022]
Abstract
Every year, more than 10 million pilgrims arrive in the Kingdom of Saudi Arabia for the Hajj or Umrah. Crowding conditions lead to high rates of respiratory infections among the pilgrims, representing a significant cause of morbidity and a major cause of hospitalization. Pre- and post-Hajj nasal specimens were prospectively obtained from a paired cohort (692 pilgrims) and from nonpaired cohorts (514 arriving and 470 departing pilgrims) from 13 countries. The countries of residence included Africa (44.2%), Asia (40.2%), the United States (8.4%) and Europe (7.2%). Nasal specimens were tested for 34 respiratory pathogens using RT-PCR. A total of 80 512 PCRs were performed. The prevalence of viruses and bacteria increased, from 7.4% and 15.4% before the Hajj to 45.4% and 31.0% after the Hajj, respectively, due to the acquisition of rhinovirus, coronaviruses (229E, HKU1, OC43), influenza A H1N1, Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus. We did not identify Middle East respiratory coronavirus carriage. At arrival, the prevalence of several viruses was clearly dependent on the pilgrim's country of origin. After Hajj participation, these viruses were isolated among pilgrims from all countries, with few exceptions. No significant differences were observed between paired and nonpaired cohort results. Our results strongly suggest that, given the particularly crowded conditions during the rituals, an international mass gathering such as the Hajj may contribute to the globalization of respiratory pathogens after the cross-contamination of pilgrims harbouring pathogens that easily spread among participants. Influenza and pneumococcal vaccination, face mask use and hand hygiene should be considered in the context of the Hajj.
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Affiliation(s)
- Z A Memish
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - A Assiri
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia
| | - A Turkestani
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia
| | - S Yezli
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia
| | - M Al Masri
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia
| | - R Charrel
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", Marseille, France
| | - T Drali
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - J Gaudart
- Equipe Biostatistiques, LERTIM, Faculté de Médecine, Marseille, France
| | - S Edouard
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - P Parola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - P Gautret
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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91
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Salez N, Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Charrel RN. Prospective and retrospective evaluation of the Cepheid Xpert® Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus. Diagn Microbiol Infect Dis 2015; 81:256-8. [PMID: 25662018 PMCID: PMC7172894 DOI: 10.1016/j.diagmicrobio.2015.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 12/02/2022]
Abstract
A total of 281 clinical specimens (nasal swabs and nasopharyngeal aspirates) were tested with the Xpert® Flu/RSV XC. The results were compared to those obtained with the real-time retro transcriptase-polymerase chain reaction assays routinely used in our laboratory. The Xpert® Flu/RSV XC showed sensitivity/specificity of 97.8%/100% and 97.9%/100% for flu and respiratory syncytial virus, respectively. Real-time RT-PCR is gold standard for diagnosis of influenza and RSV in human samples. Xpert® Flu/RSV XC assay sensitivity >97.75% and 100% specificity for both viruses. Similar performances using nasal swabs or and nasopharyngeal aspirate specimens. Turnaround time is 63 min, minimal training, suitable for point-of-care settings. No need for confirmation of the results.
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Affiliation(s)
- Nicolas Salez
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France.
| | - Antoine Nougairede
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Laetitia Ninove
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Christine Zandotti
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Remi N Charrel
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
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92
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Maloney S, Francis F, Bletchly C, Norton R. Evaluation of a commercially available synthetic RNA lipid enveloped control molecule. J Virol Methods 2014; 211:19-21. [PMID: 25447757 DOI: 10.1016/j.jviromet.2014.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/05/2014] [Accepted: 10/03/2014] [Indexed: 11/26/2022]
Abstract
Detection of viral ribonucleic acid with RT PCR is a useful tool for viral detection. One of the drawbacks of this technique is the difficulty in including an internal control molecule to ensure the validity of the extraction and amplification process. In this study the potential usefulness of a novel lipid enveloped commercially available RNA control molecule is investigated. Initial optimisation of the detection assay was performed by amplification of IC (internal control) spiked into PCR water. Thirty-two clinical respiratory samples were spiked with the IC before and after extraction and RT PCR was then performed. Inefficient extraction was simulated. Inhibition of the RT PCR was achieved by serial dilution of heparin sulfate into samples post extraction. No Targets that matched the IC (Internal Control) primers were identified in 32 extracted sputum samples as determined by the absence of non specific amplification curves. The unextracted IC had an increased CT (cycle threshold) value compared to IC that had been extracted. Inefficient extraction was detected by an increased CT. Increasing concentrations of heparin inhibited the PCR in a predictable fashion. The Bioline IC molecule provides a stable RNA IC that has acceptable performance characteristics.
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Affiliation(s)
- Samuel Maloney
- The Townsville Hospital, Townsville, Queensland, Australia; Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia.
| | - Fleur Francis
- Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia
| | - Cheryl Bletchly
- Molecular Diagnostic Unit, Pathology Queensland, Brisbane, Queensland 4006, Australia
| | - Robert Norton
- The Townsville Hospital, Townsville, Queensland, Australia; Microbiology, Pathology Queensland, Townsville, Queensland 4814, Australia.
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93
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Absence of coronaviruses, paramyxoviruses, and influenza A viruses in seabirds in the southwestern Indian Ocean. J Wildl Dis 2014; 49:1056-9. [PMID: 24502741 DOI: 10.7589/2012-09-227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We investigated circulation of coronaviruses, paramyxoviruses, and influenza A viruses in eight seabird species of the southwestern Indian Ocean. Viruses were not detected by real-time polymerase chain reactions in the 338 tested cloacal swab samples, supporting that they did not circulate in the studied colonies at the time of sampling.
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94
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Benkouiten S, Gautret P, Belhouchat K, Drali T, Nougairede A, Salez N, Memish ZA, Al Masri M, Raoult D, Brouqui P, Parola P, Charrel RN. Comparison of nasal swabs with throat swabs for the detection of respiratory viruses by real-time reverse transcriptase PCR in adult Hajj pilgrims. J Infect 2014; 70:207-10. [PMID: 25193499 PMCID: PMC7127672 DOI: 10.1016/j.jinf.2014.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/26/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Samir Benkouiten
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
| | - Philippe Gautret
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France.
| | - Khadidja Belhouchat
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Tassadit Drali
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Antoine Nougairede
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France; Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, 13385, Marseille, France
| | - Nicolas Salez
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France; Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, 13385, Marseille, France
| | - Ziad A Memish
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Malak Al Masri
- Public Health Directorate, Saudi Ministry of Health, WHO Collaborating Center for Mass Gathering Medicine, Riyadh, Saudi Arabia
| | - Didier Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
| | - Philippe Brouqui
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
| | - Philippe Parola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France
| | - Rémi N Charrel
- Institut Hospitalo-Universitaire Méditerranée Infection, 13005 Marseille, France; Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, 13385, Marseille, France
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95
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Dubot-Pérès A, Tan CYQ, de Chesse R, Sibounheuang B, Vongsouvath M, Phommasone K, Bessaud M, Gazin C, Thirion L, Phetsouvanh R, Newton PN, de Lamballerie X. SYBR green real-time PCR for the detection of all enterovirus-A71 genogroups. PLoS One 2014; 9:e89963. [PMID: 24651608 PMCID: PMC3961242 DOI: 10.1371/journal.pone.0089963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Enterovirus A71 (EV-A71) has recently become an important public health threat, especially in South-East Asia, where it has caused massive outbreaks of Hand, Foot and Mouth disease every year, resulting in significant mortality. Rapid detection of EV-A71 early in outbreaks would facilitate implementation of prevention and control measures to limit spread. Real-time RT-PCR is the technique of choice for the rapid diagnosis of EV-A71 infection and several systems have been developed to detect circulating strains. Although eight genogroups have been described globally, none of these PCR techniques detect all eight. We describe, for the first time, a SYBR Green real-time RT-PCR system validated to detect all 8 EV-A71 genogroups. This tool could permit the early detection and shift in genogroup circulation and the standardization of HFMD virological diagnosis, facilitating networking of laboratories working on EV-A71 in different regions.
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Affiliation(s)
- Audrey Dubot-Pérès
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- * E-mail:
| | - Charlene Y. Q. Tan
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
| | - Reine de Chesse
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
| | - Bountoy Sibounheuang
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Maël Bessaud
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
| | - Céline Gazin
- Laboratory of Clinical Microbiology, AP-HM Timone, University Hospital Institute for Infectious Disease and Tropical Medicine, Marseille, France
| | - Laurence Thirion
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital–Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Xavier de Lamballerie
- Unité Mixte de Recherche_D 190 “Emergence des Pathologies Virales” (Aix-Marseille University, IRD French Institute of Research for Development, EHESP French School of Public Health), Marseille, France
- Laboratory of Clinical Microbiology, AP-HM Timone, University Hospital Institute for Infectious Disease and Tropical Medicine, Marseille, France
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96
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Aherfi S, Ninove L, Zandotti C, Crepey P, Richet H, Nougairede A, de Lamballerie X, Charrel R. Increased incidence of acute parvovirus B19 infections in Marseille, France, in 2012 compared with the 2002–2011 period. Clin Microbiol Infect 2014; 20:O176-81. [DOI: 10.1111/1469-0691.12366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 07/09/2013] [Accepted: 08/10/2013] [Indexed: 11/27/2022]
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97
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Delangue J, Roca Sanchez Y, Piorkowski G, Bessaud M, Baronti C, Thirion-Perrier L, Mafayle RL, Ardaya CA, Aguilera GA, Guzman JR, Riera JL, de Lamballerie X. Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012). Virol J 2014; 11:35. [PMID: 24564892 PMCID: PMC4015617 DOI: 10.1186/1743-422x-11-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to characterise viral aetiologies of ILIs in Bolivia. METHODS It was performed in Santa Cruz city from January 2010 to September 2012, based on 564 naso-pharyngeal swabs collected in a National Reference Laboratory and real-time PCR techniques, viral cultures and phylogenetic analyses. RESULTS 50.2% of samples were positive for at least one virus with influenza viruses (Flu A: ~15%; Flu B: ~9%), rhinoviruses (~8%), coronaviruses (~5%) and hRSV (~4%) being the most frequently identified. The pattern of viral infections varied according to age groups. The elucidation rate was the highest (>60%) amongst patients under 10 yo and the lowest (<40%) amongst patients ≥60 yo. Nearly 3% of samples showed dual viral infections. Epidemiological peaks were associated with a predominant virus but generally included 30-50% of infections by different viruses. Unexpectedly, the frequency of influenza in the 0-4 yo population was very low and a complete hRSV eclipse occurred in 2011. Genetic analyses indicated that distinct evolutionary lineages of Flu A(H1N1)pdm2009, Flu A/H3N2 and Flu B have co-circulated in Bolivia in the study period, originating from Central and North America, Europe, Asia and Australia. CONCLUSION Our results emphasise the requirement for a reinforced epidemiological and genetic follow-up of influenza and other ILIs in Bolivia to further inform the preparation of vaccines used in the region, guide vaccination campaigns and improve the medical management of patients.
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Affiliation(s)
- Julie Delangue
- IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 "Emergence des Pathologies Virales", Aix Marseille Univ, 13005 Marseille, France.
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98
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Dupouey J, Ninove L, Ferrier V, Py O, Gazin C, Thirion-Perrier L, de Lamballerie X. Molecular detection of human rhinoviruses in respiratory samples: a comparison of Taqman probe-, SYBR green I- and BOXTO-based real-time PCR assays. Virol J 2014; 11:31. [PMID: 24548758 PMCID: PMC3936951 DOI: 10.1186/1743-422x-11-31] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 02/11/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human Rhinoviruses (HRV) are major causative agents of acute respiratory tract infections in all age group and important contributing factors of childhood morbidity and mortality. Clinical presentation is poorly specific and the great antigenic and genetic variability of HRVs renders the biological diagnosis complex. Here, we have evaluated several molecular diagnostic protocols, including Taqman probe-based and intercalating agent-based RT-PCR assays. METHODS 5,627 respiratory samples sent to the laboratory of Virology of the University Hospitals of Marseille, France, from March 2011 to February 2012, were tested using a real-time RT-PCR assay in the 5'NCR of the rhinoviral genome that associated a Taqman probe and the detection of DNA-BOXTO-dye complexes. A sample of 500 BOXTO-positive samples were further tested using the same probe assay (without BOXTO), and a SYBR Green assay (using the same amplification primers). The specific amplification of HRV sequences was assessed by NGS amplicon sequencing. RESULTS The Taqman probe RT-PCR assay identified 696/5,627 samples (12,4%) as HRV-positive. BOXTO-positive samples included all probe-positive samples and 1,913 additional samples, of which only 24.3% were confirmed by sequencing. The SYBR Green assay was more specific (16/550 samples were probe-negative/SYBR Green-positive, all confirmed by 5'NCR sequencing), but 3/500 samples were probe-positive/SYBR Green-negative. CONCLUSIONS Our results highlight the difficulty in detecting HRVs in clinical samples using a single molecular detection system. Amongst the 3 systems tested, the best compromise was obtained with the SYBR Green assay, which, by comparison with our probe-based assay provided an improved sensitivity without altering the detection specificity. Interestingly, a majority of probe-negative/BOXTO- or SYBR Green-positive samples were not associated with mutations in the sequence targeted by the probe. Sequence-based modifications of the secondary structure of the HRV 5'NCR may be associated with a limited access to the probe hybridisation region. Further investigations may identify a test combining a probe based- and an intercalating agent-based detection, which will significantly improve the diagnosis of HRV infections.
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Affiliation(s)
- Julien Dupouey
- IRD French Institute of Research for Development, EHESP French School of Public Health, Aix Marseille Univ, UMR_D 190 "Emergence des Pathologies Virales", Marseille 13005, France.
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99
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Descloux E, La Fuentez C, Roca Y, De Lamballerie X. Clinical significance of intra-host variability of Dengue-1 virus in venous and capillary blood. Clin Microbiol Infect 2014; 20:O167-75. [PMID: 24397875 DOI: 10.1111/1469-0691.12368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/05/2013] [Accepted: 08/10/2013] [Indexed: 11/27/2022]
Abstract
Dengue fever represents a major public health problem. Both viral and host immune factors are involved in severe infections. Humans and mosquito-vectors are infected with diverse viral populations that may play a role in viral adaptation and disease pathogenesis. Our objective was to analyse the intra-host genetic variability of dengue virus type 1 (DENV-1) in the venous and capillary blood and its relationships with the clinical presentation of dengue fever. Early serum samples were collected in 2009 from ten DENV-1-infected patients hospitalized in Santa Cruz de la Sierra, Bolivia. Partial viral envelope sequences were analysed at the inter-host and intra-host level. For each patient, an average of 56 clone sequences was analysed both in the venous sector and the capillary sector (from right and left hands). The ten consensus sequences were highly similar. The intra-host DENV-1 genetic variability was significantly lower in the venous sector than in the capillary sector, and in patients with haemorrhagic symptoms than in those without haemorrhagic symptoms, particularly in capillary samples. No relation was found with sex, age, dengue IgG-serological status, day of serum sampling, or viral load. Significant relationships were found between the clinical presentation of dengue fever and the variability of viral populations within hosts, particularly in capillary samples. The observed variability of envelope sequences at the early phase of dengue infection was not critically influenced by the previous dengue serological status of patients. An important part of viral microevolution may occur in the capillary sector and influence the mechanisms of severe forms.
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Affiliation(s)
- E Descloux
- IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 "Emergence des Pathologies Virales" Aix-Marseille Université, Marseille, France; Service de Médecine Interne et Maladies Infectieuses, Centre Hospitalier Territorial de Nouvelle Calédonie, Noumea, New Caledonia
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100
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Development of real-time RT-PCR for the detection of low concentrations of Rift Valley fever virus. J Virol Methods 2014; 195:92-9. [DOI: 10.1016/j.jviromet.2013.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 11/19/2022]
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