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Gautret P, Houhamdi L, Nguyen NN, Hoang VT, Giraud-Gatineau A, Raoult D. Corrigendum to "Does SARS-CoV-2 re-infection depend on virus variant?" [Clin Microbiol Infect 27 (9) (2021 Sep) 1374-1375]. Clin Microbiol Infect 2023; 29:1616. [PMID: 37597618 PMCID: PMC11021208 DOI: 10.1016/j.cmi.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Affiliation(s)
- Philippe Gautret
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Nhu Ngoc Nguyen
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Van Thuan Hoang
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hȏpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France.
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Sarsiat L, Garrigos T, Houhamdi L, Dauwalder O, Kuli B, Braunberger E, Belmonte O, Fournier PE, Miltgen G. Case series of 12 Bartonella quintana endocarditis from the Southwest Indian Ocean. PLoS Negl Trop Dis 2023; 17:e0011606. [PMID: 37676863 PMCID: PMC10508605 DOI: 10.1371/journal.pntd.0011606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/19/2023] [Accepted: 08/20/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Bartonella spp. are fastidious bacteria frequently identified as the cause of blood culture-negative (BCN) endocarditis. However, Bartonella infections are difficult to diagnose in routine laboratory testing and their incidence is probably underestimated. We investigated the epidemiological and clinical features of Bartonella endocarditis cases diagnosed between 2009 and 2021 on Reunion Island (Southwest Indian Ocean). METHOD We retrospectively included all patients diagnosed with Bartonella endocarditis at Reunion Island University Hospital during this period. Endocarditis was diagnosed on the basis of microbiological findings, including serological tests (IFA) and PCR on cardiac valves, and the modified Duke criteria. We used then the multispacer typing (MST) method to genotype the available Bartonella strains. FINDINGS We report 12 cases of B. quintana endocarditis on Reunion Island (83.3% in men, median patient age: 32 years). All the patients originated from the Comoros archipelago. The traditional risk factors for B. quintana infection (homelessness, alcoholism, exposure to body lice) were absent in all but two of the patients, who reported head louse infestations in childhood. Previous heart disease leading to valve dysfunction was recorded in 50% of patients. All patients underwent cardiac valve surgery and antimicrobial therapy with a regimen including doxycycline. All patients presented high C-reactive protein concentrations, anemia and negative blood cultures. The titer of IgG antibodies against Bartonella sp. exceeded 1:800 in 42% of patients. Specific PCR on cardiac valves confirmed the diagnosis of B. quintana endocarditis in all patients. Genotyping by the MST method was performed on four strains detected in preserved excised valves and was contributive for three, which displayed the MST6 genotype. CONCLUSIONS Bartonella quintana is an important cause of infective endocarditis in the Comoros archipelago and should be suspected in patients with mitral valve dysfunction and BCN from this area.
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Affiliation(s)
- Ludivine Sarsiat
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Thomas Garrigos
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Saint-Denis, La Réunion, France
| | - Linda Houhamdi
- CNR des Rickettsies, Coxiella et Bartonella, IHU-Méditerranée Infection, Marseille, France
| | - Olivier Dauwalder
- Plateau de Microbiologie Moléculaire Spécialisé et de Séquençage, Institut des Agents Infectieux, Centre de Biologie et Pathologie Nord, Hospices Civils de Lyon, Lyon, France
| | - Barbara Kuli
- Service de Maladies Infectieuses, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Eric Braunberger
- Service de Chirurgie Cardio-thoracique, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Olivier Belmonte
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Pierre-Edouard Fournier
- CNR des Rickettsies, Coxiella et Bartonella, IHU-Méditerranée Infection, Marseille, France
- UMR Vecteurs—Infections Tropicales et Méditerranéennes (VITROME), Université d’Aix-Marseille, IRD, AP-HM, SSA, IHU-Méditerranée Infection, Marseille, France
| | - Guillaume Miltgen
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
- UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Saint-Denis, La Réunion, France
- Centre Régional en Antibiothérapie (CRAtb) de La Réunion, France
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Nguyen NN, Houhamdi L, Meddeb L, Colson P, Gautret P. Reinfection with SARS-CoV-2 Omicron BA.4 and BA.5 variants. J Med Virol 2023; 95:e29033. [PMID: 37594314 DOI: 10.1002/jmv.29033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/19/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Affiliation(s)
- Nhu Ngoc Nguyen
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Linda Houhamdi
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Line Meddeb
- IHU-Méditerranée Infection, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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Hamame A, Magdy Wasfy R, Lo CI, Fenollar F, Raoult D, Fournier PE, Houhamdi L. Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota. Sci Rep 2023; 13:8465. [PMID: 37231091 DOI: 10.1038/s41598-023-35443-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.
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Affiliation(s)
- Afaf Hamame
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Reham Magdy Wasfy
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Linda Houhamdi
- IHU-Méditerranée Infection, Marseille, France.
- Aix Marseille Univ, IRD, AP-HM, Service de Santé Des Armées (SSA), VITROME, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Jumpertz M, Sevestre J, Luciani L, Houhamdi L, Fournier PE, Parola P. Bacterial Agents Detected in 418 Ticks Removed from Humans during 2014-2021, France. Emerg Infect Dis 2023; 29:701-710. [PMID: 36957992 PMCID: PMC10045685 DOI: 10.3201/eid2904.221572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Monitoring of tickborne diseases is critical for prevention and management. We analyzed 418 ticks removed from 359 patients during 2014-2021 in Marseille, France, for identification and bacteria detection. Using morphology, molecular methods, or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we identified 197 (47%) Ixodes, 136 (33%) Dermacentor, 67 (16%) Rhipicephalus, 8 (2%) Hyalomma, 6 (1%) Amblyomma, 2 (0.5%) Argas, and 2 (0.5%) Haemaphysalis tick species. We also detected bacterial DNA in 241 (58%) ticks. The most frequent bacterial pathogens were Rickettsia raoultii (17%) and R. slovaca (13%) in Dermacentor ticks, Borrelia spp. (9%) in Ixodes ticks, and R. massiliae (16%) in Rhipicephalus ticks. Among patients who were bitten, 107 had symptoms, and tickborne diseases were diagnosed in 26, including scalp eschar and neck lymphadenopathy after tick bite and Lyme borrelioses. Rapid tick and bacteria identification using a combination of methods can substantially contribute to clinical diagnosis, treatment, and surveillance of tickborne diseases.
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Ouarti B, Fonkou DMM, Houhamdi L, Mediannikov O, Parola P. Lice and lice-borne diseases in humans in Africa: a narrative review. Acta Trop 2022; 237:106709. [PMID: 36198330 DOI: 10.1016/j.actatropica.2022.106709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 01/18/2023]
Abstract
Lice are host-specific insects. Human lice include Pediculus humanus humanus (body lice) which are known to be vectors of serious human bacterial infectious diseases including epidemic typhus, relapsing fever, trench fever and plague; Pediculus humanus capitis (head lice) that frequently affect children; and Pthirus pubis, commonly known as crab lice. In Africa, human infections transmitted by lice remained poorly known and therefore, underestimated, perhaps due to the lack of diagnostic tools and professional knowledge. In this paper we review current knowledge of the microorganisms identified in human lice in the continent of Africa, in order to alert health professionals to the importance of recognising the risk of lice-related diseases.
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Affiliation(s)
- Basma Ouarti
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
| | | | - Linda Houhamdi
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
| | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France; IRD, AP-HM, MEPHI, Aix Marseille University, Marseille, France.
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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Morsli M, Boudet A, Kerharo Q, Stephan R, Salipante F, Dunyach-Remy C, Houhamdi L, Fournier PE, Lavigne JP, Drancourt M. Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France. EBioMedicine 2022; 84:104247. [PMID: 36087524 PMCID: PMC9463524 DOI: 10.1016/j.ebiom.2022.104247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis. METHODS A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software. FINDINGS Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology. INTERPRETATION In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis. FUNDING This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France; IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Université, France
| | - Agathe Boudet
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Quentin Kerharo
- IHU Méditerranée Infection, Marseille, France; Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU, Méditerranée Infection, Marseille, France
| | - Robin Stephan
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Florian Salipante
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France; Service de Biostatistique, Epidémiologie, Santé Publique, Innovation en Méthodologie, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | | | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France; VITROME, IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Jean Philippe Lavigne
- VBIC, INSERM U 1047, Université de Montpellier, France; Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France; IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Université, France; Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU, Méditerranée Infection, Marseille, France.
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Nguyen NN, Houhamdi L, Delorme L, Colson P, Gautret P. Reinfections with Different SARS-CoV-2 Omicron Subvariants, France. Emerg Infect Dis 2022; 28:2341-2343. [PMID: 36150518 PMCID: PMC9622229 DOI: 10.3201/eid2811.221109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe 188 patients in France who were successively infected with different SARS-CoV-2 Omicron subvariants, including BA.1, BA.2, and BA.5. Time between 2 infections was <90 days for 50 (26.6%) patients and <60 days for 28 (14.9%) patients. This finding suggests that definitions for SARS-CoV-2 reinfection require revision.
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Colson P, Fournier P, Delerce J, Million M, Bedotto M, Houhamdi L, Yahi N, Bayette J, Levasseur A, Fantini J, Raoult D, La Scola B. Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France. J Med Virol 2022; 94:3739-3749. [PMID: 35467028 PMCID: PMC9088576 DOI: 10.1002/jmv.27789] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022]
Abstract
Multiple SARS-CoV-2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J_AY.4-Omicron 21K/BA.1 "Deltamicron" recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1163-1421 reads and a mean nucleotide diversity of 0.1%-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening quantitative polymerase chain reaction (qPCR), we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)MarseilleFrance
| | | | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | | | | | - Nouara Yahi
- Aix‐Marseille Université, INSERM UMR S 1072MarseilleFrance
| | | | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
| | | | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
| | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance
- Aix‐Marseille Univ., Institut de Recherche pour le Développement (IRD)Microbes Evolution Phylogeny and Infections (MEPHI)MarseilleFrance
- Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
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Houhamdi L, Fournier PE. Smart apps for self-reporting clinical information. Lancet 2022; 399:1575-1576. [PMID: 35397852 PMCID: PMC8989392 DOI: 10.1016/s0140-6736(22)00453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Linda Houhamdi
- IHU Méditerranée Infection, Marseille, France, 13005; Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Université, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France, 13005.
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France, 13005; Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Université, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France, 13005
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Nguyen NN, Houhamdi L, Hoang VT, Stoupan D, Fournier PE, Raoult D, Colson P, Gautret P. High rate of reinfection with the SARS-CoV-2 Omicron variant. J Infect 2022; 85:174-211. [PMID: 35472367 PMCID: PMC9033627 DOI: 10.1016/j.jinf.2022.04.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Nhu Ngoc Nguyen
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Linda Houhamdi
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Van Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | | | - Pierre-Edouard Fournier
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Gautret
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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12
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Nguyen NN, Houhamdi L, Hoang VT, Delerce J, Delorme L, Colson P, Brouqui P, Fournier PE, Raoult D, Gautret P. SARS-CoV-2 reinfection and COVID-19 severity. Emerg Microbes Infect 2022; 11:894-901. [PMID: 35264078 PMCID: PMC8942490 DOI: 10.1080/22221751.2022.2052358] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 reinfection rate is low. The relative severity of the first and second episodes of infection remains poorly studied. In this study, we aimed at assessing the frequency of SARS-CoV-2 reinfections and comparing the severity of the first and second episodes of infection. We retrospectively included patients with SARS-CoV-2 positive RT-PCR at least 90 days after clinical recovery from a COVID-19 episode and with at least one negative RT-PCR after the first infection. Whole genome sequencing and variant-specific RT-PCR were performed and clinical symptoms and severity of infection were retrospectively documented from medical files. A total of 209 COVID-19 reinfected patients were identified, accounting for 0.4% of positive cases diagnosed from 19 March 2020 to 24 August 2021. Serology was performed in 64 patients, of whom 39 (60.1%) had antibodies against SARS-CoV-2 when sampled at the early stage of their second infection. Only seven patients (3.4%) were infected twice with the same variant. We observed no differences in clinical presentation, hospitalization rate, and transfer to ICU when comparing the two episodes of infections. Our results suggest that the severity of the second episode of COVID-19 is in the same range as that of the first infection, including patients with antibodies.
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Affiliation(s)
- Nhu Ngoc Nguyen
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Linda Houhamdi
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Van Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Jeremy Delerce
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, MEPHI, Aix-Marseille University, Marseille, France
| | - Léa Delorme
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, MEPHI, Aix-Marseille University, Marseille, France
| | - Philippe Brouqui
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, MEPHI, Aix-Marseille University, Marseille, France
| | - Pierre-Edouard Fournier
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, MEPHI, Aix-Marseille University, Marseille, France
| | - Philippe Gautret
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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13
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Colson P, Delerce J, Beye M, Levasseur A, Boschi C, Houhamdi L, Tissot-Dupont H, Yahi N, Million M, La Scola B, Fantini J, Raoult D, Fournier PE. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France. J Med Virol 2022; 94:3421-3430. [PMID: 35243660 PMCID: PMC9088623 DOI: 10.1002/jmv.27695] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
Abstract
The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Mamadou Beye
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Nouara Yahi
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France
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14
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Colson P, Fournier PE, Chaudet H, Delerce J, Giraud-Gatineau A, Houhamdi L, Andrieu C, Brechard L, Bedotto M, Prudent E, Gazin C, Beye M, Burel E, Dudouet P, Tissot-Dupont H, Gautret P, Lagier JC, Million M, Brouqui P, Parola P, Fenollar F, Drancourt M, La Scola B, Levasseur A, Raoult D. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics. Front Microbiol 2022; 12:786233. [PMID: 35197938 PMCID: PMC8859183 DOI: 10.3389/fmicb.2021.786233] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | | | | | | | | | | | | | | | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- *Correspondence: Didier Raoult,
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15
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Hoang VT, Assoumani L, Delerce J, Houhamdi L, Bedotto M, Lagier JC, Million M, Levasseur A, Fournier PE, La Scola B, Raoult D, Gautret P, Colson P. Introduction of the SARS-CoV-2 Beta variant from Comoros into the Marseille geographical area. Travel Med Infect Dis 2022; 46:102277. [PMID: 35158042 PMCID: PMC8837475 DOI: 10.1016/j.tmaid.2022.102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 10/28/2022]
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16
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Houhamdi L, Gautret P, Hoang VT, Fournier P, Colson P, Raoult D. Characteristics of the first 1,119 SARS‐CoV‐2 Omicron variant cases, in Marseille, France, November‐December 2021. J Med Virol 2022; 94:2290-2295. [PMID: 35060146 PMCID: PMC9015264 DOI: 10.1002/jmv.27613] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/10/2022]
Abstract
One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron variant cases have been diagnosed at the Institut Hospitalo‐Universitaire Méditerranée Infection, Marseille, France, between November 28, 2021, and December 31, 2021. Among the 825 patients with known vaccination status, 383 (46.4%) were vaccinated, of whom 91.9% had received at least two doses of the vaccine. Interestingly, 26.3% of cases developed SARS‐CoV‐2 infection within 21 days following the last dose of vaccine suggesting possible early production of anti‐SARS‐CoV‐2 facilitating antibodies. Twenty‐one patients have been hospitalized, one patient required intensive care, and another patient who received a vaccine booster dose died. Significantly low rates of hospitalization, transfer to Intensive Care Unit and death were observed in patients infected with Omicron as compared to those infected with Delta variant of severe acute respiratory syndrome coronavirus 2 during the same period, 26.3% of patients infected with Omicron get infected during the 3 weeks following COVID‐19 vaccination raising the question of facilitating antibodies.
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Affiliation(s)
| | - Philippe Gautret
- IHU‐Méditerranée InfectionMarseilleFrance
- Aix Marseille Univ, IRD, AP‐HM, SSA, VITROMEMarseilleFrance
| | - Van Thuan Hoang
- Thai Binh University of Medicine and PharmacyThai BinhVietnam
| | - Pierre‐Edouard Fournier
- IHU‐Méditerranée InfectionMarseilleFrance
- Aix Marseille Univ, IRD, AP‐HM, SSA, VITROMEMarseilleFrance
| | - Philippe Colson
- IHU‐Méditerranée InfectionMarseilleFrance
- Aix Marseille Univ, IRD, AP‐HM, MEPHIMarseilleFrance
| | - Didier Raoult
- IHU‐Méditerranée InfectionMarseilleFrance
- Aix Marseille Univ, IRD, AP‐HM, MEPHIMarseilleFrance
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17
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Fournier PE, Houhamdi L, Colson P, Cortaredona S, Delorme L, Cassagne C, Lagier JC, Chaudet H, Tissot-Dupont H, Giraud-Gatineau A, Fenollar F, Million M, Raoult D. SARS-CoV-2 Vaccination and Protection Against Clinical Disease: A Retrospective Study, Bouches-du-Rhône District, Southern France, 2021. Front Microbiol 2022; 12:796807. [PMID: 35116013 PMCID: PMC8803903 DOI: 10.3389/fmicb.2021.796807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/15/2021] [Indexed: 11/23/2022] Open
Abstract
From January 18th to August 13th, 2021, 13,804 unvaccinated and 1,156 patients who had received at least one COVID-19 vaccine dose were tested qPCR-positive for SARS-CoV-2 in our center. Among vaccinated patients, 949, 205 and 2 had received a single, two or three vaccine doses, respectively. Most patients (80.3%) had received the Pfizer-BioNTech vaccine. The SARS-CoV-2 variants infecting vaccinated patients varied over time, reflecting those circulating in the Marseille area, with a predominance of the Marseille-4/20A.EU2 variant from weeks 3 to 6, of the Alpha/20I variant from weeks 7 to 25, and of the Delta/21A variant from week 26. SARS-CoV-2 infection was significantly more likely to occur in the first 13 days post-vaccine injection in those who received a single dose (48.9%) than two doses (27.4%, p< 10–3). Among 161 patients considered as fully vaccinated, i.e., >14 days after the completion of the vaccinal scheme (one dose for Johnson and Johnson and two doses for Pfizer/BioNTech, Moderna and Sputnik vaccines), 10 (6.2%) required hospitalization and four (2.5%) died. Risks of complications increased with age in a nonlinear pattern, with a first breakpoint at 54, 33, and 53 years for death, transfer to ICU, and hospitalization, respectively. Among patients infected by the Delta/21A or Alpha/20I variants, partial or complete vaccination exhibited a protective effect with a risk divided by 3.1 for mortality in patients ≥ 55 years, by 2.8 for ICU transfer in patients ≥ 34 years, and by 1.8 for hospitalization in patients ≥ 54 years. Compared to partial vaccination, complete vaccination provided an even stronger protective effect, confirming effectiveness to prevent severe forms of COVID-19.
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Affiliation(s)
- Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
- *Correspondence: Pierre-Edouard Fournier,
| | | | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Sébastien Cortaredona
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Lea Delorme
- IHU Méditerranée Infection, Marseille, France
| | - Carole Cassagne
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
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18
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Boschi C, Aherfi S, Houhamdi L, Colson P, Raoult D, Scola BL. Isolation of 4000 SARS-CoV-2 shows that contagiousness is associated with viral load, not vaccine or symptomatic status. Emerg Microbes Infect 2021; 10:2276-2278. [PMID: 34792434 PMCID: PMC8648030 DOI: 10.1080/22221751.2021.2008776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022]
Abstract
Culture inoculation of 6722 nasopharyngeal samples since February 2020 allowed isolation of 3637 SARS-CoV-2 and confirmed that isolation rate is correlated to viral load, regardless symptomatology or vaccination status. Moreover, the delta variant is associated with higher viral loads and therefore higher rates of viral isolation, explaining its greater contagiousness.
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Affiliation(s)
- Celine Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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19
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Medkour H, Catheland S, Boucraut-Baralon C, Laidoudi Y, Sereme Y, Pingret JL, Million M, Houhamdi L, Levasseur A, Cabassu J, Davoust B. First evidence of human-to-dog transmission of SARS-CoV-2 B.1.160 variant in France. Transbound Emerg Dis 2021; 69:e823-e830. [PMID: 34706153 PMCID: PMC8662256 DOI: 10.1111/tbed.14359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/28/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022]
Abstract
Since the start of the coronavirus disease of 2019 (COVID-19) pandemic, several episodes of human-to-animal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission have been described in different countries. The role of pets, especially domestic dogs, in the COVID-19 epidemiology is highly questionable and needs further investigation. In this study, we report a case of COVID-19 in a French dog living in close contact with its owners who were COVID-19 patients. The dog presented rhinitis and was sampled 1 week after its owners (a man and a woman) were tested positive for COVID-19. The nasal swabs for the dog tested remained positive for SARS-CoV-2 by reverse transcription quantitative real-time PCR (RT-qPCR) 1 month following the first diagnosis. Specific anti-SARS-CoV-2 antibodies were detectable 12 days after the first diagnosis and persisted for at least 5 months as tested using enzyme-linked immunoassay (ELISA) and automated western blotting. The whole-genome sequences from the dog and its owners were 99%-100% identical (with the man and the woman's sequences, respectively) and matched the B.1.160 variant of concern (Marseille-4 variant), the most widespread in France at the time the dog was infected. This study documents the first detection of B.1.160 in pets (a dog) in France, and the first canine genome recovery of the B.1.160 variant of global concern. Moreover, given the enhanced infectivity and transmissibility of the Marseille-4 variant for humans, this case also highlights the risk that pets may potentially play a significant role in SARS-CoV-2 outbreaks and may transmit the infection to humans. We have evidence of human-to-dog transmission of the Marseille-4 variant since the owners were first to be infected. Finally, owners and veterinarians must be vigilent for canine COVID-19 when dogs are presented with respiratory clinical signs.
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Affiliation(s)
- Hacène Medkour
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | | | - Younes Laidoudi
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Youssouf Sereme
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | - Matthieu Million
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Linda Houhamdi
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | - Bernard Davoust
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
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20
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Osman IO, Levasseur A, Brechard L, Abdillahi Hassan I, Salah Abdillahi I, Ali Waberi Z, Delerce J, Bedotto M, Houhamdi L, Fournier PE, Colson P, Aboubaker MH, Raoult D, Devaux CA. Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Front Med (Lausanne) 2021; 8:737602. [PMID: 34540874 PMCID: PMC8440879 DOI: 10.3389/fmed.2021.737602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/05/2021] [Indexed: 01/08/2023] Open
Abstract
Since the start of COVID-19 pandemic the Republic of Djibouti, in the horn of Africa, has experienced two epidemic waves of the virus between April and August 2020 and between February and May 2021. By May 2021, COVID-19 had affected 1.18% of the Djiboutian population and caused 152 deaths. Djibouti hosts several foreign military bases which makes it a potential hot-spot for the introduction of different SARS-CoV-2 strains. We genotyped fifty three viruses that have spread during the two epidemic waves. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19.
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Affiliation(s)
- Ikram Omar Osman
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France.,Laboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, Djibouti
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Ludivine Brechard
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Iman Abdillahi Hassan
- Laboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, Djibouti
| | - Idil Salah Abdillahi
- Laboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, Djibouti
| | - Zeinab Ali Waberi
- Laboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, Djibouti
| | - Jeremy Delerce
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Marielle Bedotto
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | | | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Mohamed Houmed Aboubaker
- Laboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, Djibouti
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France
| | - Christian A Devaux
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
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21
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Gautret P, Houhamdi L, Nguyen NN, Hoang VT, Giraud-Gatineau A, Raoult D. Does SARS-CoV-2 re-infection depend on virus variant? Clin Microbiol Infect 2021; 27:1374-1375. [PMID: 34197931 PMCID: PMC8237371 DOI: 10.1016/j.cmi.2021.06.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Philippe Gautret
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Nhu Ngog Nguyen
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Van Thuan Hoang
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.
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22
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021. [PMID: 34451505 DOI: 10.3390/pathogens10081042.pmid:34451505;pmcid:pmc8401729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | | | | | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
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23
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021; 10:1042. [PMID: 34451505 PMCID: PMC8401729 DOI: 10.3390/pathogens10081042] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Christophe Soumagnac
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Annessi
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Lacoste
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
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24
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Brouqui P, Colson P, Melenotte C, Houhamdi L, Bedotto M, Devaux C, Gautret P, Million M, Parola P, Stoupan D, La Scola B, Lagier JC, Raoult D. COVID-19 re-infection. Eur J Clin Invest 2021; 51:e13537. [PMID: 33675046 PMCID: PMC8250303 DOI: 10.1111/eci.13537] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Philippe Brouqui
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philippe Colson
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Cléa Melenotte
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Linda Houhamdi
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | | | - Christian Devaux
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philipe Gautret
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IRD, APHM, Aix-Marseille University, VITROME, Marseille, France
| | - Matthieu Million
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philippe Parola
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IRD, APHM, Aix-Marseille University, VITROME, Marseille, France
| | | | - Bernard La Scola
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Jean-Christophe Lagier
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Didier Raoult
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
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Bedotto M, Fournier PE, Houhamdi L, Levasseur A, Delerce J, Pinault L, Padane A, Chamieh A, Tissot-Dupont H, Brouqui P, Sokhna C, Azar E, Saile R, Mboup S, Bitam I, Colson P, Raoult D. Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. J Clin Virol 2021; 139:104814. [PMID: 33836314 PMCID: PMC8011323 DOI: 10.1016/j.jcv.2021.104814] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 01/06/2023]
Abstract
Introduction The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. Materials and methods We aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant. Results All 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93 %) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 2018/3960 (51%) patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6 %) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR. Discussion Our in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in about half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.
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Affiliation(s)
- Marielle Bedotto
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Lucile Pinault
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Arrondissement 4 rue 2D1, pôle urbain de Diamniadio, Dakar, Senegal
| | - Amanda Chamieh
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France; Saint George Hospital University Medical Center, University of Balamand, Beirut, Lebanon
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Sokhna
- Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Campus International IRD-UCAD de l'IRD, Dakar, Senegal; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Eid Azar
- Saint George Hospital University Medical Center, University of Balamand, Beirut, Lebanon
| | - Rachid Saile
- Laboratory of Biology and Health, Faculty of Sciences Ben M'sik, Hassan II University of Casablanca, Morocco
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Arrondissement 4 rue 2D1, pôle urbain de Diamniadio, Dakar, Senegal
| | - Idir Bitam
- Ecole supérieure en Sciences de l'aliment et des Industries Agro-Alimentaires, Alger, Algeria
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France.
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Ayyadurai S, Houhamdi L, Lepidi H, Nappez C, Raoult D, Drancourt M. Long-term persistence of virulent Yersinia pestis in soil. Microbiology (Reading) 2008; 154:2865-2871. [PMID: 18757820 DOI: 10.1099/mic.0.2007/016154-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plague is characterized by geographical foci from which it re-emerges after decades of silence, a fact currently explained by enzootic and epizootic cycles between plague-susceptible and plague-resistant rodents. To assess the potential role of soil in plague epidemiology, we experimentally investigated whether Yersinia pestis could persist alive and virulent in soil. Sterilized soil inoculated with virulent Y. pestis biotype Orientalis was regularly sampled for 40 weeks in duplicate. Each sample was observed by acridine orange staining and immunofluorescence using an anti-Y. pestis polyclonal antibody, and DNA was extracted for PCR amplification and sequencing of the Y. pestis ureD, caf1 and pla genes. All samples were inoculated onto selective agar, and samples from soil that had been incubated for 10, 60, 165, 210 and 280 days were also inoculated into each of two BALB/c female mice. The mouse experiment was performed in triplicate. Non-inoculated, sterilized soil samples were used as negative controls. Micro-organisms fluorescing orange and detected by immunofluorescence were identified as Y. pestis in all samples. They were recovered in pure agar cultures for up to 30 weeks but thereafter were contaminated with Pseudomonas spp. Soil that had been inoculated with Y. pestis proved to be fully virulent in mice, which died with Y. pestis septicaemia and multiple organ involvement. Negative control mice showed no signs of disease. These data indicate that Y. pestis biotype Orientalis can remain viable and fully virulent after 40 weeks in soil. This study is a first step on which to base further investigations of a potential telluric reservoir for Y. pestis, which could represent an alternative mechanism for the maintenance of plague foci.
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Affiliation(s)
- Saravanan Ayyadurai
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
| | - Linda Houhamdi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
| | - Hubert Lepidi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
| | - Claude Nappez
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE, CNRS UMR 6236 - IRD 198, Faculté de Médecine, IFR48, Université de la Méditerranée, Marseille, France
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Houhamdi L, Raoult D. Different genes govern Yersinia pestis pathogenicity in Caenorhabditis elegans and human lice. Microb Pathog 2007; 44:435-7. [PMID: 18248948 DOI: 10.1016/j.micpath.2007.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 11/22/2007] [Accepted: 11/29/2007] [Indexed: 11/16/2022]
Abstract
To assess the role of virulence factors identified in Caenorhabditis elegans in the transmission of plague by lice, we infected 100 lice by feeding them on rabbits and made them bacteremic; the rabbits had been intravenously inoculated with 10(9) CFU of six different mutant Yersinia pestis strains of lower pathogenicity for C. elegans, obtained from the KIM5 strain. This strain lacks genes used for biofilm formation. High mortality rates were observed in all lice, which excreted viable bacteria in their feces. Mutants killed rabbits when infected intravenously, but mutants were not transmitted to rabbits by infected lice. We conclude that the genes governing pathogenicity in C. elegans and louse are not identical.
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Affiliation(s)
- Linda Houhamdi
- Unité des Rickettsies, Faculté de Médecine, Institut Fédératif de Recherche 48, Centre National de Recherche Scientifique, Unité Mixte de Recherche 6020, Université de la Méditerranée, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
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Houhamdi L, Lepidi H, Drancourt M, Raoult D. Experimental model to evaluate the human body louse as a vector of plague. J Infect Dis 2006; 194:1589-96. [PMID: 17083045 DOI: 10.1086/508995] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 07/28/2006] [Indexed: 11/03/2022] Open
Abstract
Yersinia pestis has been found in human body lice during plague outbreaks. To evaluate the role that the human body louse plays as a vector of plague, we allowed lice to feed on rabbits made bacteremic by intravenous inoculation of 10(9) colony-forming units of 3 strains of Y. pestis. High mortality rates were observed in all lice 2 and 3 days after infection. The lice remained infected with the strains for their life span and excreted viable organisms in their feces from day 1, although they were unable to lay eggs. The lice infected with 2 virulent strains of Y. pestis transmitted the organisms during feeding to uninfected rabbits, which became septicemic and died of plague (with 1 exception) 1 day later. Infections were transmitted to naive lice that were fed on these rabbits, showing that lice can be vectors of Y. pestis in an experimental model.
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Affiliation(s)
- Linda Houhamdi
- Unite des Rickettsies, Institut Federatif de Recherche 48, Centre National de Recherche Scientifique, Unite Mixte de Recherche 6020, Universite de la Mediterranee, Marseille cedex 5 13385, France
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29
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Rozmajzl PJ, Houhamdi L, Jiang J, Raoult D, Richards AL. Validation of a Rickettsia prowazekii-Specific Quantitative Real-Time PCR Cassette and DNA Extraction Protocols Using Experimentally Infected Lice. Ann N Y Acad Sci 2006; 1078:617-9. [PMID: 17114790 DOI: 10.1196/annals.1374.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The presence of R. prowazekii in lice using R. prowazekii-specific qPCR cassettes showed the changes of the rickettsial burden in the lice post-infection.
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Houhamdi L, Raoult D. Experimental infection of human body lice with Acinetobacter baumannii. Am J Trop Med Hyg 2006; 74:526-31. [PMID: 16606978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
The human body louse is currently recognized as a vector of Rickettsia prowazekii, Borrelia recurrentis, and Bartonella quintana. Previous studies have reported the isolation of Acinetobacter baumannii from the body lice of homeless patients. To study how the body louse acquires A. baumannii, we infected a rabbit by infusing 2 x 10(6) colony-forming units of the louse strain of A. baumannii. Two hundred body lice were infected by feeding on the bacteremic rabbit and compared with 200 uninfected lice and two groups of 200 lice feeding on rabbits infected either with another strain of A. baumannii or A. lwoffii. Each louse group received maintenance feedings once a day on another seronegative rabbit. Body lice that fed on rabbits infused with each Acinetobacter species demonstrated a generalized infection. The body lice did not transmit their infection to the nurse rabbit by bite while feeding or to their progeny (eggs and larvae). The lice excreted living Acinetobacter species within their feces. Only the louse strain of A. baumannii was pathogenic for the body louse. An increased mortality rate was observed between the second and third days post-infection; however, they remained infected for their lifespan.
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Affiliation(s)
- Linda Houhamdi
- Unité des Rickettsies, Institut Fédératif de Recherche 48, Centre National de Recherche Scientifique, Marseille, France
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Abstract
The classic epidemiological model of plague is an infection of rodents that is transmitted to human beings by rodent ectoparasites. This model fits with observations of sporadic and limited outbreaks, but hardly explains the persistence of plague foci for millennia or the epidemiological features drawn from the descriptions of historical pandemics. A comprehensive review of the published data, including scientific papers published in France between 1920 and 1940, allows the completion of the epidemiological chain by introducing soil as a reservoir, burrowing rodents as a first link, and human ectoparasites as the main driving force for pandemics. Modern studies are needed to confirm the validity of this controversial model and to assess the relative contribution of each link in the various epidemiological presentations of plague. If confirmed, these data should be taken into account to update public-health policies and bioterrorism risk management, particularly among ectoparasite-infested people.
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Affiliation(s)
- Michel Drancourt
- Unité des Rickettsies CNRS UMR 6020, IRF 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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32
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Abstract
The classic epidemiological model of plague is an infection of rodents that is transmitted to human beings by rodent ectoparasites. This model fits with observations of sporadic and limited outbreaks, but hardly explains the persistence of plague foci for millennia or the epidemiological features drawn from the descriptions of historical pandemics. A comprehensive review of the published data, including scientific papers published in France between 1920 and 1940, allows the completion of the epidemiological chain by introducing soil as a reservoir, burrowing rodents as a first link, and human ectoparasites as the main driving force for pandemics. Modern studies are needed to confirm the validity of this controversial model and to assess the relative contribution of each link in the various epidemiological presentations of plague. If confirmed, these data should be taken into account to update public-health policies and bioterrorism risk management, particularly among ectoparasite-infested people.
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Affiliation(s)
- Michel Drancourt
- Unité des Rickettsies CNRS UMR 6020, IRF 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Houhamdi L, Raoult D. Experimentally infected human body lice (pediculus humanus humanus) as vectors of Rickettsia rickettsii and Rickettsia conorii in a rabbit model. Am J Trop Med Hyg 2006; 74:521-5. [PMID: 16606977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
The human body louse, the natural vector of Rickettsia prowazekii, is able to experimentally transmit the normally flea-borne rickettsia R. typhi, suggesting that the relationships between the body louse and rickettsiae are not specific. We used our experimental infection model to test the ability of body lice to transmit two prevalent tick-borne rickettsiae. Each of two rabbits was made bacteremic by injecting intravenously 2 x 10(6) plaque-forming units of either R. rickettsii or R. conorii. Four hundred body lice were infected by feeding on the bacteremic rabbit and were compared with 400 uninfected lice. Each louse group was fed once a day on a separate seronegative rabbit. The survival of infected lice was not different from that of uninfected controls. Lice remained infected for their lifespan, excreted R. rickettsii and R. conorii in their feces, but did not transmit the infection to their progeny. The nurse rabbit of uninfected lice remained asymptomatic and seronegative. Those rabbits used to feed infected lice developed bacteremia and seroconverted. Although the body louse is not a known vector of spotted fevers, it was able in our study to acquire, maintain, and transmit both R. rickettsii and R. conorii.
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Affiliation(s)
- Linda Houhamdi
- Unité des Rickettsies, Institut Fédératif de Recherche 48, Centre National de Recherche Scientifique, Marseille, France
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Raoult D, Dutour O, Houhamdi L, Jankauskas R, Fournier PE, Ardagna Y, Drancourt M, Signoli M, La VD, Macia Y, Aboudharam G. Evidence for louse-transmitted diseases in soldiers of Napoleon's Grand Army in Vilnius. J Infect Dis 2005; 193:112-20. [PMID: 16323139 DOI: 10.1086/498534] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Accepted: 07/29/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Many soldiers in Napoleon's Grand Army died of infectious diseases during its retreat from Russia. Because soldiers were commonly infested with body lice, it has been speculated that louse-borne infectious diseases, such as epidemic typhus (caused by Rickettsia prowazekii), were common. METHODS We investigated this possibility during recent excavations of a mass grave of Napoleon's soldiers in Vilnius, Lithuania. Segments of 5 body lice, identified morphologically and by polymerase chain reaction (PCR) amplification and sequencing, were found in earth from the grave that also contained fragments of soldiers' uniforms. RESULTS DNA of Bartonella quintana (the agent of trench fever) was identified by PCR and sequencing in 3 of the lice. Similarly, PCR and sequencing of dental pulp from the remains of 35 soldiers revealed DNA of B. quintana in 7 soldiers and DNA of R. prowazekii in 3 other soldiers. CONCLUSIONS Our results show that louse-borne infectious diseases affected nearly one-third of Napoleon's soldiers buried in Vilnius and indicate that these diseases might have been a major factor in the French retreat from Russia.
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Affiliation(s)
- Didier Raoult
- Unite des Rickettsies, Centre National de la Recherche Scientifique (CNRS) Unite Mixte de Recherche (UMR) 6020, Universite de la Mediterranee, Faculte de Medecine, Marseille, France.
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Houhamdi L, Raoult D. Excretion of living Borrelia recurrentis in feces of infected human body lice. J Infect Dis 2005; 191:1898-906. [PMID: 15871124 DOI: 10.1086/429920] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Accepted: 12/17/2004] [Indexed: 11/03/2022] Open
Abstract
Louse-borne relapsing fever (LBRF), caused by Borrelia recurrentis, is 1 of the most dangerous arthropod-borne diseases. Infection is thought to occur through louse crushing. Lice feces have not been shown to contain living borreliae. We infected 800 body lice by feeding them on a rabbit made spirochetemic by the injection of 2 x 106 borreliae. The life span of infected lice was not shortened. Once infected, lice remained infected for life but did not transmit borreliae to their progeny or to nurse rabbits. B. recurrentis infection was observed throughout lice and spread into hemolymph on day 5 after infection. We describe 2 unprecedented phenomena. In hemolymph, B. recurrentis formed clumps of aggregated borreliae. Using immunofluorescence assay, transmission electron microscopy, and culture, we detected borreliae excreted in lice feces beginning on day 14 after infection. We conclude that, similar to epidemic typhus and trench fever, transmission of LBRF may be caused by lice feces.
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Affiliation(s)
- Linda Houhamdi
- Unite des Rickettsies, Institut Federatif de Recherche 48, Centre National de Recherche Scientifique, Unite Mixte de Recherche 6020, Universite de la Mediterranee, Faculte de Medecine, Marseille, France
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Houhamdi L, Parola P, Raoult D. [Lice and lice-borne diseases in humans]. Med Trop (Mars) 2005; 65:13-23. [PMID: 15903070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Among the three lice which parasite the human being, the human body louse, Pediculus humanus humanus, is a vector of infectious diseases. It lives and multiplies in clothes and human infestation is associated with cold weather and a lack of hygiene. Three pathogenic bacteria are transmitted by the body louse: 1) Rickettsia prowazekii, the agent of epidemic typhus of which the most recent outbreak (and the largest since World War II) was observed during the civil war in Burundi; 2) Borrelia recurrentis, the agent of relapsing fever, historically responsible of massive outbreaks in Eurasia and Africa, which prevails currently in Ethiopia and neighboring countries; 3) Bartonella quintana, the agent of trench fever, bacillary angiomatosis, chronic bacteremia, endocarditis, and lymphadenopathy. Body louse infestation, associated with a decline in social and hygienic conditions provoked by civil unrest and economic instability, is reemergent worldwide. Recently, a forth human pathogen, Acinetobacter baumannii, has been associated to the body louse.
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Affiliation(s)
- L Houhamdi
- L 'Unité des Rickettsies, CNRS UMR 6020, Marseille, France
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Abstract
Rickettsia typhi and R. felis are flea-transmitted human pathogenic rickettsial species. To investigate the distributional dynamics of these rickettsiae we designed a micro-immunofluorescence assay (MIF) using species-specific monoclonal antibodies (MAbs) applied to flea cryosections. Our assay was performed in less than 3 h and its applicability was demonstrated by the detection of R. typhi in 50 artificially infected human body lice but in none of 50 uninfected lice. With MIF, we identified 31 positive among 32 fleas proven with PCR to be naturally infected with R. felis; and 7 positive among 32 fleas proven with PCR to be naturally infected with R. typhi. No cross-detection was observed with both MAbs. Fresh R. felis-infected fleas were significantly more MIF-positive than long conserved R. typhi-infected fleas (31/32 vs. 7/32, P < 0.01). This discrepancy may be linked to degradation of antigens by long-term freezing. For R. typhi-infected fleas, our assay was significantly more efficient when applied to fleas in early stages of infection (less than 15 days) by comparison with fleas frozen more than 20 days after infection (7/15 vs. 0/17, P = 0.01). This difference may be related to an antigenic modification caused by selection pressure in the vector and host process. The sensitivity of the described method did not exceed 47% (7/15) for R. typhi but, in contrast, was 97% for R. felis. Thus, our method appears to be useful for surveillance in R. felis infections, but requires further studies for the detection of R. typhi.
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Affiliation(s)
- R Fang
- Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de Méedecine, 13385 Marseilles, France
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Abstract
Murine (endemic) typhus caused by Rickettsia typhi, one of the most widely distributed arthropod-borne diseases, is transmitted to humans mainly by the oriental rat flea. The human body louse, Pediculus humanus corporis, has been suspected to have a role in the transmission of R. typhi to humans. To evaluate the potential role of Pediculus humanus corporis as a vector of murine typhus, we used R. typhi in an experimental model of human body louse infection previously used with R. prowazekii. A rabbit was made bacteremic by inoculating it with 2 x 10(6) plaque-forming units of R. typhi; it remained bacteremic for at least 59 hours. Two hundred body lice infected by feeding on the bacteremic rabbit were compared to 200 uninfected control lice. Each louse population was fed once a day on the abdomen of a seronegative rabbit. On day 8 post-infection, as a result of disruption of the gut cells and leakage of the blood meal into the hemolymph, four infected lice became bright red and died within four hours. The life span of infected lice was 20 days less than that of the controls. Infected lice did not transmit R. typhi to their progeny (eggs and larvae) as demonstrated by PCR amplification and cell culture. With an immunofluorescence assay, R. typhi was detected in feces from day 7 post-infection, and the organism remained viable in feces for up to 80 days as demonstrated by cell culture. From the 21st day post-infection, the rabbit used to feed the R. typhi-infected lice developed an immunoglobulin response with a titer of 1:50 increasing to 1:200 at the 42nd day post-infection. It showed no clinical signs of infection. The rabbit that was used to feed uninfected lice remained seronegative. Although body lice are not clearly identified vectors of R. typhi, it seems that under certain circumstances they could transmit R. typhi.
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Affiliation(s)
- Linda Houhamdi
- Unité des rickettsies, IFR 48 CNRS UMR 6020, Université de la Méditerranée Faculté de Médecine, 13385 Marseilles cedex 5, France
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Houhamdi L, Fournier PE, Fang R, Lepidi H, Raoult D. An experimental model of human body louse infection with Rickettsia prowazekii. J Infect Dis 2002; 186:1639-46. [PMID: 12447741 DOI: 10.1086/345373] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2002] [Revised: 08/15/2002] [Indexed: 11/03/2022] Open
Abstract
Rickettsia prowazekii is transmitted to humans by the body louse. A new experimental model of body louse infection with R. prowazekii is reported here. Eight hundred human lice were infected by feeding on a rabbit that was made bacteremic by injecting 2x106 plaque-forming units of R. prowazekii. The bacterium invaded the stomach cells and was released in feces, in which it was detected 5 days after infection. At day 6 after infection, as a result of the cell burst and the spread of erythrocytes in the hemolymph, the louse became bright red and died within 4 h. The life span of infected lice was shortened by 20-23 days, compared with that of uninfected control lice. Infected lice did not transmit R. prowazekii to their progeny. Through cell culture, rickettsiae were cultivated from fecal samples up to 10 days after their emission. The administration of doxycycline to the rabbit during louse feeding did not cure lice from R. prowazekii infection.
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Affiliation(s)
- Linda Houhamdi
- Unité des Rickettsies, Institut Fédératif de Recheche 48, Centre National de la Recherche Scientifique, Université de la Méditerranée, Marseille, France
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Abstract
In order to identify Rickettsia prowazekii in lice, we developed a panel of 29 representative monoclonal antibodies selected from 187 positive hybridomas made by fusing splenocytes of immunized mice with SP2/0-Ag14 myeloma cells. Immunoblotting revealed that 15 monoclonal antibodies reacted with the lipopolysaccharide-like (LPS-L) antigen and 14 reacted with the epitopes of a 120-kDa protein. Only typhus group rickettsiae reacted with the monoclonal antibodies against LPS-L. R. felis, a recently identified rickettsial species, did not react with these monoclonal antibodies, confirming that it is not antigenically related to the typhus group. Monoclonal antibodies against the 120-kDa protein were highly specific for R. prowazekii. We successfully applied a selected monoclonal antibody against the 120-kDa protein to detect by immunofluorescence assay R. prowazekii in smears from 56 wild and laboratory lice, as well as in 10 samples of louse feces infected or not infected with the organism. We have developed a simple, practical, and specific diagnostic assay for clinical specimens and large-scale epidemiological surveys with a sensitivity of 91%. These monoclonal antibodies could be added to the rickettsial diagnostic panel and be used to differentiate R. prowazekii from other rickettsial species.
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Affiliation(s)
- Rong Fang
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculty of Medicine, 13385 Marseille, France
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