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Hide M, Michel G, Legueult K, Pin R, Leonard S, Simon L, Bañuls AL, Delaunay P, Marty P, Pomares C. Asymptomatic Leishmania infantum infection in dogs and dog owners in an endemic area in southeast France. Parasite 2024; 31:16. [PMID: 38530209 DOI: 10.1051/parasite/2024019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
The prevalence of asymptomatic leishmaniasis in dogs and their owners in the main endemic areas of France has not been studied to date. The objective of this study was to quantify asymptomatic Leishmania infantum infection in southeast France in healthy people and their dogs using molecular and serological screening techniques. We examined the presence of parasitic DNA using specific PCR targeting kinetoplast DNA (kDNA) and specific antibodies by serology (ELISA for dogs and Western blot for humans) among immunocompetent residents and their dogs in the Alpes-Maritimes. Results from 343 humans and 607 dogs were included. 46.9% (n = 161/343) of humans and 18.3% (n = 111/607) of dogs were PCR positive; 40.2% of humans (n = 138/343) and 9.9% of dogs (n = 60/607) were serology positive. Altogether, 66.2% of humans (n = 227) and 25.7% of dogs (n = 156) had positive serologies and/or positive PCR test results. Short-haired dogs were more frequently infected (71.8%, n = 112) than long-haired dogs (12.2%, n = 19) (p = 0.043). Dogs seemed to be more susceptible to asymptomatic infection according to their breed types (higher infection rates in scenthounds, gun dogs and herding dogs) (p = 0.04). The highest proportion of dogs and human asymptomatic infections was found in the Vence Region, corresponding to 28.2% (n = 20/71) of dogs and 70.5% (n = 31/44) of humans (4.5/100,000 people). In conclusion, the percentage of infections in asymptomatic humans is higher than in asymptomatic dogs in the studied endemic area. It is questionable whether asymptomatic infection in humans constitutes a risk factor for dogs.
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Affiliation(s)
- Mallorie Hide
- MIVEGEC, Université de Montpellier, IRD, CNRS, 911 av Agropolis, 34090, Montpellier, France
| | - Gregory Michel
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, 151 route Saint Antoine de Ginestière, BP 2 3194 06204, Nice, France
| | - Kevin Legueult
- Département de Santé Publique, UR2CA, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, 151, route de Saint Antoine de Ginestière, CS 23079 06202, Nice, France
| | - Raphaelle Pin
- Laboratoire Vétérinaire Départemental, 105 route des Chappes, BP 107 06902, Sophia-Antipolis, France
| | - Susana Leonard
- MIVEGEC, Université de Montpellier, IRD, CNRS, 911 av Agropolis, 34090, Montpellier, France
| | - Loïc Simon
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, 151 route Saint Antoine de Ginestière, BP 2 3194 06204, Nice, France - Service de Parasitologie Mycologie, CHU Nice, 151, route de Saint Antoine de Ginestière, CS 23079 06202, Nice, France
| | - Anne-Laure Bañuls
- MIVEGEC, Université de Montpellier, IRD, CNRS, 911 av Agropolis, 34090, Montpellier, France
| | - Pascal Delaunay
- Service de Parasitologie Mycologie, CHU Nice, 151, route de Saint Antoine de Ginestière, CS 23079 06202, Nice, France
| | - Pierre Marty
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, 151 route Saint Antoine de Ginestière, BP 2 3194 06204, Nice, France - Service de Parasitologie Mycologie, CHU Nice, 151, route de Saint Antoine de Ginestière, CS 23079 06202, Nice, France
| | - Christelle Pomares
- Centre Méditerranéen de Médecine Moléculaire (C3M), U1065, Université Côte d'Azur, Inserm, 151 route Saint Antoine de Ginestière, BP 2 3194 06204, Nice, France - Service de Parasitologie Mycologie, CHU Nice, 151, route de Saint Antoine de Ginestière, CS 23079 06202, Nice, France
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Huy NQ, Linh NC, Son NT, Ngoc DB, Tam TTT, Hang LTT, Thuyet BT, Song LH, Van Quyen D, Hayer J, Bañuls AL, Sy BT. Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalized for stroke. J Glob Antimicrob Resist 2024:S2213-7165(24)00036-5. [PMID: 38408562 DOI: 10.1016/j.jgar.2024.02.009] [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: 09/16/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
OBJECTIVES Burkholderia dolosa is a clinically important opportunistic pathogen in inpatients. Here we characterized an extensively drug-resistant and hypervirulent B. dolosa isolate from a patient hospitalized for stroke. METHODS Resistance to 41 antibiotics was tested with the agar disc diffusion, minimum inhibitory concentration, or broth microdilution method. The complete genome was assembled using short-reads and long-reads and the hybrid de novo assembly method. Allelic profiles obtained by multilocus sequence typing were analyzed using the PubMLST database. Antibiotic-resistance and virulence genes were predicted in silico using public databases and the "baargin" workflow. B. dolosa N149 phylogenetic relationships with all available B. dolosa strains and Burkholderia cepacia complex strains were analyzed using the pangenome obtained with Roary. RESULTS B. dolosa N149 displayed extensive resistance to 31 antibiotics and intermediate resistance to 4 antibiotics. The complete genome included three circular chromosomes (6,338,630 bp in total) and one plasmid (167,591 bp). Genotypic analysis revealed various gene clusters (acr, amr, amp, emr, ade, bla and tet) associated with resistance to 35 antibiotic classes. The major intrinsic resistance mechanisms were multidrug efflux pump alterations, inactivation and reduced permeability of targeted antibiotics. Moreover, 91 virulence genes (encoding proteins involved in adherence, formation of capsule, biofilm and colony, motility, phagocytosis inhibition, secretion systems, protease secretion, transmission and quorum sensing) were identified. B. dolosa N149 was assigned to a novel sequence type (ST2237) and formed a mono-phylogenetic clade separated from other B. dolosa strains. CONCLUSION This study provided insights into the antimicrobial resistance and virulence mechanisms of B. dolosa.
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Affiliation(s)
- Nguyen Quang Huy
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.
| | - Nguyen Cam Linh
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Nguyen Thai Son
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Do Bich Ngoc
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Tran Thi Thanh Tam
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Le Thi Thu Hang
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Bui Thanh Thuyet
- Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Le Huu Song
- Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Dong Van Quyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Juliette Hayer
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam; UMR MIVEGEC (University of Montpellier- IRD-CNRS), Montpellier, France
| | - Anne-Laure Bañuls
- LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam; UMR MIVEGEC (University of Montpellier- IRD-CNRS), Montpellier, France
| | - Bui Tien Sy
- Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research, Hanoi, Vietnam.
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Mohamed HS, Galal L, Hayer J, Benavides JA, Bañuls AL, Dupont C, Conquet G, Carrière C, Dumont Y, Didelot MN, Michon AL, Jean-Pierre H, Aboubaker MH, Godreuil S. Genomic epidemiology of carbapenemase-producing Gram-negative bacteria at the human-animal-environment interface in Djibouti city, Djibouti. Sci Total Environ 2023; 905:167160. [PMID: 37730061 DOI: 10.1016/j.scitotenv.2023.167160] [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] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The emergence of carbapenem resistance is a major public health threat in sub-Saharan Africa but remains poorly understood, particularly at the human-animal-environment interface. This study provides the first One Health-based study on the epidemiology of Carbapenemase-Producing Gram-Negative Bacteria (CP-GNB) in Djibouti City, Djibouti, East Africa. In total, 800 community urine samples and 500 hospital specimens from humans, 270 livestock fecal samples, 60 fish samples, and 20 water samples were collected and tested for carbapenem resistance. The overall estimated CP-GNB prevalence was 1.9 % (32/1650 samples) and specifically concerned 0.3 % of community urine samples, 2.8 % of clinical specimens, 2.6 % of livestock fecal samples, 11.7 % of fish samples, and 10 % of water samples. The 32 CP-GNB included 19 Escherichia coli, seven Acinetobacter baumannii, five Klebsiella pneumoniae, and one Proteus mirabilis isolate. Short-read (Illumina) and long-read (Nanopore) genome sequencing revealed that carbapenem resistance was mainly associated with chromosomal carriage of blaNDM-1, blaOXA-23, blaOXA-48, blaOXA-66, and blaOXA-69 in A. baumannii, and with plasmid carriage in Enterobacterales (blaNDM-1 and blaOXA-181 in E. coli, blaNDM-1, blaNDM-5 and blaOXA-48 in K. pneumoniae, and blaNDM-1 in P. mirabilis). Moreover, 17/32 CP-GNB isolates belonged to three epidemic clones: (1) A. baumannii sequence type (ST) 1697,2535 that showed a distribution pattern consistent with intra- and inter-hospital dissemination; (2) E. coli ST10 that circulated at the human-animal-environment interface; and (3) K. pneumoniae ST147 that circulated at the human-environment interface. Horizontal exchanges probably contributed to carbapenem resistance dissemination in the city, especially the blaOXA-181-carrying ColKP3-IncX3 hybrid plasmid that was found in E. coli isolates belonging to different STs. Our study highlights that despite a relatively low CP-GNB prevalence in Djibouti City, plasmids harboring carbapenem resistance circulate in humans, animals and environment. Our findings stress the need to implement preventive and control measures for reducing the circulation of this potentially emerging public health threat.
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Affiliation(s)
- Hasna Saïd Mohamed
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Hôpital Général Peltier de Djibouti, Djibouti ville, Djibouti; Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti
| | - Lokman Galal
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.
| | - Juliette Hayer
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Julio A Benavides
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Doctorado en Medicina de la Conservación y Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
| | - Anne-Laure Bañuls
- UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; LMI DRISA, Montpellier, France
| | - Chloé Dupont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Guilhem Conquet
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Christian Carrière
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Marie-Noëlle Didelot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Anne-Laure Michon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Mohamed Houmed Aboubaker
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City, Djibouti; Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti City 696, Djibouti
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; UMR MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France; Jeune Equipe Associée à l'IRD (JEAI), FASORAM, Montpellier, France
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Kniha E, Dvořák V, Koblmüller S, Prudhomme J, Ivović V, Hoxha I, Oerther S, Heitmann A, Lühken R, Bañuls AL, Sereno D, Michelutti A, Toniolo F, Alarcón-Elbal PM, Bravo-Barriga D, González MA, Lucientes J, Colella V, Otranto D, Bezerra-Santos MA, Kunz G, Obwaller AG, Depaquit J, Alić A, Kasap OE, Alten B, Omeragic J, Volf P, Walochnik J, Sebestyén V, Trájer AJ. Reconstructing the post-glacial spread of the sand fly Phlebotomus mascittii Grassi, 1908 (Diptera: Psychodidae) in Europe. Commun Biol 2023; 6:1244. [PMID: 38066195 PMCID: PMC10709326 DOI: 10.1038/s42003-023-05616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Phlebotomine sand flies (Diptera: Phlebotominae) are the principal vectors of Leishmania spp. (Kinetoplastida: Trypanosomatidae). In Central Europe, Phlebotomus mascittii is the predominant species, but largely understudied. To better understand factors driving its current distribution, we infer patterns of genetic diversity by testing for signals of population expansion based on two mitochondrial genes and model current and past climate and habitat suitability for seven post-glacial maximum periods, taking 19 climatic variables into account. Consequently, we elucidate their connections by environmental-geographical network analysis. Most analyzed populations share a main haplotype tracing back to a single glacial maximum refuge area on the Mediterranean coasts of South France, which is supported by network analysis. The rapid range expansion of Ph. mascittii likely started in the early mid-Holocene epoch until today and its spread possibly followed two routes. The first one was through northern France to Germany and then Belgium, and the second across the Ligurian coast through present-day Slovenia to Austria, toward the northern Balkans. Here we present a combined approach to reveal glacial refugia and post-glacial spread of Ph. mascittii and observed discrepancies between the modelled and the current known distribution might reveal yet overlooked populations and potential further spread.
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Affiliation(s)
- Edwin Kniha
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Vít Dvořák
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Jorian Prudhomme
- UMR MIVEGEC (Université de Montpellier-IRD-CNRS), Institute of Research for Development, Montpellier, France
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Vladimir Ivović
- Department of Biodiversity, FAMNIT, University of Primorska, Koper-Capodistria, Slovenia
| | - Ina Hoxha
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sandra Oerther
- Institute of Global Health, Heidelberg University, Heidelberg, Germany
- German Mosquito Control Association (KABS), Speyer, Germany
- Institute for Dipterology (IfD), Speyer, Germany
| | - Anna Heitmann
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Renke Lühken
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Research Group Vector Control, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anne-Laure Bañuls
- UMR MIVEGEC (Université de Montpellier-IRD-CNRS), Institute of Research for Development, Montpellier, France
| | - Denis Sereno
- UMR MIVEGEC (Université de Montpellier-IRD-CNRS), Institute of Research for Development, Montpellier, France
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP, Parasite Infectiology and Public Health Research group. IRD, CIRAD, Montpellier, France
| | - Alice Michelutti
- Laboratory of Parasitology, Micology and Medical Entomology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Federica Toniolo
- Laboratory of Parasitology, Micology and Medical Entomology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Pedro M Alarcón-Elbal
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos (PASAPTA), Facultad de Veterinaria, Universidad CEU Cardenal Herrera, Valencia, Spain
- Laboratorio de investigación de Entomología, Departamento de Zoología, Facultad de Ciencias Biológicas, Bloque B, Universidad de Valencia, Valencia, Spain
| | - Daniel Bravo-Barriga
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonosis and Emerging Diseases (ENZOEM), University of Cordoba, Cordoba, Spain
| | - Mikel A González
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
- Applied Zoology and Animal Conservation Group, University of the Balearic Islands (UIB), Palma de Mallorca, Spain
| | - Javier Lucientes
- Animal Health Department, The AgriFood Institute of Aragon (IA2), School of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Vito Colella
- Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Bari, Italy
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran
| | | | - Gernot Kunz
- Institute of Biology, University of Graz, Graz, Austria
| | - Adelheid G Obwaller
- Division of Science, Research and Development, Federal Ministry of Defence, Vienna, Austria
| | - Jerome Depaquit
- Université de Reims Champagne Ardenne, ESCAPE EA7510, USC ANSES VECPAR, SFR Cap Santé, UFR de Pharmacie, Reims, France
| | - Amer Alić
- Department of Clinical Sciences of Veterinary Medicine, Faculty of Veterinary Medicine, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Ozge Erisoz Kasap
- Department of Biology, Ecology Section, Faculty of Science, VERG Laboratories, Hacettepe University, Ankara, Turkey
| | - Bulent Alten
- Department of Biology, Ecology Section, Faculty of Science, VERG Laboratories, Hacettepe University, Ankara, Turkey
| | - Jasmin Omeragic
- Department of Pathobiology and Epidemiology, Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Viktor Sebestyén
- University of Pannonia, Sustainability Solutions Research Lab, Veszprém, Hungary
| | - Attila J Trájer
- University of Pannonia, Sustainability Solutions Research Lab, Veszprém, Hungary.
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Nguyen QH, Le TTH, Nguyen ST, Nguyen KOT, Quyen DV, Hayer J, Bañuls AL, Tran TTT. Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients. Front Microbiol 2023; 14:1094119. [PMID: 37323902 PMCID: PMC10265513 DOI: 10.3389/fmicb.2023.1094119] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates. Methods The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination. Results The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 β-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the β-lactamase gene clusters in plasmid contigs that carried the same AMR genes. Discussion Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.
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Affiliation(s)
- Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi Thu Hang Le
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Son Thai Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Kieu-Oanh Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Dong Van Quyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Juliette Hayer
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- UMR MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Anne-Laure Bañuls
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- UMR MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Tam Thi Thanh Tran
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
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6
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Ha HTA, Nguyen PTL, Hung TTM, Tuan LA, Thuy BT, Lien THM, Thai PD, Thanh NH, Bich VTN, Anh TH, Hanh NTH, Minh NT, Thanh DP, Mai SNT, The HC, Trung NV, Thu NH, Duong TN, Anh DD, Ngoc PT, Bañuls AL, Choisy M, van Doorn HR, Suzuki M, Hoang TH. Prevalence and Associated Factors of optrA-Positive- Enterococcus faecalis in Different Reservoirs around Farms in Vietnam. Antibiotics (Basel) 2023; 12:954. [PMID: 37370273 DOI: 10.3390/antibiotics12060954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Linezolid is an antibiotic of last resort for the treatment of infections caused by Gram-positive bacteria, including vancomycin-resistant enterococci. Enterococcus faecalis, a member of enterococci, is a significant pathogen in nosocomial infections. E. faecalis resistance to linezolid is frequently related to the presence of optrA, which is often co-carried with fex, phenicol exporter genes, and erm genes encoding macrolide resistance. Therefore, the common use of antibiotics in veterinary might promote the occurrence of optrA in livestock settings. This is a cross-sectional study aiming to investigate the prevalence of optrA positive E. faecalis (OPEfs) in 6 reservoirs in farms in Ha Nam province, Vietnam, and its associated factors and to explore genetic relationships of OPEfs isolates. Among 639 collected samples, the prevalence of OPEfs was highest in flies, 46.8% (51/109), followed by chickens 37.3% (72/193), dogs 33.3% (17/51), humans 18.7% (26/139), wastewater 16.4% (11/67) and pigs 11.3%, (14/80). The total feeding area and total livestock unit of the farm were associated with the presence of OPEfs in chickens, flies, and wastewater. Among 186 OPEfs strains, 86% were resistant to linezolid. The presence of optrA was also related to the resistant phenotype against linezolid and levofloxacin of E. faecalis isolates. Close genotypic relationships identified by Pulsed Field Gel Electrophoresis between OPEfs isolates recovered from flies and other reservoirs including chickens, pigs, dogs, and wastewater suggested the role of flies in the transmission of antibiotic-resistant pathogens. These results provided warnings of linezolid resistance although it is not used in livestock.
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Affiliation(s)
- Hoang Thi An Ha
- Hanoi Medical University, Hanoi 100000, Vietnam
- Department of Microbiology, Vinh Medical University, Vinh 431000, Vietnam
| | | | - Tran Thi Mai Hung
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Le Anh Tuan
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Bui Thanh Thuy
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | | | - Pham Duy Thai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Nguyen Ha Thanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | | | | | - Ngo Thi Hong Hanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Nguyen Thi Minh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam
| | - Si-Nguyen T Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Vu Trung
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | | | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
| | - Pham Thi Ngoc
- National Institute of Veterinary Research, Hanoi 100000, Vietnam
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Centre IRD, 34394 Montpellier, France
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi 100000, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo 162-0052, Japan
| | - Tran Huy Hoang
- Hanoi Medical University, Hanoi 100000, Vietnam
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam
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7
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Laroche L, Ayhan N, Charrel R, Bañuls AL, Prudhomme J. Persistence of Toscana virus in sugar and blood meals of phlebotomine sand flies: epidemiological and experimental consequences. Sci Rep 2023; 13:5608. [PMID: 37019992 PMCID: PMC10076283 DOI: 10.1038/s41598-023-32431-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/27/2023] [Indexed: 04/07/2023] Open
Abstract
Many virological studies have tested the persistence of enveloped RNA viruses in various environmental and laboratory conditions and shown their short-term persistence. In this article, we analyzed Toscana virus (TOSV) infectivity, a pathogenic sandfly-borne phlebovirus, in two different conditions: in the sugar meal and blood meal of sand flies. Our results showed that TOSV RNA was detectable up to 15 days in sugar solution at 26 °C and up to 6 h in blood at 37 °C. Moreover, TOSV remains infective for 7 days in sugar solution and for minimum 6 h in rabbit blood. TOSV has shown persistent infectivity/viability under different conditions, which may have important epidemiological consequences. These results strengthen new hypotheses about the TOSV natural cycle, such as the possibility of horizontal transmission between sand flies through infected sugar meal.
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Affiliation(s)
- Lison Laroche
- UMR MIVEGEC, Université de Montpellier - IRD 224 - CNRS 5290, 911 Avenue Agropolis, 34394, Montpellier, France.
| | - Nazli Ayhan
- UVE, Aix Marseille Université - IRD 190 - Inserm 1207 - AP-HM Hôpitaux Universitaires de Marseille, Marseille, France
| | - Rémi Charrel
- UVE, Aix Marseille Université - IRD 190 - Inserm 1207 - AP-HM Hôpitaux Universitaires de Marseille, Marseille, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC, Université de Montpellier - IRD 224 - CNRS 5290, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Jorian Prudhomme
- UMR MIVEGEC, Université de Montpellier - IRD 224 - CNRS 5290, 911 Avenue Agropolis, 34394, Montpellier, France
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
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8
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Sawadogo Y, Galal L, Belarbi E, Zongo A, Schubert G, Leendertz F, Kanteh A, Sesay AK, Erhart A, Bañuls AL, Tarnagda Z, Godreuil S, Tinto H, Ouedraogo AS. Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa. Viruses 2022; 14:v14122788. [PMID: 36560792 PMCID: PMC9782145 DOI: 10.3390/v14122788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. METHODS Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. RESULTS The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. CONCLUSIONS This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.
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Affiliation(s)
- Yacouba Sawadogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
| | - Lokman Galal
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
| | | | - Arsène Zongo
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
| | | | | | - Abdoulie Kanteh
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Abdul Karim Sesay
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Annette Erhart
- Disease Control and Elimination Theme, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Anne-Laure Bañuls
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Zékiba Tarnagda
- Laboratoire National de Référence-Grippe (LNR-G), Institut de Recherche en Sciences de la Santé, Ouagadougou 03 BP 7192, Burkina Faso
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Halidou Tinto
- Centre National de la Recherche Scientifique et Technologique/Institut de Recherche en Sciences de la Santé (CNRST/IRSS), Nanoro BP 18, Burkina Faso
| | - Abdoul-Salam Ouedraogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
- Correspondence: or
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9
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Prudhomme J, Mazza T, Hagen S, Cassan C, Toty C, Senghor MW, Niang AA, Faye B, Bañuls AL. New Microsatellite Markers for Genetic Studies on Sergentomyia schwetzi (Diptera: Psychodidae): A Suspected Vector of Leishmania infantum (Trypanosomatida: Trypanosomatidae) in the Canine Leishmaniasis Focus of Mont-Rolland, Senegal. J Med Entomol 2022; 59:2170-2175. [PMID: 35980597 PMCID: PMC9667725 DOI: 10.1093/jme/tjac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Visceral leishmaniasis is not endemic in West Africa, but prevalence of canine leishmaniasis and seroprevalence of Leishmania infantum infection in humans are high in the Mont Rolland community (Thiès region, Senegal). Previous studies in this area showed that Sergentomyia schwetzi could be the potential vector of Le. infantum. To precisely describe the biology and population structure of this potential vector, we identified eight novel microsatellite loci to characterize Se. schwetzi populations. We tested these loci in Se. schwetzi populations from five locations at Mont Rolland (Thiès, Senegal). All the loci were polymorphic, with a mean of 17.25 alleles (observed heterozygosity: 0.455). We did not detect any evidence of scoring errors due to stuttering and large allele dropout. Moreover, several of these loci were also amplified in six other sand fly species (Sergentomyia magna, Sergentomyia dubia, Sergentomyia minuta, Phlebotomus duboscqi, Phlebotomus perniciosus, and Phlebotomus ariasi). These preliminary results demonstrate the utility of these microsatellite markers for Se. schwetzi (and for the other sand fly species) population genetic studies.
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Affiliation(s)
| | - Thomas Mazza
- UMR MIVEGEC (Université Montpellier - IRD - CNRS), Centre IRD, F34394 Montpellier, France
| | - Sophie Hagen
- UMR MIVEGEC (Université Montpellier - IRD - CNRS), Centre IRD, F34394 Montpellier, France
| | - Cécile Cassan
- UMR MIVEGEC (Université Montpellier - IRD - CNRS), Centre IRD, F34394 Montpellier, France
| | - Céline Toty
- UMR MIVEGEC (Université Montpellier - IRD - CNRS), Centre IRD, F34394 Montpellier, France
| | | | | | - Babacar Faye
- Service de Parasitologie – Mycologie Faculté de Médecine, Pharmacie et Odontologie, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Anne-Laure Bañuls
- UMR MIVEGEC (Université Montpellier - IRD - CNRS), Centre IRD, F34394 Montpellier, France
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10
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Nguyen PTL, Ngo THH, Tran TMH, Vu TNB, Le VT, Tran HA, Pham DT, Nguyen HT, Tran DL, Nguyen TPL, Nguyen TTT, Tran ND, Dang DA, Bañuls AL, Choisy M, van Doorn HR, Suzuki M, Tran HH. Genomic epidemiological analysis of mcr-1-harboring Escherichia coli collected from livestock settings in Vietnam. Front Vet Sci 2022; 9:1034610. [PMID: 36387375 PMCID: PMC9643773 DOI: 10.3389/fvets.2022.1034610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/05/2022] [Indexed: 09/19/2023] Open
Abstract
Livestock has been implicated as a reservoir for antimicrobial resistance (AMR) genes that can spread to humans when antimicrobials are used in animals for food production to treat clinical diseases and prevent and control common disease events. In Vietnam, mcr-1-harboring Escherichia coli (MCRPEC) strains have been isolated from humans, animals (chickens, pigs, and dogs) feces, flies, foods, and the environment (rainwater, well water, and irrigation water) in communities and from clinical specimens in hospitals. The relationship between levels of AMR in livestock and its occurrence in humans is complex and is driven by many factors. We conducted whole genome sequencing of MCRPEC to analyze the molecular epidemiological characteristics, history, and relatedness of 50 isolates obtained in 2019 from different reservoirs in farms and markets in Ha Nam province, Vietnam. 34 sequence types (STs) with 3 new STs were identified in multilocus sequence typing analysis: ST12945 and ST12946 from chicken feces, and ST12947 from flies. The AMR phenotypes of 50 MCRPEC isolates were as follows: ampicillin (100%, 50/50), cefotaxime (10%, 5/50), gentamicin (60%, 30/50), amikacin (8%, 4/50), meropenem (6%, 3/50), ceftazidime (18%, 9/50), colistin (24%, 12/50) and ciprofloxacin (80%, 40/50). All 50 MCRPEC isolates were identified as MDR. 100% (50/50) isolates carried AMR genes, ranging from 5 to 22 genes. The most prevalent plasmid replicon types carrying mcr-1 were IncP-1 (17/37, 45.9%), IncX4 (7/37, 18.9%), and IncHI2/IncHI2A (6/37, 16.2%). These data suggest that the epidemiology of the mcr-1 gene is mostly determined by plasmid spreading instead of clonal dissemination of MCRPE strains. The co-occurrence of several STs such as ST10, ST48, ST155, ST206, ST2705 in various sample types, joined to the higher prevalence of a few types of Inc plasmids, confirms the dissemination of the mcr-1 carrying plasmids in E. coli clones established in livestock. 5 over 8 STs identified in flies (ST206, ST2705, ST155, ST10, and ST48) suggested the fly contribution in the transmission of AMR bacteria in environments. These popular STs also occur in human samples and 100% of the human samples were positive for the mcr-1 gene.
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Affiliation(s)
| | | | | | | | - Viet Thanh Le
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | | | - Duy Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ha Thanh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dieu Linh Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Center IRD, Montpellier, France
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Huy Hoang Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
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11
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Nguyen PTL, Tran HTM, Tran HA, Pham TD, Luong TM, Nguyen TH, Nguyen LTP, Nguyen TTT, Hoang HTA, Nguyen C, Tran DN, Dang AD, Suzuki M, Le TV, Bañuls AL, Choisy M, Van Doorn RH, Tran HH. Carriage of Plasmid-Mediated Colistin Resistance-1-Positive Escherichia coli in Humans, Animals, and Environment on Farms in Vietnam. Am J Trop Med Hyg 2022; 107:65-71. [PMID: 35895375 PMCID: PMC9294698 DOI: 10.4269/ajtmh.21-1203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/18/2021] [Accepted: 03/27/2022] [Indexed: 07/30/2023] Open
Abstract
Plasmid-Mediated Colistin Resistance 1 (mcr-1) was first reported in 2015 and is a great concern to human health. In this study, we investigated the prevalence of mcr-1 and mcr-1-positive Escherichia coli (MCRPEC) and the association in infection status among various reservoirs connected to livestock. The study was conducted in 70 poultry and swine farms in a commune in Ha Nam province, northern Vietnam. Samples were collected from farmers, food animals, domestic animals, and farm environments (flies and wastewater) for polymerase chain reaction (PCR) screening for mcr-1 gene and species identification of PCR positive isolates. Among 379 obtained mcr-1 positives isolates, Escherichia coli was the major identified, varying from 50% (2/4) in dog feces to 100% (31/31) in humans feces isolates. The prevalence of MCRPEC was 14.4% (20/139), 49.7% (96/193), 31.3% (25/80), 36.7% (40/109), 26.9% (18/67), and 3.9% (2/51) in humans, chickens, pigs, flies, wastewater, and dogs, respectively. The study identified association between MCRPEC infection status in humans and flies (OR = 3.4), between flies and chickens (OR = 5.3), and between flies and pigs (OR = 9.0). Farmers' age and farm livestock unit were also associated factors of MCRPEC infection status in humans (OR = 5.1 and 1.05, respectively). These findings bring new knowledge on antibiotic resistance in livestock setting and important suggestions on potential role of flies in the transmission of mcr-1 resistance gene.
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Affiliation(s)
| | | | | | - Thai Duy Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tan Minh Luong
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thanh Ha Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | - Chi Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Association of Public Health Laboratories, Silver Spring, Maryland
| | - Duong Nhu Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anh Duc Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Thanh Viet Le
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Centre IRD, Montpellier, France
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Rogier H. Van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Huy Hoang Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Hanoi Medical University, Hanoi, Vietnam
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12
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Delvallez G, Badell E, Cheng S, Meng S, Tong V, Norman J, Toubiana J, Vandelannoote K, Bañuls AL, Hide M, Brisse S. Non-toxigenic Corynebacterium diphtheriae in hallux ulceration. J Infect Dev Ctries 2022; 16:1118-1121. [PMID: 35797309 DOI: 10.3855/jidc.16153] [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: 11/28/2021] [Accepted: 01/22/2022] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Toxigenic Corynebacterium diphtheriae causes classical diphtheria. Skin infections by toxigenic or non-toxigenic Corynebacterium diphtheriae are prevalent in the tropics but are rarely reported. CASE PRESENTATION We report the identification of a non-toxigenic Corynebacterium diphtheriae (biovar Gravis) isolate in a 52-year-old Cambodian male. The patient presented purulent and non-healing ulcerations on the right hallux. The wound has healed after 7 days of antibiotic therapy with a favourable outcome. CONCLUSIONS This case represents, to our knowledge, the first report of Corynebacterium diphtheriae in Cambodia in the last 10 years, and highlights the lack of diagnosis and notifications of diphtheria. It is important to raise awareness among clinicians and to set up diphtheria surveillance in Cambodia.
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Affiliation(s)
- Gauthier Delvallez
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sokleaph Cheng
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Soda Meng
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Judy Norman
- Mercy Medical Center Cambodia, Phnom Penh, Cambodia
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Koen Vandelannoote
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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13
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Kocher A, Cornuault J, Gantier JC, Manzi S, Chavy A, Girod R, Dusfour I, Forget PM, Ginouves M, Prévot G, Guégan JF, Bañuls AL, de Thoisy B, Murienne J. Biodiversity and vector-borne diseases: host dilution and vector amplification occur simultaneously for Amazonian leishmaniases. Mol Ecol 2022; 32:1817-1831. [PMID: 35000240 DOI: 10.1111/mec.16341] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022]
Abstract
Changes in biodiversity may impact infectious disease transmission through multiple mechanisms. We explored the impact of biodiversity changes on the transmission of Amazonian leishmaniases, a group of wild zoonoses transmitted by phlebotomine sand flies (Psychodidae), which represent an important health burden in a region where biodiversity is both rich and threatened. Using molecular analyses of sand fly pools and blood-fed dipterans, we characterized the disease system in forest sites in French Guiana undergoing different levels of human-induced disturbance. We show that the prevalence of Leishmania parasites in sand flies correlates positively with the relative abundance of mammal species known as Leishmania reservoirs. In addition, Leishmania reservoirs tend to dominate in less diverse mammal communities, in accordance with the dilution effect hypothesis. This results in a negative relationship between Leishmania prevalence and mammal diversity. On the other hand, higher mammal diversity is associated with higher sand fly density, possibly because more diverse mammal communities harbor higher biomass and more abundant feeding resources for sand flies, although more research is needed to identify the factors that shape sand fly communities. As a consequence of these antagonistic effects, decreased mammal diversity comes with an increase of parasite prevalence in sand flies, but has no detectable impact on the density of infected sand flies. These results represent additional evidence that biodiversity changes may simultaneously dilute and amplify vector-borne disease transmission through different mechanisms that need to be better understood before drawing generalities on the biodiversity-disease relationship.
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Affiliation(s)
- Arthur Kocher
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France.,MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.,Institut Pasteur de la Guyane, Cayenne, France.,Transmission, Infection, Diversification & Evolution Group, Max-Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Josselin Cornuault
- Real Jardín Botánico CSIC, Plaza Murillo 2, 28014, Madrid, Spain.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jean-Charles Gantier
- Laboratoire des Identifications Fongiques et Entomo-parasitologiques, Mennecy, France
| | - Sophie Manzi
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France
| | - Agathe Chavy
- Institut Pasteur de la Guyane, Cayenne, France.,TBIP, Université de Guyane, 97300, Cayenne, France
| | | | | | - Pierre-Michel Forget
- Muséum National d'Histoire Naturelle, UMR-7179 MECADEV (Mécanismes Adaptatifs et Evolution), MNHN-CNRS, Brunoy, France
| | - Marine Ginouves
- TBIP, Université de Guyane, 97300, Cayenne, France.,Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR9017-CIIL Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Ghislaine Prévot
- TBIP, Université de Guyane, 97300, Cayenne, France.,Université de Lille, CNRS, Inserm, Institut Pasteur de Lille, U1019-UMR9017-CIIL Centre d'Infection et d'Immunité de Lille, 59000, Lille, France
| | - Jean-François Guégan
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France.,INRAE, Cirad, Université de Montpellier, UMR ASTRE, Montpellier, France
| | | | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, France.,Association Kwata, Cayenne, French Guiana
| | - Jérôme Murienne
- Laboratoire Évolution et Diversité Biologique (UMR5174 EDB) - CNRS, IRD, Université Toulouse III Paul Sabatier - Toulouse, France
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14
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Vu SN, Tran HS, Tran VP, Tran CT, Tran ND, Dang DA, Nguyen TY, Vu TL, Ngo KP, Nguyen VH, Hoàng NA, Cassan C, Prudhomme J, Depaquit J, Rahola N, Bañuls AL. Taxonomical insights and ecology of sandfly (Diptera, Psychodidae) species in six provinces of Northern Vietnam. Parasite 2021; 28:85. [PMID: 34928207 PMCID: PMC8686828 DOI: 10.1051/parasite/2021080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/26/2021] [Indexed: 11/14/2022] Open
Abstract
We studied sandfly (Diptera: Psychodidae) populations in six provinces of Vietnam. This work explores the diversity of sandfly species according to the province, as well as environment, and updated information on public health since leishmaniasis cases were reported in two provinces. Sandflies were collected using 428 CDC light traps from May 30 to October 13, 2016 and identified based on the morphology of the cibarium, pharynx and/or male genitalia or female spermathecae. A total of 2585 sandflies belonging to five genera and 13 identified species were collected. The main species were: the Sergentomyia barraudi group (12.53%), Se. sylvatica (9.63%) and Phlebotomus stantoni (3.95%). In all, 294 Sergentomyia specimens classified as Se. sp2 and Se. sp3 and a heterogeneous group, herein called Se. und_sp., showed unknown morphological characteristics requiring further studies. We provide detailed comments about morphological description and taxonomical identification in order to help standardization of sandfly classification in Southeast Asia. We observed differentiation according to the provinces in terms of density and species richness, with Lang Son having the highest density and Ninh Binh having the highest species richness. The majority of specimens were collected in rock caves and outdoors, suggesting mainly cavernicolous and exophilic characters of sandfly species in Northern Vietnam. However, specimens were also collected in intra- and peri-domiciliary sites. It is worth noting that Ph. stantoni was the main species found in dog sheds and indoors, and in particular in a leishmaniasis patient's house.
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Affiliation(s)
- Sinh Nam Vu
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Hai Son Tran
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Vu Phong Tran
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Cong Tu Tran
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Thi Yen Nguyen
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Thi Lieu Vu
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Khanh Phuong Ngo
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Viet Hoang Nguyen
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Ngọc Anh Hoàng
- National Institute of Hygiene and Epidemiology, 1 Yec-Xanh Street, Hai Ba Trung District, 100000 Hanoi, Vietnam
| | - Cécile Cassan
- MIVEGEC, UMR Univ Montpellier-IRD-CNRS, Centre IRD Montpellier - 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 05, France
| | - Jorian Prudhomme
- MIVEGEC, UMR Univ Montpellier-IRD-CNRS, Centre IRD Montpellier - 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 05, France
| | - Jérôme Depaquit
- EA7510 ESCAPE, USC ANSES "VECPAR", UFR Pharmacie, Université de Reims Champagne-Ardenne, 51096 Reims, France
| | - Nil Rahola
- MIVEGEC, UMR Univ Montpellier-IRD-CNRS, Centre IRD Montpellier - 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 05, France
| | - Anne-Laure Bañuls
- MIVEGEC, UMR Univ Montpellier-IRD-CNRS, Centre IRD Montpellier - 911 Avenue Agropolis, BP64501, 34394 Montpellier Cedex 05, France
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15
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Linh TD, Thu NH, Shibayama K, Suzuki M, Yoshida L, Thai PD, Anh DD, Duong TN, Trinh HS, Thom VP, Nga LTV, Phuong NTK, Thuyet BT, Walsh TR, Thanh LV, Bañuls AL, van Doorn HR, Van Anh T, Hoang TH. Expansion of KPC-producing Enterobacterales in four large hospitals in Hanoi, Vietnam. J Glob Antimicrob Resist 2021; 27:200-211. [PMID: 34607061 PMCID: PMC8692232 DOI: 10.1016/j.jgar.2021.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/15/2020] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES The incidence of carbapenem resistance among nosocomial Gram-negative bacteria in Vietnam is high and increasing, including among Enterobacterales. In this study, we assessed the presence of one of the main carbapenemase genes, blaKPC, among carbapenem-resistant Enterobacterales (CRE) from four large hospitals in Hanoi, Vietnam, between 2010 and 2015, and described their key molecular characteristics. METHODS KPC-producing Enterobacterales were detected using conventional PCR and were further analysed using S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and whole-genome sequencing (WGS) for sequence typing and genetic characterisation. RESULTS blaKPC genes were detected in 122 (20.4%) of 599 CRE isolates. blaKPC-carrying plasmids were diverse in size. Klebsiella pneumoniae harbouring blaKPC genes belonged to ST15 and ST11, whereas KPC-producing Escherichia coli showed more diverse sequence types including ST3580, ST448, ST709 and ST405. Genotypic relationships supported the hypothesis of circulation of a population of 'resident' resistant bacteria in one hospital through the years and of transmission among these hospitals via patient transfer. WGS results revealed co-carriage of several other antimicrobial resistance genes and three different genetic contexts of blaKPC-2. Among these, the combination of ISEcp1-blaCTX-M and ISKpn27-blaKPC-ΔISKpn6 on the same plasmid is reported for the first time. CONCLUSION We describe the dissemination of blaKPC-expressing Enterobacterales in four large hospitals in Hanoi, Vietnam, since 2010, which may have started earlier, along with their resistance patterns, sequence types, genotypic relationship, plasmid sizes and genetic context, thereby contributing to the overall picture of the antimicrobial resistance situation in Enterobacterales in Vietnam.
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Affiliation(s)
- Tran Dieu Linh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen Hoai Thu
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - LayMint Yoshida
- Institute of Tropical Diseases, Nagasaki University, Nagasaki, Japan
| | - Pham Duy Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | | | | | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Cardiff University, Cardiff, UK
| | - Le Viet Thanh
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), Centre IRD, Montpellier, France
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Tran Huy Hoang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam; Hanoi Medical University, Hanoi, Vietnam.
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16
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Abstract
Toscana virus (TOSV) is an emerging pathogen in the Mediterranean area and is neuroinvasive in its most severe form. Basic knowledge on TOSV biology is limited. We conducted a systematic review on travel-related infections to estimate the TOSV incubation period. We estimated the incubation period at 12.1 days.
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17
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Chevenet F, Fargette D, Guindon S, Bañuls AL. EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. BMC Bioinformatics 2021; 22:463. [PMID: 34579644 PMCID: PMC8474961 DOI: 10.1186/s12859-021-04386-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/20/2021] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret. RESULT We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions. CONCLUSION The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org .
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Affiliation(s)
- François Chevenet
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France. .,LIRMM, CNRS, Université de Montpellier, Montpellier, France.
| | - Denis Fargette
- IPME, IRD, CIRAD, Université de Montpellier, Montpellier, France
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18
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Tran HA, Vu TNB, Trinh ST, Tran DL, Pham HM, Ngo THH, Nguyen MT, Tran ND, Pham DT, Dang DA, Shibayama K, Suzuki M, Yoshida LM, Trinh HS, Le VT, Vu PT, Luu TVN, Bañuls AL, Trinh KL, Tran VA, Tran HH, van Doorn HR. Resistance mechanisms and genetic relatedness among carbapenem-resistant Pseudomonas aeruginosa isolates from three major hospitals in Hanoi, Vietnam (2011-15). JAC Antimicrob Resist 2021; 3:dlab103. [PMID: 34322671 PMCID: PMC8313516 DOI: 10.1093/jacamr/dlab103] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Background MDR bacteria including carbapenem-resistant Pseudomonas aeruginosa are recognized as an important cause of hospital-acquired infections worldwide. This investigation seeks to determine the molecular characterization and antibiotic resistance genes associated with carbapenem-resistant P. aeruginosa. Methods We conducted WGS and phylogenetic analysis of 72 carbapenem-resistant P. aeruginosa isolated from hospital-acquired infection patients from August 2011 to March 2015 in three major hospitals in Hanoi, Vietnam. Results We identified three variants of IMP gene, among which blaIMP-15 was the most frequent (n = 34) in comparison to blaIMP-26 (n = 2) and blaIMP-51 (n = 12). We observed two isolates with imipenem MIC >128 mg/L that co-harboured blaIMP-15 and blaDIM-1 genes and seven isolates (imipenem MIC > 128 mg/L) with a blaKPC-1 gene from the same hospital. MLST data shows that these 72 isolates belong to 18 STs and phylogenetic tree analysis has divided these isolates into nine groups. Conclusions Our results provide evidence that not only blaIMP-26 but other IMP variants such as blaIMP-15 and blaIMP-51 genes and several STs (ST235, ST244, ST277, ST310, ST773 and ST3151) have been disseminating in healthcare settings in Vietnam. In addition, we report the emergence of two isolates belonging to ST1240 and ST3340 that harboured two important carbapenemase genes (blaIMP-15 and blaDIM-1) and seven isolates belonging to ST3151 of P. aeruginosa that carried the blaKPC-1 gene in Vietnam, which could potentially cause serious restricted availability of treatment options in healthcare settings.
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Affiliation(s)
| | | | - Son Tung Trinh
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Dieu Linh Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ha My Pham
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | | | | | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duy Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Lay-Myint Yoshida
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | | | - Viet Thanh Le
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | | | - Anne-Laure Bañuls
- MIVEGEC Univ Montpellier-IRD-CNRS, Centre IRD, Montpellier, France.,LMI DRISA, Hanoi, Vietnam
| | | | | | - Huy Hoang Tran
- Hanoi Medical University, Hanoi, Vietnam.,National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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19
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Nguyen TVA, Anthony RM, Cao TTH, Bañuls AL, Nguyen VAT, Vu DH, Nguyen NV, Alffenaar JWC. Delamanid Resistance: Update and Clinical Management. Clin Infect Dis 2021; 71:3252-3259. [PMID: 32521000 DOI: 10.1093/cid/ciaa755] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/05/2020] [Indexed: 12/29/2022] Open
Abstract
Delamanid, a-first-in-class bicyclic nitroimidazole, was recently approved for multidrug-resistant tuberculosis treatment. Pitted against the hope for improving treatment outcomes is the threat of the rapid resistance emergence. This review provides information on the mechanisms of action, resistance emergence, and drug susceptibility testing (DST) for delamanid. Delamanid resistance has already been reported in both in vitro experiments and clinical settings. Although mutations conferring delamanid resistance have been identified in fbiA, fbiB, fbiC, ddn, and fgd1 genes of Mycobacterium tuberculosis, knowledge about the molecular resistance mechanisms is limited, and there remains no standardized DST method. The rapid acquisition of delamanid resistance emphasizes the need for optimal use of new drugs, the need for drug resistance surveillance, and a comprehensive understanding of drug resistance mechanisms. Further studies are necessary to investigate genetic and phenotypic changes that determine clinically relevant delamanid resistance to help develop a rapid delamanid DST.
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Affiliation(s)
- Thi Van Anh Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, Hanoi, Vietnam
| | - Richard M Anthony
- Tuberculosis reference laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thi Thu Huyen Cao
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Hanoi, Vietnam.,MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Van Anh Thi Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology of Vietnam, Hanoi, Vietnam
| | - Dinh Hoa Vu
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | | | - Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead hospital, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
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20
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Cheng S, Hide M, Pheng SH, Kerléguer A, Delvallez G, Sam S, Mao TE, Nguyen TVA, Bañuls AL. Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study. Infect Drug Resist 2021; 14:1089-1104. [PMID: 33762833 PMCID: PMC7982564 DOI: 10.2147/idr.s289907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background Due to the emergence of Mycobacterium tuberculosis (M.tb) clinical isolates resistant to most potent first-line drugs (FLD), second-line drugs (SLD) are being prescribed more frequently. We explore the genetic characteristics and molecular mechanisms of M.tb isolates phenotypically resistant to SLD, including pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) isolates. Methods Drug-resistant (DR) M.tb isolates collected from 2012 to 2017 were tested using sequencing and phenotypic drug susceptibility testing. Genotypes were determined to explore their links with SLD resistance patterns. Results Of the 272 DR M.tb isolates, 6 non-multidrug resistant (non-MDR) isolates were fluoroquinolones (FQ)-resistant, 3 were XDR and 16 were pre-XDR (14 resistant to FQ and 2 to second-line injectable drugs). The most frequent mutations in FQ-resistant and second-line injectable drugs resistant isolates were gyrA D94G (15/23) and rrs a1401g (3/5), respectively. Seventy-five percent of pre-XDR isolates and 100% of XDR isolates harbored mutations conferring resistance to pyrazinamide. All XDR isolates belonged to the Beijing genotype, of which one, named XDR+, was resistant to all drugs tested. One cluster including pre-XDR and XDR isolates was observed. Conclusion This is the first description of SLD resistance in Cambodia. The data suggest that the proportion of XDR and pre-XDR isolates remains low but is on the rise compared to previous reports. The characterization of the XDR+ isolate in a patient who refused treatment underlines the risk of transmission in the population. In addition, genotypic results show, as expected, that the Beijing family is the main involved in pre-XDR and XDR isolates and that the spread of the Beijing pre-XDR strain is capable of evolving into XDR strain. This study strongly indicates the need for rapid interventions in terms of diagnostic and treatment to prevent the spread of the pre-XDR and XDR strains and the emergence of more resistant ones.
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Affiliation(s)
- Sokleaph Cheng
- Institut Pasteur du Cambodge and Ministry of Health, Phnom Penh, Cambodia.,Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
| | - Sok Heng Pheng
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Alexandra Kerléguer
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Gauthier Delvallez
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophan Sam
- Cambodian Health Committee, Phnom Penh, Cambodia
| | - Tan Eang Mao
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Thi Van Anh Nguyen
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Martinique, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
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21
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Ouchar Mahamat O, Kempf M, Lounnas M, Tidjani A, Hide M, Benavides JA, Carrière C, Bañuls AL, Jean-Pierre H, Ouedraogo AS, Dumont Y, Godreuil S. Epidemiology and prevalence of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in humans, animals and the environment in West and Central Africa. Int J Antimicrob Agents 2020; 57:106203. [PMID: 33075511 DOI: 10.1016/j.ijantimicag.2020.106203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/29/2020] [Accepted: 10/11/2020] [Indexed: 12/17/2022]
Abstract
Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) are widespread. Here we used the 'One Health' approach to determine knowledge gaps on ESBL-E and CPE in West and Central Africa. We searched all articles on ESBL-E and CPE in these African regions published in PubMed, African Journals Online and Google Scholar from 2000 onwards. Among the 1201 articles retrieved, we selected 165 studies (West Africa, 118; Central Africa, 47) with data from 22 of the 26 West and Central Africa countries. Regarding the settings, 136 articles focused only on humans (carriage and/or infection), 6 articles on humans and animals, 13 on animals, 1 on humans and the environment, 8 on the environment and 1 on humans, animals and environments. ESBL-E prevalence ranged from 11-72% in humans and 7-79% in aquatic environments (wastewater). In animals, ESBL-E prevalence hugely varied: 0% in cattle, 11-36% in chickens, 20% in rats, 21-71% in pigs and 32-75% in dogs. The blaCTX-M-15 gene was the predominant ESBL-encoding gene and was associated with plasmids of incompatibility groups F, H, K, Y, N, I1 and R. CPE were studied only in humans. Class B metallo-β-lactamases (NDM) and class D oxacillinases (OXA-48 and OXA-181) were the most common carbapenemases. Our results show major knowledge gaps, particularly on ESBL and CPE in animals and the environment, that might limit antimicrobial resistance management in these regions. The results also emphasise the urgent need to improve active surveillance programmes in each country and to support antimicrobial stewardship.
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Affiliation(s)
- Oumar Ouchar Mahamat
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France; Service de laboratoire, Hôpital de la Mère et de l'Enfant, N'Djaména, Chad.
| | - Marie Kempf
- CRCINA, INSERM, Université de Nantes, Université d'Angers, Angers, France, and Laboratoire de Bactériologie-Hygiène, Institut de Biologie en Santé - PBH, CHU Angers, Angers, France
| | - Manon Lounnas
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | | | - Mallorie Hide
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Julio A Benavides
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile; Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Christian Carrière
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France; Laboraoire Mixte International, DRISA, IRD, Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | | | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France; Laboraoire Mixte International, DRISA, IRD, Montpellier, France
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22
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Bouzinbi N, Marcy O, Bertolotti T, Chiron R, Bemer P, Pestel-Caron M, Peuchant O, Guet-Revillet H, Fangous MS, Héry-Arnaud G, Ouedraogo AS, Bañuls AL, Godreuil S. Evaluation of the GenoType NTM-DR assay performance for the identification and molecular detection of antibiotic resistance in Mycobacterium abscessus complex. PLoS One 2020; 15:e0239146. [PMID: 32976521 PMCID: PMC7518582 DOI: 10.1371/journal.pone.0239146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/31/2020] [Indexed: 12/04/2022] Open
Abstract
The first objective of this study was to determine the GenoType NTM-DR assay performance for subspecies identification in Mycobacterium abscessus complex isolates. The second objective was to evaluate the GenoType NTM-DR assay ability to detect clarithromycin and amikacin resistance in M. abscessus complex isolates compared with drug susceptibility testing (DST) and PCR sequencing of the erm(41), rrl and rrs genes. The concordance between the GenoType NTM-DR and MLST results concerning subspecies identification was 100%. The wild type and mutated alleles of the rrl and rrs genes were detected by the GenoType NTM-DR assay and PCR sequencing with 100% (115/115) agreement. Similarly, 100% concordance between GenoType NTM-DR and DST was observed for clarithromycin and amikacin testing. Sensitivity for the detection of clarithromycin and amikacin resistance was 100%. The GenoType NTM-DR assay provides a robust and complementary tool to the gold standard methods (MLST and broth microdilution) for subspecies identification and drug resistance detection.
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Affiliation(s)
- Nicolas Bouzinbi
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Olivier Marcy
- Bordeaux Population Health Centre U1219, Université de Bordeaux, Bordeaux, France
| | - Thibault Bertolotti
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Raphael Chiron
- Cystic Fibrosis Centre, University Hospital of Montpellier, Montpellier, France
| | - Pascale Bemer
- Bacteriology-Hospital Hygiene Department, University Hospital of Nantes, Nantes University, Nantes, France
| | - Martine Pestel-Caron
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Olivia Peuchant
- USC EA 3671 Infections Humaines à Mycoplasmes et à Chlamydiae, Univ. Bordeaux, Bordeaux, France
| | - Hélène Guet-Revillet
- CHU de Toulouse, Laboratoire de Bactériologie-Hygiène, Institut Fédératif de Biologie, Toulouse, France
| | - Marie-Sarah Fangous
- Bacteriology-Hospital Hygiene Department, University Hospital of Brest, Brest University, Brest, France
| | - Geneviève Héry-Arnaud
- Bacteriology-Hospital Hygiene Department, University Hospital of Brest, Brest University, Brest, France
| | | | - Anne-Laure Bañuls
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
- LMI Drug Resistance in South East Asia “DRISA”, IRD Montpellier, Montpellier, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
- LMI Drug Resistance in South East Asia “DRISA”, IRD Montpellier, Montpellier, France
- * E-mail:
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23
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Prudhomme J, De Meeûs T, Toty C, Cassan C, Rahola N, Vergnes B, Charrel R, Alten B, Sereno D, Bañuls AL. Altitude and hillside orientation shapes the population structure of the Leishmania infantum vector Phlebotomus ariasi. Sci Rep 2020; 10:14443. [PMID: 32879357 PMCID: PMC7468129 DOI: 10.1038/s41598-020-71319-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/15/2020] [Indexed: 12/19/2022] Open
Abstract
Despite their role in Leishmania transmission, little is known about the organization of sand fly populations in their environment. Here, we used 11 previously described microsatellite markers to investigate the population genetic structure of Phlebotomus ariasi, the main vector of Leishmania infantum in the region of Montpellier (South of France). From May to October 2011, we captured 1,253 Ph. ariasi specimens using sticky traps in 17 sites in the North of Montpellier along a 14-km transect, and recorded the relevant environmental data (e.g., altitude and hillside). Among the selected microsatellite markers, we removed five loci because of stutter artifacts, absence of polymorphism, or non-neutral evolution. Multiple regression analyses showed the influence of altitude and hillside (51% and 15%, respectively), and the absence of influence of geographic distance on the genetic data. The observed significant isolation by elevation suggested a population structure of Ph. ariasi organized in altitudinal ecotypes with substantial rates of migration and positive assortative mating. This organization has implications on sand fly ecology and pathogen transmission. Indeed, this structure might favor the global temporal and spatial stability of sand fly populations and the spread and increase of L. infantum cases in France. Our results highlight the necessity to consider sand fly populations at small scales to study their ecology and their impact on pathogens they transmit.
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Affiliation(s)
- Jorian Prudhomme
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France.
| | | | - Céline Toty
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | - Cécile Cassan
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | - Nil Rahola
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | - Baptiste Vergnes
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
| | - Remi Charrel
- Unité des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), 13385, Marseille, France
| | - Bulent Alten
- ESRL Laboratories, Department of Biology, Ecology Section, Faculty of Science, Hacettepe University, 0680, Beytepe, Ankara, Turkey
| | - Denis Sereno
- INTERTRYP, IRD, Cirad, Univ Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- MIVEGEC Univ Montpellier, IRD, CNRS, Centre IRD, 911 avenue Agropolis, 34394, Montpellier, France
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24
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Vaselek S, Prudhomme J, Myskova J, Lestinova T, Spitzova T, Bañuls AL, Volf P. Comparative Study of Promastigote- and Amastigote-Initiated Infection of Leishmania infantum (Kinetoplastida: Trypanosomatidae) in Phlebotomus perniciosus (Diptera: Psychodidae) Conducted in Different Biosafety Level Laboratories. J Med Entomol 2020; 57:601-607. [PMID: 31702779 PMCID: PMC7044723 DOI: 10.1093/jme/tjz199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Indexed: 06/10/2023]
Abstract
Sand flies (Diptera: Psychodidae) are natural vectors of Leishmania. For the initiation of sand fly experimental infections either Leishmania amastigotes or promastigotes can be used. In order to obtain comparable results, it is necessary to adjust and standardize procedures. During this study, we conducted promastigote- and amastigote-initiated infections of Leishmania infantum Nicolle, 1908 parasites in Phlebotomus (Larroussius) perniciosus Newstead, 1911 in two laboratories with different levels of biosafety protection. Protocol originally designed for a biosafety level 2 facility was modified for biosafety level 3 facility and infection parameters were compared. Particularly, specially designed plastic containers were used for blood feeding; feeders were placed outside the sand fly cage, on the top of the mesh; feeding was performed inside the climatic chamber; separation of engorged females was done in Petri dishes kept on ice; engorged females were kept in the cardboard containers until dissection. All experiments, conducted in both laboratories, resulted in fully developed late stage infections with high number of parasites and colonization of the stomodeal valve. We demonstrated that protocol originally designed for biosafety level 2 facilities can be successfully modified for other biosafety facilities, depending on the special requirements of the individual institution/laboratory.
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Affiliation(s)
- Slavica Vaselek
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Jorian Prudhomme
- UMR MIVEGEC (IRD - CNRS - University of Montpellier), IRD center, 911 avenue Agropolis, Montpellier, France
| | - Jitka Myskova
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Tereza Lestinova
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Tatiana Spitzova
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD - CNRS - University of Montpellier), IRD center, 911 avenue Agropolis, Montpellier, France
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
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25
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Ayhan N, Prudhomme J, Laroche L, Bañuls AL, Charrel RN. Broader Geographical Distribution of Toscana Virus in the Mediterranean Region Suggests the Existence of Larger Varieties of Sand Fly Vectors. Microorganisms 2020; 8:microorganisms8010114. [PMID: 31947561 PMCID: PMC7022675 DOI: 10.3390/microorganisms8010114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Toscana virus (TOSV) is endemic in the Mediterranean basin, where it is transmitted by sand flies. TOSV can infect humans and cause febrile illness as well as neuroinvasive infections affecting the central and peripheral nervous systems. Although TOSV is a significant human pathogen, it remains neglected and there are consequently many gaps of knowledge. Recent seroepidemiology studies and case reports showed that TOSV’s geographic distribution is much wider than was assumed a decade ago. The apparent extension of the TOSV circulation area raises the question of the sandfly species that are able to transmit the virus in natural conditions. Phlebotomus (Ph.)perniciosus and Ph. perfiliewi were historically identified as competent species. Recent results suggest that other species of sand flies could be competent for TOSV maintenance and transmission. Here we organize current knowledge in entomology, epidemiology, and virology supporting the possible existence of additional phlebotomine species such as Ph. longicuspis, Ph. sergenti, Ph. tobbi, Ph. neglectus, and Sergentomyia minuta in TOSV maintenance. We also highlight some of the knowledge gaps to be addressed in future studies.
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Affiliation(s)
- Nazli Ayhan
- Unité des Virus Emergents (Aix-Marseille Univ–IRD 190–Inserm 1207–IHU Méditerranée Infection), 13005 Marseille, France;
- Unité de Virologie EA7310 Bioscope, Université de Corse Pasquale Paoli (UCPP), 20250 Corte, France
- Correspondence: (N.A.); (J.P.); Tel.: +33-782-202794 (N.A.); +33-621-504351 (J.P.)
| | - Jorian Prudhomme
- UMR MIVEGEC (IRD—CNRS—Université de Montpellier), 911 avenue Agropolis, F34394 Montpellier, France; (L.L.); (A.-L.B.)
- Correspondence: (N.A.); (J.P.); Tel.: +33-782-202794 (N.A.); +33-621-504351 (J.P.)
| | - Lison Laroche
- UMR MIVEGEC (IRD—CNRS—Université de Montpellier), 911 avenue Agropolis, F34394 Montpellier, France; (L.L.); (A.-L.B.)
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD—CNRS—Université de Montpellier), 911 avenue Agropolis, F34394 Montpellier, France; (L.L.); (A.-L.B.)
| | - Remi N. Charrel
- Unité des Virus Emergents (Aix-Marseille Univ–IRD 190–Inserm 1207–IHU Méditerranée Infection), 13005 Marseille, France;
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26
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Vu NS, Tran SH, Tran PV, Tran TC, Tran DN, Dang AD, Nguyen YT, Vu LT, Ngo PK, Nguyen HV, Cassan C, Nguyen CV, Rahola N, Bañuls AL. Diversity and Ecology of Sand Flies (Diptera: Psychodidae), Potential Vectors of Leishmania in the Quang Ninh Province, Vietnam. J Med Entomol 2020; 57:259-265. [PMID: 31346619 DOI: 10.1093/jme/tjz129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Indexed: 06/10/2023]
Abstract
The study aims to make an update on the distribution and ecology of sand flies in the Quang Ninh province, Northern Vietnam, where Leishmania cases were reported in 2001. Seventeen sites were chosen in three districts of the province: Ha Long, Cam Pha, and Hoanh Bo. Phlebotomine sand flies were collected using 68 CDC light traps from May 30 to 3 June 2016. Captured specimens were transferred individually into Eppendorf tubes with 90% ethanol. The sand fly heads and genitalia were removed and were mounted in Euparal after successive different baths. Specimen identification was determined based on the morphology of the cibarium, pharynx, and/or male genitalia or female spermathecae. A total of 416 sand flies (125 females, 283 males) belonging to four genera were collected and 10 sand fly species were identified: Sergentomyia silvatica, Se. barraudi, Se. hivernus, Se. bailyi, Phlebotomus mascomai, Ph. stantoni, Ph. yunshengensis, Ph. betisi, Chinius junlianensis, Idiophlebotomus longiforceps. The Sergentomyia genus prevailed (79.7% of the collected sand flies), followed by the Phlebotomus genus (13.7%), the Chinius genus (6.1%), and the Idiophlebotomus genus (0.8%). Besides these well-defined taxa, five specimens, named sp1, showed unknown morphological characteristics, requiring further study. The majority of sand flies were collected in rock caves suggesting the cavernicolous character of the species in the Quang Ninh province. However, specimens were also collected in intra and peridomiciliary sites in which Ph. stantoni and Se. hivernus were found as the main species. It is worth noting that two Ph. stantoni were found in the house of a patient affected by Leishmania.
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Affiliation(s)
- Nam Sinh Vu
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Son Hai Tran
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Phong Vu Tran
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Tu Cong Tran
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duong Nhu Tran
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anh Duc Dang
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Yen Thi Nguyen
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Lieu Thi Vu
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Phuong Khanh Ngo
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hoang Viet Nguyen
- Medical Entomology and Zoology Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Cécile Cassan
- MIVEGEC, UMR IRD-CNRS-Univ Montpellier, Centre IRD Montpellier, Montpellier, France
| | - Chau Van Nguyen
- Department of Entomology, National Institute of Malariology Parasitology and Entomology, Hanoi, Vietnam
| | - Nil Rahola
- MIVEGEC, UMR IRD-CNRS-Univ Montpellier, Centre IRD Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- MIVEGEC, UMR IRD-CNRS-Univ Montpellier, Centre IRD Montpellier, Montpellier, France
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27
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Ouchar Mahamat O, Tidjani A, Lounnas M, Hide M, Benavides J, Somasse C, Ouedraogo AS, Sanou S, Carrière C, Bañuls AL, Jean-Pierre H, Dumont Y, Godreuil S. Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in hospital and community settings in Chad. Antimicrob Resist Infect Control 2019; 8:169. [PMID: 31695911 PMCID: PMC6824111 DOI: 10.1186/s13756-019-0626-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 07/22/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Background Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) remains poorly documented in Africa. The objective of this study was to determine the prevalence of ESBL-PE fecal carriage in Chad. Methods In total, 200 fresh stool samples were collected from 100 healthy community volunteers and 100 hospitalized patients from January to March 2017. After screening using ESBL-selective agar plates and species identification by MALDI-TOF mass spectrometry, antibiotic susceptibility was tested using the disk diffusion method, and ESBL production confirmed with the double-disc synergy test. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method. Results ESBL-PE fecal carriage prevalence was 44.5% (51% among hospitalized patients vs 38% among healthy volunteers; p < 0.05). ESBL-producing isolates were mostly Escherichia coli (64/89) and Klebsiella pneumoniae (16/89). PCR and sequencing showed that 98.8% (87/89) of ESBL-PE harbored blaCTX-M genes: blaCTX-M-15 in 94.25% (82/87) and blaCTX-M-14 in 5.75% (5/87). Phylogroup determination by quadruplex PCR indicated that ESBL-producing E. coli isolates belonged to group A (n = 17; 27%), C (n = 17; 27%), B2 (n = 9; 14%), B1 (n = 8; 13%), D (n = 8; 13%), E (n = 1; 1.6%), and F (n = 1; 1.6%). The ST131 clone was identified in 100% (9/9) of E. coli B2 strains. Conclusions The high fecal carriage rate of ESBL-PE associated with CTX-M-15 in hospital and community settings of Chad highlights the risk for resistance transmission between non-pathogenic and pathogenic bacteria.
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Affiliation(s)
- Oumar Ouchar Mahamat
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,Service de laboratoire Hôpital de la Mère et de l'Enfant, N'Djaména, Chad
| | | | - Manon Lounnas
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Mallorie Hide
- 2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Julio Benavides
- 57 Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Calèbe Somasse
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Abdoul-Salam Ouedraogo
- Service de bactériologie-virologie, Département des laboratoires, Centre Hospitalier Universitaire Souro Sanou, Bobo Dioulasso, Burkina Faso
| | - Soufiane Sanou
- Service de bactériologie-virologie, Département des laboratoires, Centre Hospitalier Universitaire Souro Sanou, Bobo Dioulasso, Burkina Faso
| | - Christian Carrière
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- 2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,7Laboraoire Mixte International, DRISA, IRD, Montpellier, France
| | - Hélène Jean-Pierre
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Yann Dumont
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Sylvain Godreuil
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,7Laboraoire Mixte International, DRISA, IRD, Montpellier, France
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28
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Somphavong S, Berland JL, Gauthier M, Vu TT, Nguyen QH, Iem V, Vongvichit P, Inthavong D, Akkhavong V, Chanthavilay P, Soundala S, Keovichit I, Paranhos-Baccalà G, Paboriboune P, Nguyen TVA, Bañuls AL. First insights into the genetic characteristics and drug resistance of Mycobacterium tuberculosis population collected during the first national tuberculosis prevalence survey of Lao PDR (2010-2011). BMC Infect Dis 2019; 19:851. [PMID: 31615439 PMCID: PMC6794770 DOI: 10.1186/s12879-019-4435-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 09/21/2018] [Accepted: 08/30/2019] [Indexed: 01/27/2023] Open
Abstract
Background In Lao People’s Democratic Republic (PDR), tuberculosis (TB) prevalence was estimated at 540/100,000 in 2011. Nevertheless, little is known about the genetic characteristics and anti-TB drug resistance of the Mycobacterium tuberculosis population. The main objective of this work was to study the genetic characteristics and drug resistance of M. tuberculosis population collected during the first National TB Prevalence Survey (TBPS) of Lao PDR (2010–2011). Methods Two hundred and twenty two isolates collected during TBPS (2010–2011) were analyzed with the GenoType MTBDRplus test for M. tuberculosis identification and drug resistance detection. Then, 206 of the 222 isolates were characterized by spoligotyping and MIRU-VNTR typing. Results Among the 222 M. tuberculosis isolates, 11 were mono-resistant to isoniazid and 2 were resistant to isoniazid and rifampicin (MDR-TB), using the GenoType MTBDRplus test. Among the 202 genetically characterized isolates, the East African-Indian (EAI) family was predominant (76.7%) followed by the Beijing (14.4%) and T (5.5%) families. EAI isolates came from all the country provinces, whereas Beijing isolates were found mainly in the northern and central provinces. A higher proportion of Beijing isolates was observed in people younger than 35 years compared to EAI. Moreover, the percentage of drug resistance was higher among Beijing (17.2%) than EAI (5.2%) isolates, and the two MDR-TB isolates belonged to the Beijing family. Combined analysis of the MIRU-VNTR and spoligotyping results (n = 202 isolates) revealed an estimated clustering rate of 11% and the occurrence of mini-outbreaks of drug-resistant TB caused by Beijing genotypes. Conclusions The EAI family, the ancient and endemic family in Asia, is predominant in Lao PDR whereas the prevalence of Beijing, the most harmful M. tuberculosis family for humans, is still low, differently from neighboring countries. However, its association with drug resistance, its presence in young patients and its potential association with recent transmission suggest that the Beijing family could change TB epidemiological pattern in Lao PDR. Therefore, efficient TB control and surveillance systems must be maintained and reinforced to prevent the emergence of highly transmissible and drug-resistant strains in Lao PDR, as observed in neighboring countries. Electronic supplementary material The online version of this article (10.1186/s12879-019-4435-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silaphet Somphavong
- Centre d'Infectiologie Lao-Christophe Mérieux, Vientiane, Lao PDR. .,MIVEGEC (IRD-CNRS-Université de Montpellier), Centre IRD, Montpellier, France. .,LMI "Drug Resistance in South East Asia, DRISA", Hanoi, Vietnam.
| | - Jean-Luc Berland
- Laboratoire des Pathogènes Émergents, Fondation Mérieux, Lyon, France
| | - Marie Gauthier
- Laboratoire des Pathogènes Émergents, Fondation Mérieux, Lyon, France
| | - Thi Thuong Vu
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Quang Huy Nguyen
- LMI "Drug Resistance in South East Asia, DRISA", Hanoi, Vietnam.,Department of Pharmacological, Medical and Agronomical Biotechnology, University of Science and Technology of Hanoi, Academy of Science and Technology, Hanoi, Vietnam
| | - Vibol Iem
- National reference laboratory for tuberculosis, Vientiane, Lao PDR
| | | | - Donekham Inthavong
- National reference laboratory for tuberculosis, Vientiane, Lao PDR.,National Tuberculosis Control Program, Vientiane, Lao PDR
| | | | | | | | | | | | | | - Thi Van Anh Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), Centre IRD, Montpellier, France.,LMI "Drug Resistance in South East Asia, DRISA", Hanoi, Vietnam
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29
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Nguyen TVA, Anthony RM, Bañuls AL, Nguyen TVA, Vu DH, Alffenaar JWC. Bedaquiline Resistance: Its Emergence, Mechanism, and Prevention. Clin Infect Dis 2019; 66:1625-1630. [PMID: 29126225 DOI: 10.1093/cid/cix992] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bedaquiline, a new antituberculosis drug, has already been used in >50 countries. The emergence of bedaquiline resistance is alarming, as it may result in the rapid loss of this new drug. This article aims to review currently identified mechanisms of resistance and the emergence of bedaquiline resistance, and discuss strategies to delay the resistance acquisition. In vitro and clinical studies as well as reports from compassionate use have identified the threat of bedaquiline resistance and cross-resistance with clofazimine, emphasizing the crucial need for the systematic surveillance of resistance. Currently known mechanisms of resistance include mutations within the atpE, Rv0678, and pepQ genes. The development of standardized drug susceptibility testing (DST) for bedaquiline is urgently needed. Understanding any target and non-target-based mechanisms is essential to minimize resistance development and treatment failure and help to develop appropriate DST for bedaquiline and genetic-based resistance screening.
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Affiliation(s)
- Thi Van Anh Nguyen
- Department of Pharmacological, Medical, Agronomical Biotechnology, University of Science and Technology of Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, Hanoi, Vietnam
| | - Richard M Anthony
- Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Hanoi, Vietnam.,Institute of Research for Development, Montpellier, France.,Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology of Vietnam
| | - Thi Van Anh Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology of Vietnam
| | - Dinh Hoa Vu
- Department of Clinical Pharmacy and National Drug Information and Adverse Drug Reaction Monitoring Centre, Hanoi University of Pharmacy, Vietnam
| | - Jan-Willem C Alffenaar
- University of Groningen, University Medical Center Groningen, Clinical Pharmacy and Pharmacology, The Netherlands
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Siala M, Cassan C, Smaoui S, Kammoun S, Marouane C, Godreuil S, Hachicha S, Mhiri E, Slim L, Gamara D, Messadi-Akrout F, Bañuls AL. A first insight into genetic diversity of Mycobacterium bovis isolated from extrapulmonary tuberculosis patients in South Tunisia assessed by spoligotyping and MIRU VNTR. PLoS Negl Trop Dis 2019; 13:e0007707. [PMID: 31532767 PMCID: PMC6750577 DOI: 10.1371/journal.pntd.0007707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Introduction In Tunisia, almost 77% of clinically and bacteriologically diagnosed cases of extrapulmonary tuberculosis (EPTB) are zoonotic TB, caused by M. bovis. Although several studies have analyzed bovine TB in cattle in Tunisia, no study has evaluated the risk of transmission to humans in such an endemic country. We aimed to study the genetic diversity of M. bovis human isolates, to ascertain the causes of human EPTB infection by M. bovis and to investigate the distribution and population structure of this species in Tunisia. Materials and methods A total of 110 M. bovis isolates taken from patients with confirmed EPTB were characterized by spoligotyping and MIRU-VNTR typing methods. Results Among the 15 spoligotypes detected in our study, 6 (SB0120, SB0121, SB2025, SB1200, SB1003 and SB0134) were the most prevalent (83.5%) of which SB0120, SB0121 and SB2025 were the most prevailing. MIRU-VNTR typing method showed a high genotypic and genetic diversity. The genetic differentiation based on MIRU-VNTR was significant between populations from South East (Tataouine, Medenine) and Central West (Gafsa, Sidi Bouzid, Kasserine) regions. Of note, 13/15 (86.7%) spoligotypes detected in our study were previously identified in cattle in Tunisia with different frequencies suggesting a peculiar ability of some genotypes to infect humans. Using combined spoligotyping and MIRU-VNTR method, a high clustering rate of 43.9% was obtained. Our results underlined that human EPTB due to M. bovis was more commonly found in female gender and in young patients. Most of our patients, 66.4% (73/110) were raw milk or derivatives consumers, whereas 30.9% (34/110) patients would have contracted EPTB through contact with livestock. The findings suggest that the transmission of Zoonotic TB caused by M. bovis to humans mainly occurred by oral route through raw milk or derivatives. Conclusion Our study showed the urgent need of a better veterinary control with the implementation of effective and comprehensive strategies in order to reach a good protection of animals as well as human health. In South Tunisia, the prevalence of bovine TB is high with Mycobacterium bovis as causative agent and cattle as reservoir of the bacteria. However as previously mentioned in several studies, M. bovis is also responsible for human extrapulmonary tuberculosis (EPTB) cases in South Tunisia. Despite the veterinary and medical problems, M. bovis is still little studied. In this context, this work aimed to study the molecular epidemiology of M. bovis in EPTB patients in south Tunisia in order to determine the main risk factors of transmission. Our results underlined that SB0120, SB0121 and SB2025, previously described in cattle in Tunisia, represent the predominant genotypes. The findings highlighted that human EPTB caused by M. bovis mainly occurred through the consumption of raw milk or derivatives. These data demonstrate the urgent need to implement strategies for preventing and controlling zoonotic TB.
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Affiliation(s)
- Mariam Siala
- Department of Biology, Preparatory Institute for Engineering Studies, Sfax, University of Sfax-Tunisia
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, Sfax, University of Sfax-Tunisia
- * E-mail:
| | - Cécile Cassan
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
| | - Salma Smaoui
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Sana Kammoun
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Chema Marouane
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Sylvain Godreuil
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, CHU de Montpellier, France
| | - Salma Hachicha
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Emna Mhiri
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
- Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A. Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Leila Slim
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
- Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A. Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Dhikrayet Gamara
- Basic Health Care Management, Ministry of Health, Tunis, Tunisia
| | - Férièle Messadi-Akrout
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Anne-Laure Bañuls
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
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Vergnes B, Gazanion E, Mariac C, Du Manoir M, Sollelis L, Lopez-Rubio JJ, Sterkers Y, Bañuls AL. A single amino acid substitution (H451Y) in Leishmania calcium-dependent kinase SCAMK confers high tolerance and resistance to antimony. J Antimicrob Chemother 2019; 74:3231-3239. [DOI: 10.1093/jac/dkz334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
For almost a century, antimonials have remained the first-line drugs for the treatment of leishmaniasis. However, little is known about their mode of action and clinical resistance mechanisms.
Objectives
We have previously shown that Leishmania nicotinamidase (PNC1) is an essential enzyme for parasite NAD+ homeostasis and virulence in vivo. Here, we found that parasites lacking the pnc1 gene (Δpnc1) are hypersusceptible to the active form of antimony (SbIII) and used these mutant parasites to better understand antimony’s mode of action and the mechanisms leading to resistance.
Methods
SbIII-resistant WT and Δpnc1 parasites were selected in vitro by a stepwise selection method. NAD(H)/NADP(H) dosages and quantitative RT–PCR experiments were performed to explain the susceptibility differences observed between strains. WGS and a marker-free CRISPR/Cas9 base-editing approach were used to identify and validate the role of a new resistance mutation.
Results
NAD+-depleted Δpnc1 parasites were highly susceptible to SbIII and this phenotype could be rescued by NAD+ precursor or trypanothione precursor supplementation. Δpnc1 parasites could become resistant to SbIII by an unknown mechanism. WGS revealed a unique amino acid substitution (H451Y) in an EF-hand domain of an orphan calcium-dependent kinase, recently named SCAMK. When introduced into a WT reference strain by base editing, the H451Y mutation allowed Leishmania parasites to survive at extreme concentrations of SbIII, potentiating the rapid emergence of resistant parasites.
Conclusions
These results establish that Leishmania SCAMK is a new central hub of antimony’s mode of action and resistance development, and uncover the importance of drug tolerance mutations in the evolution of parasite drug resistance.
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Affiliation(s)
| | | | | | | | | | | | - Yvon Sterkers
- MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France
- Department of Parasitology-Mycology, Faculty of Medicine, University Hospital Center of Montpellier, Univ. Montpellier, Montpellier, France
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Nguyen TNA, Anton-Le Berre V, Bañuls AL, Nguyen TVA. Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review. Front Microbiol 2019; 10:794. [PMID: 31057511 PMCID: PMC6477542 DOI: 10.3389/fmicb.2019.00794] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 10/04/2018] [Accepted: 03/28/2019] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations.
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Affiliation(s)
- Thi Ngoc Anh Nguyen
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Anne-Laure Bañuls
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thi Van Anh Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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Ouchar Mahamat O, Lounnas M, Hide M, Dumont Y, Tidjani A, Kamougam K, Abderrahmane M, Benavides J, Solassol J, Bañuls AL, Jean-Pierre H, Carrière C, Godreuil S. High prevalence and characterization of extended-spectrum ß-lactamase producing Enterobacteriaceae in Chadian hospitals. BMC Infect Dis 2019; 19:205. [PMID: 30819135 PMCID: PMC6396450 DOI: 10.1186/s12879-019-3838-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 07/15/2018] [Accepted: 02/20/2019] [Indexed: 11/15/2022] Open
Abstract
Background Extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) represent a major problem in the management of nosocomial infections. However, ESBL-PE are not systematically monitored in African countries. The aim of this study was to determine ESBL-PE prevalence in patients from three hospitals in N’Djamena, the capital city of Chad, and to characterize the genetic origin of the observed resistance. Methods From January to March 2017, 313 non-duplicate isolates were recovered from various clinical specimens obtained from 1713 patients in the three main hospitals of N’Djamena. Bacterial species were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Susceptibility to 28 antibiotics was tested using the disk diffusion method on Müller-Hinton agar, and ESBL production was confirmed with the double-disc synergy test. The most prevalent ESBL genes associated with the observed resistance were detected using multiplex PCR followed by double-stranded DNA sequencing. Results Among the 313 isolates, 197 belonged to the Enterobacteriaceae family. The overall ESBL-PE prevalence was 47.72% (n = 94/197), with a higher rate among inpatients compared with outpatients (54.13% vs. 34.37%). ESBL-PE prevalence was highest in older patients (≥60 years of age). E. coli was the most common ESBL-producer organism (63.8%), followed by K. pneumoniae (21.2%). ESBL-PE were mainly found in urine samples (75%). The CTX-M-1 group was dominant (96.7% of the 94 ESBL-PE isolates, CTX-M-15 enzyme), followed by the CTX-M-9 group (4.1%). 86% of resistant isolates harbored more than one ESBL-encoding gene. ESBL production was also associated with the highest levels of resistance to non-β-lactam drugs. Conclusions The prevalence of ESBL-PE harboring resistant genes encoding ESBLs of the CTX-M-1 group was high (48%) among clinical isolates of three main hospitals in Chad, suggesting an alarming spread of ESBL-PE among patients. Electronic supplementary material The online version of this article (10.1186/s12879-019-3838-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oumar Ouchar Mahamat
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France. .,UMR MIVEGEC IRD-CNRS-Université de Montpellier, Laboratory of Bacteriology CHU, Arnaud de Villeneuve 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France. .,Service de laboratoire, Hôpital de la Mère et de l'Enfant, N'Djaména, Chad.
| | - Manon Lounnas
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,UMR MIVEGEC IRD-CNRS-Université de Montpellier, Laboratory of Bacteriology CHU, Arnaud de Villeneuve 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - Mallorie Hide
- UMR MIVEGEC IRD-CNRS-Université de Montpellier, Laboratory of Bacteriology CHU, Arnaud de Villeneuve 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - Yann Dumont
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France
| | | | - Kadidja Kamougam
- Service de laboratoire, Hôpital Général des Références Nationale, N'Djaména, Chad
| | | | - Julio Benavides
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jérôme Solassol
- Centre Hospitalier Universitaire de Montpellier, Département Bio-pathologie cellulaire et tissulaire des tumeurs, Université de Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC IRD-CNRS-Université de Montpellier, Laboratory of Bacteriology CHU, Arnaud de Villeneuve 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France.,Laboraoire Mixte International DRISA, IRD, Montpellier, France
| | - Hélène Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France
| | - Christian Carrière
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France
| | - Sylvain Godreuil
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Université de Montpellier, Montpellier, France.,UMR MIVEGEC IRD-CNRS-Université de Montpellier, Laboratory of Bacteriology CHU, Arnaud de Villeneuve 371 avenue du doyen Gaston Giraud, 34295, Montpellier Cedex 5, France.,Laboraoire Mixte International DRISA, IRD, Montpellier, France
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Cassan C, Diagne CA, Tatard C, Gauthier P, Dalecky A, Bâ K, Kane M, Niang Y, Diallo M, Sow A, Brouat C, Bañuls AL. Leishmania major and Trypanosoma lewisi infection in invasive and native rodents in Senegal. PLoS Negl Trop Dis 2018; 12:e0006615. [PMID: 29958273 PMCID: PMC6042788 DOI: 10.1371/journal.pntd.0006615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/12/2018] [Accepted: 06/17/2018] [Indexed: 11/19/2022] Open
Abstract
Bioinvasion is a major public health issue because it can lead to the introduction of pathogens in new areas and favours the emergence of zoonotic diseases. Rodents are prominent invasive species, and act as reservoirs in many zoonotic infectious diseases. The aim of this study was to determine the link between the distribution and spread of two parasite taxa (Leishmania spp. and Trypanosoma lewisi) and the progressive invasion of Senegal by two commensal rodent species (the house mouse Mus musculus domesticus and the black rat Rattus rattus). M. m. domesticus and R. rattus have invaded the northern part and the central/southern part of the country, respectively. Native and invasive rodents were caught in villages and cities along the invasion gradients of both invaders, from coastal localities towards the interior of the land. Molecular diagnosis of the two trypanosomatid infections was performed using spleen specimens. In the north, neither M. m. domesticus nor the native species were carriers of these parasites. Conversely, in the south, 17.5% of R. rattus were infected by L. major and 27.8% by T. lewisi, while very few commensal native rodents were carriers. Prevalence pattern along invasion gradients, together with the knowledge on the geographical distribution of the parasites, suggested that the presence of the two parasites in R. rattus in Senegal is of different origins. Indeed, the invader R. rattus could have been locally infected by the native parasite L. major. Conversely, it could have introduced the exotic parasite T. lewisi in Senegal, the latter appearing to be poorly transmitted to native rodents. Altogether, these data show that R. rattus is a carrier of both parasites and could be responsible for the emergence of new foci of cutaneous leishmaniasis, or for the transmission of atypical human trypanosomiasis in Senegal.
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Affiliation(s)
- Cécile Cassan
- MIVEGEC, IRD, CNRS, Univ. Montpellier, Montpellier, France
| | - Christophe A. Diagne
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
| | - Caroline Tatard
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Philippe Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Khalilou Bâ
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
| | - Mamadou Kane
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
| | - Youssoupha Niang
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
| | - Mamoudou Diallo
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
| | - Aliou Sow
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Campus ISRA/IRD de Bel Air, Dakar, Sénégal
| | - Carine Brouat
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Lehrter V, Bañuls AL, Léger N, Rioux JA, Depaquit J. Phlebotomus (Paraphlebotomus) chabaudi and Phlebotomus riouxi: closely related species or synonyms? ACTA ACUST UNITED AC 2017; 24:47. [PMID: 29194032 PMCID: PMC5711378 DOI: 10.1051/parasite/2017050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 05/20/2017] [Accepted: 11/09/2017] [Indexed: 11/14/2022]
Abstract
Phlebotomus riouxi Depaquit, Killick-Kendrick & Léger 1998 was described as a species closely related to Phlebotomus chabaudi Croset, Abonnenc & Rioux 1970, differing mainly by the size and number of setae of the coxite basal lobe. Molecular studies carried out on several populations from Algeria and Tunisia and based on mitochondrial genes cytochrome b (Cytb) and cytochrome oxidase I (COI) supported the typological validity of these two species. Recently, specimens from a single population in southern Tunisia were morphologically identified as Ph. riouxi, Ph. chabaudi and intermediates, but were clustered in the same clade according to their Cytb and nuclear gene elongation factor-1 α (EF-1α) sequences. These species were thus synonymized. To further explore this synonymy, we carried out a molecular study on specimens from Algeria and Tunisia using the same molecular markers and a part of 28S rDNA. We did not find any morphologically intermediate specimens in our sampling. We highlighted differences between the genetic divergence rates within and between the two species for the three markers and we identified new haplotypes. The sequence analysis did not reveal any signature of introgression in allopatric nor in sympatric populations such as in the Ghomrassen population. Phylogenetic analyses based on our specimens revealed that the two main clades are Ph. chabaudi and Ph. riouxi, in agreement with the morphological identification. These results support the validity of Ph. riouxi and Ph. chabaudi as typological species.
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Affiliation(s)
- Véronique Lehrter
- EA 4688 - USC ANSES VECPAR, SFR Cap Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC, IRD - CNRS - Université de Montpellier, 911 avenue Agropolis, 34394 Montpellier, France
| | - Nicole Léger
- EA 4688 - USC ANSES VECPAR, SFR Cap Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims, France
| | - Jean-Antoine Rioux
- Faculté de Médecine, Université de Montpellier, 2 rue de l'École de Médecine, 34000 Montpellier, France
| | - Jérôme Depaquit
- EA 4688 - USC ANSES VECPAR, SFR Cap Santé, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims, France
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Kocher A, de Thoisy B, Catzeflis F, Valière S, Bañuls AL, Murienne J. iDNA screening: Disease vectors as vertebrate samplers. Mol Ecol 2017; 26:6478-6486. [PMID: 28926155 DOI: 10.1111/mec.14362] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/28/2017] [Accepted: 09/12/2017] [Indexed: 01/13/2023]
Abstract
In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology.
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Affiliation(s)
- Arthur Kocher
- CNRS, Université Toulouse III Paul Sabatier, ENFA;, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France.,IRD 224, CNRS 5290, Université de Montpellier, UMR MIVEGEC, Montpellier, France
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana.,Association Kwata, Cayenne, French Guiana
| | - François Catzeflis
- Institut des Sciences de l'Evolution, Case Courrier 064, CNRS UMR-5554, Université Montpellier-2, Montpellier, France
| | - Sophie Valière
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Anne-Laure Bañuls
- IRD 224, CNRS 5290, Université de Montpellier, UMR MIVEGEC, Montpellier, France
| | - Jérôme Murienne
- CNRS, Université Toulouse III Paul Sabatier, ENFA;, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
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Nguyen HQ, Nguyen NV, Contamin L, Tran THT, Vu TT, Nguyen HV, Nguyen NLT, Nguyen ST, Dang AD, Bañuls AL, Nguyen VAT. Quadruple-first line drug resistance in Mycobacterium tuberculosis in Vietnam: What can we learn from genes? Infect Genet Evol 2017; 50:55-61. [PMID: 28214557 DOI: 10.1016/j.meegid.2017.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/13/2017] [Accepted: 02/13/2017] [Indexed: 12/15/2022]
Abstract
In Vietnam, a country with high tuberculosis (137/100.000 population) and multidrug-resistant (MDR)-TB burdens (7.8/100.000 population), little is known about the molecular signatures of drug resistance in general and more particularly of second line drug (SLD) resistance. This study is specifically focused on Mycobacterium tuberculosis isolates resistant to four first-line drugs (FLDs) that make TB much more difficult to treat. The aim is to determine the proportion of SLD resistance in these quadruple drug resistant isolates and the genetic determinants linked to drug resistance to better understand the genetic processes leading to quadruple and extremely drug resistance (XDR). 91 quadruple (rifampicin, isoniazid, ethambutol and streptomycin) FLD resistant and 55 susceptible isolates were included. Spoligotyping and 24-locus MIRU-VNTR techniques were performed and 9 genes and promoters linked to FLD and SLD resistance were sequenced. SLD susceptibility testing was carried out on a subsample of isolates. High proportion of quadruple-FLD resistant isolates was resistant to fluoroquinolones (27%) and second-line injectable drugs (30.2%) by drug susceptibility testing. The sequencing revealed high mutation diversity with prevailing mutations at positions katG315, inhA-15, rpoB531, embB306, rrs1401, rpsL43 and gyrA94. The sensitivity and specificity were high for most drug resistances (>86%), but the sensitivity was lower for injectable drug resistances (<69%). The mutation patterns revealed 23.1% of pre-XDR and 7.7% of XDR isolates, mostly belonging to Beijing family. The genotypic diversity and the variety of mutations reflect the existence of various evolutionary paths leading to FLD and SLD resistance. Nevertheless, particular mutation patterns linked to high-level resistance and low fitness costs seem to be favored.
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Affiliation(s)
- Huy Quang Nguyen
- UMR MIVEGEC (224 IRD-5290 CNRS-Université de Montpellier), Institute of Research for Development, Montpellier, France; Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam; Department of Biotechnology-Pharmacology, University of Science and Technology of Hanoi, Hanoi, Viet Nam; LMI Drug Resistance in South East Asia (DRISA), NIHE, Hanoi, Viet Nam.
| | - Nhung Viet Nguyen
- Viet Nam National Tuberculosis Programme, Hanoi, Viet Nam; Viet Nam Association for Tuberculosis and Lung Disease, Hanoi, Viet Nam
| | - Lucie Contamin
- UMR MIVEGEC (224 IRD-5290 CNRS-Université de Montpellier), Institute of Research for Development, Montpellier, France; Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam; LMI Drug Resistance in South East Asia (DRISA), NIHE, Hanoi, Viet Nam
| | - Thanh Hoa Thi Tran
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Thuong Thi Vu
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Hung Van Nguyen
- Department of Microbiology, National Lung Hospital, Hanoi, Viet Nam
| | | | - Son Thai Nguyen
- Department of Microbiology, Military Medical University, Hanoi, Viet Nam
| | - Anh Duc Dang
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Anne-Laure Bañuls
- UMR MIVEGEC (224 IRD-5290 CNRS-Université de Montpellier), Institute of Research for Development, Montpellier, France; Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam; LMI Drug Resistance in South East Asia (DRISA), NIHE, Hanoi, Viet Nam
| | - Van Anh Thi Nguyen
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
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Prudhomme J, Cassan C, Hide M, Toty C, Rahola N, Vergnes B, Dujardin JP, Alten B, Sereno D, Bañuls AL. Ecology and morphological variations in wings of Phlebotomus ariasi (Diptera: Psychodidae) in the region of Roquedur (Gard, France): a geometric morphometrics approach. Parasit Vectors 2016; 9:578. [PMID: 27842606 PMCID: PMC5109773 DOI: 10.1186/s13071-016-1872-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/03/2016] [Indexed: 12/03/2022] Open
Abstract
Background Phlebotomus ariasi Tonnoir, 1921, is the predominant sand fly species in the Cevennes region and a proven vector of Leishmania infantum, which is the main pathogen of visceral and canine leishmaniasis in the south of France. Even if this species is widely present in Western Mediterranean countries, its biology and ecology remain poorly known. The main goals of this work are to investigate the phenotypic variation of P. ariasi at a local scale in a region characterized by climatic and environmental fluctuations, and to determine if slope and altitude could affect the sand fly phenotypes. Results Sand flies were captured along a 14 km-long transect in 2011 from May to October. At the same time, environmental data such as altitude and slope were also collected. Morphological analysis of P. ariasi wings was performed by a geometric morphometrics approach. We found morphological variation among local populations of P. ariasi. Strong shape and size variations were observed in the course of the season (particularly in June and July) for both genders. During June, we highlighted differences in wing phenotypes according to altitude for both sexes and to slope and station for females. Conclusions The phenotypic variations observed in P. ariasi along the studied transect indicated these populations are subjected to environmental pressures. Nevertheless, it seems that sand flies are more sensitive to extrinsic factors in June and July, suggesting a phenotypic plasticity.
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Affiliation(s)
- Jorian Prudhomme
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France.
| | - Cécile Cassan
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
| | - Mallorie Hide
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
| | - Céline Toty
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
| | - Nil Rahola
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
| | - Baptiste Vergnes
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
| | | | - Bulent Alten
- Department of Biology, Ecology Section, Faculty of Science, Hacettepe University, HU-ESRL-VERG Laboratories, Beytepe, Ankara, 0680, Turkey
| | - Denis Sereno
- UMR INTERTRYP (IRD - CIRAD 177), Centre IRD, Montpellier, F34394, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 avenue Agropolis, Montpellier, F34394, France
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Ouedraogo AS, Dunyach-Remy C, Kissou A, Sanou S, Poda A, Kyelem CG, Solassol J, Bañuls AL, Van De Perre P, Ouédraogo R, Jean-Pierre H, Lavigne JP, Godreuil S. High Nasal Carriage Rate of Staphylococcus aureus Containing Panton-Valentine leukocidin- and EDIN-Encoding Genes in Community and Hospital Settings in Burkina Faso. Front Microbiol 2016; 7:1406. [PMID: 27679613 PMCID: PMC5020597 DOI: 10.3389/fmicb.2016.01406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
The objectives of the present study were to investigate the rate of S.aureus nasal carriage and molecular characteristics in hospital and community settings in Bobo Dioulasso, Burkina Faso. Nasal samples (n = 219) were collected from 116 healthy volunteers and 103 hospitalized patients in July and August 2014. Samples were first screened using CHROMagar Staph aureus chromogenic agar plates, and S. aureus strains were identified by mass spectrometry. Antibiotic susceptibility was tested using the disk diffusion method on Müller-Hinton agar. All S. aureus isolates were genotyped using DNA microarray. Overall, the rate of S. aureus nasal carriage was 32.9% (72/219) with 29% in healthy volunteers and 37% in hospital patients. Among the S. aureus isolates, only four methicillin-resistant S. aureus (MRSA) strains were identified and all in hospital patients (3.9%). The 72 S. aureus isolates from nasal samples belonged to 16 different clonal complexes, particularly to CC 152-MSSA (22 clones) and CC1-MSSA (nine clones). Two clones were significantly associated with community settings: CC1-MSSA and CC45-MSSA. The MRSA strains belonged to the ST88-MRSA-IV or the CC8-MRSA-V complex. A very high prevalence of toxinogenic strains 52.2% (36/69), containing Panton-Valentine leucocidin- and EDIN-encoding genes, was identified among the S. aureus isolates in community and hospital settings. This study provides the first characterization of S. aureus clones and their genetic characteristics in Burkina Faso. Altogether, it highlights the low prevalence of antimicrobial resistance, high diversity of methicillin-sensitive S. aureus clones and high frequency of toxinogenic S. aureus strains.
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Affiliation(s)
- Abdoul-Salam Ouedraogo
- Centre Hospitalier Universitaire Souro SanouBobo Dioulasso, Burkina Faso; Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de MontpellierMontpellier, France; Université de MontpellierMontpellier, France; Institut National de la Santé et de la Recherche Médicale U1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to PreventionMontpellier, France
| | - Catherine Dunyach-Remy
- Institut National de la Santé et de la Recherche Médicale U1047, Université de MontpellierNîmes, France; Service de Microbiologie, Centre Hospitalier Universitaire CaremeauNîmes, France
| | - Aimée Kissou
- Centre Hospitalier Universitaire Souro Sanou Bobo Dioulasso, Burkina Faso
| | - Soufiane Sanou
- Centre Hospitalier Universitaire Souro Sanou Bobo Dioulasso, Burkina Faso
| | - Armel Poda
- Centre Hospitalier Universitaire Souro Sanou Bobo Dioulasso, Burkina Faso
| | - Carole G Kyelem
- Centre Hospitalier Universitaire Souro Sanou Bobo Dioulasso, Burkina Faso
| | - Jérôme Solassol
- Department of Biopathology, Centre Hospitalier Universitaire MontpellierMontpellier, France; Department of Clinical Oncoproteomics, Montpellier Cancer InstituteMontpellier, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD 224 - Centre National de la Recherche Scientifique 5290 - Université de Montpellier) Montpellier, France
| | - Philippe Van De Perre
- Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de MontpellierMontpellier, France; Université de MontpellierMontpellier, France; Institut National de la Santé et de la Recherche Médicale U1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to PreventionMontpellier, France
| | - Rasmata Ouédraogo
- Centre Hospitalier Universitaire Souro Sanou Bobo Dioulasso, Burkina Faso
| | - Hélène Jean-Pierre
- Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de Montpellier Montpellier, France
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale U1047, Université de MontpellierNîmes, France; Service de Microbiologie, Centre Hospitalier Universitaire CaremeauNîmes, France
| | - Sylvain Godreuil
- Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de MontpellierMontpellier, France; Université de MontpellierMontpellier, France; Institut National de la Santé et de la Recherche Médicale U1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to PreventionMontpellier, France
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Nguyen VAT, Bañuls AL, Tran THT, Pham KLT, Nguyen TS, Nguyen HV, Nguyen NLT, Nguyen NLT, Dang DA, Marks GB, Choisy M. Mycobacterium tuberculosis lineages and anti-tuberculosis drug resistance in reference hospitals across Viet Nam. BMC Microbiol 2016; 16:167. [PMID: 27464737 PMCID: PMC4964266 DOI: 10.1186/s12866-016-0784-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/19/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis, the tuberculosis (TB) pathogen, despite a low level of genetic diversity, has revealed a high variety of biological and epidemiological characteristics linked to their lineages, such as transmissibility, fitness and propensity to acquire drug resistance. This has important implications for the epidemiology of TB. We conducted this first countrywide cross-sectional study to identify the prevalent M. tuberculosis lineages and to assess their epidemiological associations and their relation to drug resistance. The study was conducted among isolates acquired in reference hospitals across Vietnam. Isolates with drug susceptibility testing profiles were identified for their lineages by spoligotyping. Logistic regression was used to investigate the association of M. tuberculosis lineages with location, age and sex of the patients and drug resistance levels. RESULTS Results showed that the most prevalent lineage was Beijing (55.4 %), followed by EAI (27.5 %), T (6.4 %), LAM (1.3 %), Haarlem (1 %) and Zero type (0.3 %). The proportion of Beijing isolates in the North (70.4 %) and the South (68 %) was higher than in the Centre (28 %) (OR = 1.7 [95 % CI: 1.4-2.0], p < 0.0001), whereas the proportion of EAI isolates in the North (7.1 %) and the South (17 %) was much lower compared with the Centre (59 %) (OR = 0.5 [95 % CI: 0.4-0.6], p < 0.0001). Overall, Beijing isolates were the most likely to be drug-resistant and EAI isolates were the least likely to be drug-resistant, except in the South of Vietnam where EAI is also highly drug-resistant. The proportion of Beijing isolates was significantly higher (p < 0.01), and the proportion of EAI isolates was significantly lower (p < 0.05) in younger patients. The proportion of drug-resistance was higher in isolates collected from male patients and from patients in the middle age groups. CONCLUSIONS The findings suggest ongoing replacement of EAI lineage, which is mainly more drug-susceptible with highly drug-resistant Beijing lineage in all studied regions of Vietnam. Male patients of working ages should be the focus for better control to prevent the emergence of drug-resistant TB.
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Affiliation(s)
- Van Anh Thi Nguyen
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, 10000 Vietnam
| | - Anne-Laure Bañuls
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
- MIVEGEC (IRD 224-CNRS 5290-Université de Montpellier), Centre IRD, Montpellier, France
| | - Thanh Hoa Thi Tran
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - Kim Lien Thi Pham
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - Thai Son Nguyen
- Department of Microbiology, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - Hung Van Nguyen
- Department of Microbiology, National Lung Hospital, Hanoi, Vietnam
| | - Ngoc Lan Thi Nguyen
- Department of Microbiology, Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam
| | | | - Duc Anh Dang
- Department of Bacteriology, National Institute of Hygiene Epidemiology, Hanoi, Vietnam
| | - Guy B. Marks
- Woolcock Institute of Medical Research, University of Sydney, Sydney, Australia
- South Western Sydney Clinical School, UNSW, Sydney, Australia
| | - Marc Choisy
- MIVEGEC (IRD 224-CNRS 5290-Université de Montpellier), Centre IRD, Montpellier, France
- Oxford University Clinical Research Unit, Hanoi, Vietnam
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Kocher A, Gantier JC, Gaborit P, Zinger L, Holota H, Valiere S, Dusfour I, Girod R, Bañuls AL, Murienne J. Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding. Mol Ecol Resour 2016; 17:172-182. [PMID: 27292284 DOI: 10.1111/1755-0998.12556] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.
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Affiliation(s)
- Arthur Kocher
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France.,UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 Avenue Agropolis, F34394, Montpellier, France
| | - Jean-Charles Gantier
- Laboratoire des Identifications Fongiques et Entomo-parasitologiques, Mennecy, France
| | - Pascal Gaborit
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Lucie Zinger
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
| | - Helene Holota
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
| | - Sophie Valiere
- GeT-PlaGe, Genotoul, INRA Auzeville, 31326, Castanet-Tolosan, France
| | - Isabelle Dusfour
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de la Guyane, 23 Avenue Pasteur, BP 6010, 97306, Cayenne Cedex, French Guiana
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD 224 - CNRS 5290 - Université de Montpellier), 911 Avenue Agropolis, F34394, Montpellier, France
| | - Jerome Murienne
- CNRS, Université Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), Toulouse, France
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Cassan C, Dione MM, Dereure J, Diedhiou S, Bucheton B, Hide M, Kako C, Gaye O, Senghor M, Niang AA, Bañuls AL, Faye B. First insights into the genetic diversity and origin of Leishmania infantum in Mont Rolland (Thiès region, Senegal). Microbes Infect 2016; 18:412-420. [DOI: 10.1016/j.micinf.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
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Chazel M, Marchandin H, Keck N, Terru D, Carrière C, Ponsoda M, Jacomo V, Panteix G, Bouzinbi N, Bañuls AL, Choisy M, Solassol J, Aubry A, Godreuil S. Evaluation of the SLOMYCO Sensititre(®) panel for testing the antimicrobial susceptibility of Mycobacterium marinum isolates. Ann Clin Microbiol Antimicrob 2016; 15:30. [PMID: 27150659 PMCID: PMC4858841 DOI: 10.1186/s12941-016-0145-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/27/2016] [Indexed: 12/30/2022] Open
Abstract
Background The agar dilution method is currently considered as the reference method for Mycobacterium marinum drug susceptibility testing (DST). As it is time-consuming, alternative methods, such as the E-test, were evaluated for M.marinum DST, but without success. The SLOMYCO Sensititre® panel, recently commercialized by TREK Diagnostic Systems (Cleveland, OH), can be used for DST in slow-growing mycobacteria and for antimicrobial agents recommended by the Clinical and Laboratory Standards Institute (CLSI) for M.marinum DST. The main goal of this work was to evaluate the SLOMYCO Sensititre® panel method for DST in M.marinum isolates from human patients and fish relative to the reference agar dilution method. Methods/Results The reproducibility of the minimum inhibitory concentration (MIC) determination (±1 log2 dilution) was very good for both the agar dilution method and SLOMYCO Sensititre® panel (>90 % agreement). The percentage essential agreement between methods varied, depending on the drug: between 97 and 75 % for ciprofloxacin, moxifloxacin, linezolid, isoniazid, clarithromycin, amikacin, rifabutin and rifampin, 74 % for trimethoprim, 72 % for doxycycline, 70 % for sulfamethoxazole, 59 % for streptomycin, 33 % for ethambutol and only 2.2 % for ethionamide. When the agar dilution and SLOMYCO Sensititre® panel results were converted into interpretive criteria, the category agreement was 100 % for amikacin, ciprofloxacin, clarithromycin, moxifloxacin, rifabutin, sulfamethoxazole and trimethoprim, 98 % for ethambutol and 96 % for rifampin and no agreement for doxycycline. Conclusions The SLOMYCO Sensititre® panel method could provide a potential alternative to the reference agar dilution method, when DST in M.marinum is required, except for doxycycline.
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Affiliation(s)
- Marion Chazel
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France
| | - Hélène Marchandin
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France.,UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, Laboratoire de Bactériologie, U.F.R. des Sciences Pharmaceutiques et Biologiques, Montpellier, France
| | - Nicolas Keck
- Laboratoire Départemental Vétérinaire de l'Hérault, Montpellier, France
| | - Dominique Terru
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France
| | - Christian Carrière
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France.,Department of Bacteriology-Virology, INSERM U1058 "Pathogenesis and Control of Chronic Infections", Université Montpellier-EFS, CHU Arnaud de Villeneuve 371 avenue du Doyen Gaston Giraud, 34295, Montpellier, France.,Université Montpellier, Montpellier, France
| | | | | | | | - Nicolas Bouzinbi
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224, Université de Montpellier, Montpellier, France
| | - Marc Choisy
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224, Université de Montpellier, Montpellier, France
| | - Jérôme Solassol
- Université Montpellier, Montpellier, France.,Department of Biopathology, CHRU Montpellier, Montpellier, France.,Department of Clinical Oncoproteomic, Montpellier Cancer Institute, Montpellier, France
| | - Alexandra Aubry
- Centre National de Référence des Mycobactéries et de la Résistance aux Antituberculeux, Paris, France.,Laboratoire de Bactériologie-Hygiène Paris, AP-HP, Hôpital Pitié-Salpêtrière, 75013, Paris, France.,Centre for Immunology and Microbial Infections, team 13, Sorbonne Universités, UPMC Univ Paris 06, U1135, 75013, Paris, France.,INSERM, U1135, Paris, France
| | - Sylvain Godreuil
- Département de Bactériologie-Virologie, CHRU Montpellier, Montpellier, France. .,Department of Bacteriology-Virology, INSERM U1058 "Pathogenesis and Control of Chronic Infections", Université Montpellier-EFS, CHU Arnaud de Villeneuve 371 avenue du Doyen Gaston Giraud, 34295, Montpellier, France. .,Université Montpellier, Montpellier, France.
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Abstract
Although leishmaniases are endemic in 98 countries, they are still considered neglected tropical diseases. Leishmaniases are characterized by the emergence of new virulent and asymptomatic strains of Leishmania spp. and, as a consequence, by a very diverse clinical spectrum. To fight more efficiently these parasites, the mechanisms of host defense and of parasite virulence need to be thoroughly investigated. To this aim, animal models are widely used. However, the results obtained with these models are influenced by several experimental parameters, such as the mouse genetic background, parasite genotype, inoculation route/infection site, parasite dose and phlebotome saliva. In this review, we propose an update on their influence in the two main clinical forms of the disease: cutaneous and visceral leishmaniases.
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Affiliation(s)
- Corinne Loeuillet
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR IRD 224-CNRS 5290, Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR IRD 224-CNRS 5290, Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Mallorie Hide
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR IRD 224-CNRS 5290, Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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Ngoc Thi Vu B, J Jafari A, Aardema M, Kieu Thi Tran H, Ngoc Thi Nguyen D, Tuyet Dao T, Vu Nguyen T, Khanh Tran T, Kim Thi Nguyen C, Fox A, Bañuls AL, Thwaites G, Van Nguyen K, Wertheim HFL. Population structure of colonizing and invasive Staphylococcus aureus strains in northern Vietnam. J Med Microbiol 2016; 65:298-305. [PMID: 26758688 DOI: 10.1099/jmm.0.000220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is an important global health problem worldwide. There is still scarce information on the population structure of S. aureus strains in Asia, where the majority of the world population lives. This study characterized the diversity of S. aureus strains in northern Vietnam through multilocus sequence typing (MLST). Eighty-five carriage isolates from the community and 77 invasive isolates from the clinical setting were selected and tested for meticillin resistance and the presence of Panton-Valentine leukocidin (PVL). MLST was performed on these isolates, of which CC59 (25.4 %), CC188 (17.3 %) and CC45 (16.7 %) were the predominant clonal complexes (CCs). CC59 carriage isolates had significantly lower rates of meticillin-resistant S. aureus (MRSA) than their corresponding clinical group isolates (32 vs 83 %). There were no significant differences in rates of MRSA between carriage isolates and clinical isolates of CC45 and CC188. CC59 carriage isolates were significantly lower in rates of PVL+ than CC59 clinical isolates (32 vs 83 %), but the converse was shown in CC45 isolates (14 vs 0 %, respectively). This study revealed vast differences in the molecular epidemiology and population structure of S. aureus in community and clinical settings in Vietnam. Nevertheless, the data underline the spread of virulent and/or resistant strains (MRSA and/or PVL+) in the community, suggesting the necessity for further surveillance to determine the mechanism of transmission of these strains (i.e. MRSA/PVL+) outside clinical settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Annette Fox
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.,Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
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Prudhomme J, Rahola N, Toty C, Cassan C, Roiz D, Vergnes B, Thierry M, Rioux JA, Alten B, Sereno D, Bañuls AL. Ecology and spatiotemporal dynamics of sandflies in the Mediterranean Languedoc region (Roquedur area, Gard, France). Parasit Vectors 2015; 8:642. [PMID: 26683841 PMCID: PMC4684629 DOI: 10.1186/s13071-015-1250-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/06/2015] [Indexed: 01/10/2023] Open
Abstract
Background Phlebotomine sandflies are hematophagous insects widely present in Western Mediterranean countries and known for their role as Leishmania vectors. During the last ten years, the risk of leishmaniasis re-emergence has increased in France. However, sandfly biology and ecology in the South of France remain poorly known because the last detailed study on their spatiotemporal dynamics was performed over 30 years ago. The aim of the present study was to update our knowledge on sandfly ecology by determining their spatiotemporal dynamics and by investigating the relationship between environmental/climatic factors and the presence and abundance of sandflies in the South of France. Methods An entomological survey was carried out during three years (2011–2013) along a 14 kilometer-long transect. The findings were compared with the data collected along the same transect in 1977. Data loggers were placed in each station and programmed to record temperature and relative humidity every six hours between April 2011 and November 2014. Several environmental factors (such as altitude, slope and wall orientation (North, East, West and South)) were characterized at each station. Results Four sandfly species were collected: Phlebotomus ariasi and Sergentomyia minuta, which were predominant, Ph. perniciosus and Ph. mascittii. Sandfly activity within the studied area started in May and ended in October with peaks in July-August at the optimum average temperature. We found a positive effect of altitude and temperature and a negative effect of relative humidity on Ph. ariasi and Se. minuta presence. We detected interspecific differences and non-linear effects of these climatic variables on sandfly abundance. Although the environment has considerably changed in 30 years, no significant difference in sandfly dynamics and species diversity was found by comparing the 1977 and 2011–2013 data. Conclusion Our study shows that this area maintains a rich sandfly fauna with high Ph. ariasi population density during the active season. This represents a risk for Leishmania transmission. The analysis revealed that the presence and abundance of Ph. ariasi and Se. minuta were differently correlated with the environmental and climatic factors. Comparison with the data collected in 1977 highlighted the sandfly population stability, suggesting that they can adapt, in the short and long term, to changing ecosystems.
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Affiliation(s)
- Jorian Prudhomme
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Nil Rahola
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Céline Toty
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Cécile Cassan
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - David Roiz
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Baptiste Vergnes
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Magali Thierry
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
| | - Jean-Antoine Rioux
- Faculté de Médecine, Université Montpellier, 2 rue Ecole de médecine, 34000, Montpellier, France.
| | - Bulent Alten
- Faculty of Science, Department of Biology, Ecology Section, ESRL Laboratories, Hacettepe University, 0680 Beytepe, Ankara, Turkey.
| | - Denis Sereno
- UMR INTERTRYP (IRD - CIRAD 177), Centre IRD, F34394, Montpellier, France.
| | - Anne-Laure Bañuls
- Centre IRD, UMR MIVEGEC (IRD 224 - CNRS 5290 - Université Montpellier), F34394, Montpellier, France.
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Harrabi M, Bettaieb J, Ghawar W, Toumi A, Zaâtour A, Yazidi R, Chaâbane S, Chalghaf B, Hide M, Bañuls AL, Ben Salah A. Spatio-temporal Genetic Structuring of Leishmania major in Tunisia by Microsatellite Analysis. PLoS Negl Trop Dis 2015; 9:e0004017. [PMID: 26302440 PMCID: PMC4547700 DOI: 10.1371/journal.pntd.0004017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/30/2015] [Indexed: 01/06/2023] Open
Abstract
In Tunisia, cases of zoonotic cutaneous leishmaniasis caused by Leishmania major are increasing and spreading from the south-west to new areas in the center. To improve the current knowledge on L. major evolution and population dynamics, we performed multi-locus microsatellite typing of human isolates from Tunisian governorates where the disease is endemic (Gafsa, Kairouan and Sidi Bouzid governorates) and collected during two periods: 1991–1992 and 2008–2012. Analysis (F-statistics and Bayesian model-based approach) of the genotyping results of isolates collected in Sidi Bouzid in 1991–1992 and 2008–2012 shows that, over two decades, in the same area, Leishmania parasites evolved by generating genetically differentiated populations. The genetic patterns of 2008–2012 isolates from the three governorates indicate that L. major populations did not spread gradually from the south to the center of Tunisia, according to a geographical gradient, suggesting that human activities might be the source of the disease expansion. The genotype analysis also suggests previous (Bayesian model-based approach) and current (F-statistics) flows of genotypes between governorates and districts. Human activities as well as reservoir dynamics and the effects of environmental changes could explain how the disease progresses. This study provides new insights into the evolution and spread of L. major in Tunisia that might improve our understanding of the parasite flow between geographically and temporally distinct populations. In Tunisia, zoonotic cutaneous leishmaniasis (ZCL) constitutes a significant public health problem. Since 1884, the Gafsa, Kairouan and Sidi Bouzid governorates are the most endemic areas of ZCL. This study used a multi-locus microsatellite typing approach to study the evolution and the population dynamics of Leishmania major in Tunisia. Within the same area, in twenty years, parasite populations evolved by producing a genetically differentiated population, probably better adapted to the ecosystem. In agreement with the reported human cases of ZCL, the genetic data on samples from the three governorates shows that the disease did not spread according to a geographical gradient. Furthermore, L. major flows seem to still occur between governorates and neighboring districts. This study suggests that environmental changes, human activities and reservoir systems have influenced the spread and evolution of L. major populations. Our findings provide important knowledge on the epidemiology of L. major in Tunisia and might help understanding why the disease is still spreading from the south to the center, despite the control measures that have been put into place.
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Affiliation(s)
- Myriam Harrabi
- Institut Pasteur, Tunis, Tunisia
- Faculté des Sciences de Bizerte-Université de Carthage, Tunis, Tunisia
- * E-mail:
| | | | | | | | | | | | | | | | - Mallorie Hide
- UMR MIVEGEC (IRD 224-CNRS5290-Universités Montpellier 1 et 2), Centre IRD, Montpellier, France
| | - Anne-Laure Bañuls
- UMR MIVEGEC (IRD 224-CNRS5290-Universités Montpellier 1 et 2), Centre IRD, Montpellier, France
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Tomás-Pérez M, Hide M, Riera C, Montoya L, Bañuls AL, Ribera E, Portús M, Fisa R. Multilocus microsatellite typing of Leishmania infantum isolates in monitored Leishmania/HIV coinfected patients. Parasit Vectors 2015. [PMID: 26198004 PMCID: PMC4511019 DOI: 10.1186/s13071-015-0989-9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Leishmania infantum is the main etiological agent of both visceral and cutaneous clinical forms of leishmaniasis in the Mediterranean area. Leishmania/HIV coinfection in this area is characterized by a chronic course and frequent recurrences of clinical episodes. The present study using Multilocus Microsatellite Typing (MLMT) analysis, a highly discriminative tool, aimed to genetically characterize L. infantum isolates taken from monitored Leishmania/HIV coinfected patients presenting successive clinical episodes. Methods In this study, by the analysis of 20 microsatellite loci, we studied the MLMT profiles of 25 L. infantum isolates from 8 Leishmania/HIV coinfected patients who had experienced several clinical episodes. Two to seven isolates per patient were taken before and after treatment, during clinical and non-clinical episodes, with time intervals of 6 days to 29 months. Genetic diversity, clustering and phenetic analyses were performed. Results MLMT enabled us to study the genetic characteristics of the 25 L. infantum isolates, differentiating 18 genotypes, corresponding to a genotypic diversity of 0.72. Fifteen genotypes were unique in the total sample set and only 3 were repeated, 2 of which were detected in different patients. Both clustering and phylogenetic analyses provided insights into the genetic links between the isolates; in five patients isolates showed clear genetic links: either the genotype was exactly the same or only slightly different. In contrast, the isolates of the other three patients were dispersed in different clusters and some could be the result of mixing between populations. Conclusions Our data indicated a great MLMT variability between isolates from coinfected patients and no predominant genotype was observed. Despite this, almost all clinical episodes could be interpreted as a relapse rather than a reinfection. The results showed that diverse factors like an intrapatient evolution over time or culture bias could influence the parasite population detected in the patient, making it difficult to differentiate between relapse and reinfection.
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Affiliation(s)
- Míriam Tomás-Pérez
- Laboratory of Parasitology, Faculty of Pharmacy, Universitat de Barcelona, Avda Joan XXIII s/n, 08028, Barcelona, Spain.
| | - Mallorie Hide
- MIVEGEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France.
| | - Cristina Riera
- Laboratory of Parasitology, Faculty of Pharmacy, Universitat de Barcelona, Avda Joan XXIII s/n, 08028, Barcelona, Spain.
| | - Liliana Montoya
- Laboratory of Parasitology, Faculty of Pharmacy, Universitat de Barcelona, Avda Joan XXIII s/n, 08028, Barcelona, Spain.
| | - Anne-Laure Bañuls
- MIVEGEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France.
| | - Esteve Ribera
- Infectious Diseases Department and Microbiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Montserrat Portús
- Laboratory of Parasitology, Faculty of Pharmacy, Universitat de Barcelona, Avda Joan XXIII s/n, 08028, Barcelona, Spain.
| | - Roser Fisa
- Laboratory of Parasitology, Faculty of Pharmacy, Universitat de Barcelona, Avda Joan XXIII s/n, 08028, Barcelona, Spain.
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Rougeron V, De Meeûs T, Bañuls AL. Response to Tibayrenc et al.: can recombination in Leishmania parasites be so rare? Trends Parasitol 2015; 31:280-1. [PMID: 26142922 DOI: 10.1016/j.pt.2015.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 11/20/2022]
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Brunel AS, Bañuls AL, Marchandin H, Bouzinbi N, Morquin D, Jumas-Bilak E, Corne P. Methicillin-sensitive Staphylococcus aureus CC398 in intensive care unit, France. Emerg Infect Dis 2015; 20:1511-5. [PMID: 25148514 PMCID: PMC4178408 DOI: 10.3201/eid2009.130225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During testing for Staphylococcus aureus in an intensive care unit in France in 2011, we found that methicillin-sensitive S. aureus clonal complex 398 was the most frequent clone (29/125, 23.2%). It was isolated from patients (5/89, 5.6%), health care workers (2/63, 3.2%), and environmental sites (15/864,1.7%). Results indicate emergence of this clone in a hospital setting.
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