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Saint-Hilaire M, Plumain D, Thomé JP, Adam C, Scholl G, Vedy S, Ferdinand S, Talarmin A, Guyomard-Rabenirina S. Validation of an HPLC-MS/MS method with QuEChERS extraction using isotopic dilution to analyze chlordecone in human serum. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123894. [PMID: 37837856 DOI: 10.1016/j.jchromb.2023.123894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/05/2023] [Accepted: 09/23/2023] [Indexed: 10/16/2023]
Abstract
Until 1993, chlordecone (CLD) was extensively used in banana fields in French West Indies. In a previous study, CLD was detected in 90 % of Martinican and Guadeloupean adult's serum. In order to simplify the analyses of CLD in the serum, a new QuEChERS-HPLC-MS/MS method was implemented and validated by the Pasteur Institute of Guadeloupe (IPG). This method was validated with accuracy profiles according to the French Standard NF V03-110 plus the ISO 15189 and European guidelines. Linearity, repeatability, accuracy, intermediate precision, specificity, limit of detection (LOD), limit of quantification (LOQ) and uncertainty were determined. The accuracy profile allowed the method to be validated between 0.06 µg L-1 and 1.00 µg L-1 of serum. The LOD was 0.02 µg L-1, the LOQ was 0.06 µg L-1 and the uncertainty of the method was 21 %. A comparison of 49 serum samples between the IPG (LC-MS/MS) and the LEAE-CART (GC-HRMS) laboratories demonstrated that this new method can reliably determine CLD in human serum. Stability tests were performed and duration of the storage of raw samples and extracts before analysis by HPLC-MS/MS. Raw samples were stable after collection for at least one week at 5 °C or 25 °C and for at least 3 months at -20 °C. Extracts in acetonitrile were stable for at least 1 month at -20 °C. These stability results facilitate the daily use of the method. This method should help the entire population of Guadeloupe and Martinique by allowing a routinely analyzed for CLD and will be useful for future projects aimed at improving population health monitoring.
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Affiliation(s)
- Maïlie Saint-Hilaire
- Institut Pasteur Guadeloupe, Morne Joliviere, 97139 Les Abymes, Guadeloupe, France.
| | - Didier Plumain
- Institut Pasteur Guadeloupe, Morne Joliviere, 97139 Les Abymes, Guadeloupe, France
| | - Jean-Pierre Thomé
- Université de Liège, LEAE -CART, Freshwater and Oceanic Sciences Unit of Research (FOCUS), B6C, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Catherine Adam
- Université de Liège, LEAE -CART, Freshwater and Oceanic Sciences Unit of Research (FOCUS), B6C, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Georges Scholl
- Université de Liège, CART, Molecular Systems Unit of Research (MolSys), B6C, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Serge Vedy
- Institut Pasteur Guadeloupe, Morne Joliviere, 97139 Les Abymes, Guadeloupe, France
| | - Séverine Ferdinand
- Institut Pasteur Guadeloupe, Morne Joliviere, 97139 Les Abymes, Guadeloupe, France
| | - Antoine Talarmin
- Institut Pasteur Guadeloupe, Morne Joliviere, 97139 Les Abymes, Guadeloupe, France
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Gamiette G, Ferdinand S, Couvin D, Dard C, Talarmin A. The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses. Parasit Vectors 2023; 16:276. [PMID: 37563598 PMCID: PMC10416417 DOI: 10.1186/s13071-023-05872-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Angiostrongylus cantonensis (rat lungworm) is the main pathogen responsible for eosinophilic meningitis in humans. One of its intermediate snail hosts, Achatina fulica, was already present in many countries around the world before it appeared in the West Indies in the late 1980s. In the French territories in the Caribbean and northern South America, the first cases of human neuroangiostrongyliasis were reported in Martinique, Guadeloupe and French Guiana in 2002, 2013 and 2017, respectively. In order to better characterize angiostrongyliasis in Guadeloupe, particularly its geographical origin and route of introduction, we undertook molecular characterization of adult worms of Angiostrongylus cantonensis and its intermediate host Achatina fulica. METHODS Genomic DNA of adult Angiostrongylus cantonensis and Achatina fulica was extracted and amplified by polymerase chain reaction (PCR) targeting the mitochondrial genes cytochrome B and C for A. cantonensis and 16S ribosomal RNA for A. fulica. The PCR products were sequenced and studied by phylogenetic analysis. RESULTS Cytochrome B and cytochrome C molecular markers indicate a monophyletic lineage of A. cantonensis adult worms in Guadeloupe. Two sequences of A. fulica were identified. CONCLUSIONS These results confirm the recent introduction of both Angiostrongylus cantonensis and Achatina fulica into Guadeloupe. Achatina fulica in Guadeloupe shares a common origin with those in Barbados and New Caledonia, while Angiostrongylus cantonensis in Guadeloupe shares a common origin with those in Brazil, Hawaii and Japan.
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Affiliation(s)
- Gelixa Gamiette
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France.
| | - Séverine Ferdinand
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
| | - Céline Dard
- Institute for Advanced Biosciences, Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209-CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Antoine Talarmin
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
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Pot M, Ducat C, Reynaud Y, Couvin D, Ferdinand S, Breurec S, Talarmin A, Guyomard-Rabenirina S. Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies. BMC Genom Data 2023; 24:16. [PMID: 36906565 PMCID: PMC10007730 DOI: 10.1186/s12863-023-01116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
OBJECTIVES The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment. DATA DESCRIPTION ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Célia Ducat
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-À-Pitre, France
- grid.7429.80000000121866389Centre for Clinical Investigation 1424, INSERM, Pointe-À-Pitre/Les Abymes, France
- Laboratory of Clinical Microbiology, University Hospital Centre of Guadeloupe, Pointe-À-Pitre/Les Abymes, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-À-Pitre, France
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Dereeper A, Gruel G, Pot M, Couvin D, Barbier E, Bastian S, Bambou JC, Gelu-Simeon M, Ferdinand S, Guyomard-Rabenirina S, Passet V, Martino F, Piveteau P, Reynaud Y, Rodrigues C, Roger PM, Roy X, Talarmin A, Tressieres B, Valette M, Brisse S, Breurec S. Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies). Microbiol Spectr 2022; 10:e0124222. [PMID: 36094181 PMCID: PMC9603589 DOI: 10.1128/spectrum.01242-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022] Open
Abstract
Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of the Klebsiella pneumoniae species complex (KpSC) and identify the routes of transmission between human and nonhuman sources due to its insularity, small population size, and small area. Here, we report an analysis of 590 biological samples, 546 KpSC isolates, and 331 genome sequences collected between January 2018 and May 2019. The KpSC appears to be common whatever the source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged to K. pneumoniae sensu stricto (phylogroup Kp1), and all but one were recovered from the hospital setting. The distribution of species and phylogroups across the different niches was clearly nonrandom, with a distinct separation of Kp1 and Klebsiella variicola (Kp3). The most frequent sequence types (STs) (≥5 isolates) were previously recognized as high-risk multidrug-resistant (MDR) clones, namely, ST17, ST307, ST11, ST147, ST152, and ST45. Only 8 out of the 63 STs (12.7%) associated with human isolates were also found in nonhuman sources. A total of 22 KpSC isolates were defined as hypervirulent: 15 associated with human infections (9.8% of all human isolates), 4 (8.9%) associated with dogs, and 3 (15%) associated with pigs. Most of the human isolates (33.3%) belonged to the globally successful sublineage CG23-I. ST86 was the only clone shared by a human and a nonhuman (dog) source. Our work shows the limited transmission of KpSC isolates between human and nonhuman sources and points to the hospital setting as a cornerstone of the spread of MDR clones and antibiotic resistance genes. IMPORTANCE In this study, we characterized the presence and genomic features of isolates of the Klebsiella pneumoniae species complex (KpSC) from human and nonhuman sources in Guadeloupe (French West Indies) in order to identify the reservoirs and routes of transmission. This is the first study in an island environment, an ideal setting that limits the contribution of external imports. Our data showed the limited transmission of KpSC isolates between the different compartments. In contrast, we identified the hospital setting as the epicenter of antibiotic resistance due to the nosocomial spread of successful multidrug-resistant (MDR) K. pneumoniae clones and antibiotic resistance genes. Ecological barriers and/or limited exposure may restrict spread from the hospital setting to other reservoirs and vice versa. These results highlight the need for control strategies focused on health care centers, using genomic surveillance to limit the spread, particularly of high-risk clones, of this important group of MDR pathogens.
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Affiliation(s)
- Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Elodie Barbier
- UMR AgroEcologie, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Moana Gelu-Simeon
- Hepato-Gastroenterology Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | - Virginie Passet
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Frederic Martino
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Carla Rodrigues
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Pierre-Marie Roger
- Infectious Disease Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
| | - Xavier Roy
- Veterinary Clinic, Baie-Mahault, Guadeloupe
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Benoit Tressieres
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
| | - Marc Valette
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sylvain Brisse
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
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Pot M, Reynaud Y, Couvin D, Dereeper A, Ferdinand S, Bastian S, Foucan T, Pommier JD, Valette M, Talarmin A, Guyomard-Rabenirina S, Breurec S. Emergence of a Novel Lineage and Wide Spread of a blaCTX-M-15/IncHI2/ST1 Plasmid among Nosocomial Enterobacter in Guadeloupe. Antibiotics (Basel) 2022; 11:1443. [PMID: 36290101 PMCID: PMC9598596 DOI: 10.3390/antibiotics11101443] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 04/04/2024] Open
Abstract
Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The blaCTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant blaCTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Tania Foucan
- Operational Hygiene Team, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Jean-David Pommier
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Marc Valette
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | | | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97157 Pointe-à-Pitre, France
- INSERM, Center for Clinical Investigation 1424, 97139 Les Abymes, France
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Moco V, Cazenave D, Garnier M, Pot M, Marcelino I, Talarmin A, Guyomard-Rabenirina S, Breurec S, Ferdinand S, Dereeper A, Reynaud Y, Couvin D. getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories. BMC Bioinformatics 2022; 23:268. [PMID: 35804320 PMCID: PMC9264741 DOI: 10.1186/s12859-022-04809-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Background Biological sequences are increasing rapidly and exponentially worldwide. Nucleotide sequence databases play an important role in providing meaningful genomic information on a variety of biological organisms. Results The getSequenceInfo software tool allows to access sequence information from various public repositories (GenBank, RefSeq, and the European Nucleotide Archive), and is compatible with different operating systems (Linux, MacOS, and Microsoft Windows) in a programmatic way (command line) or as a graphical user interface. getSequenceInfo or gSeqI v1.0 should help users to get some information on queried sequences that could be useful for specific studies (e.g. the country of origin/isolation or the release date of queried sequences). Queries can be made to retrieve sequence data based on a given kingdom and species, or from a given date. This program allows the separation between chromosomes and plasmids (or other genetic elements/components) by arranging each component in a given folder. Some basic statistics are also performed by the program (such as the calculation of GC content for queried assemblies). An empirically designed nucleotide ratio is calculated using nucleotide information in order to tentatively provide a “NucleScore” for studied genome assemblies. Besides the main gSeqI tool, other additional tools have been developed to perform various tasks related to sequence analysis. Conclusion The aim of this study is to democratize the use of public repositories in programmatic ways, and to facilitate sequence data analysis in a pedagogical perspective. Output results are available in FASTA, FASTQ, Excel/TSV or HTML formats. The program is freely available at: https://github.com/karubiotools/getSequenceInfo. getSequenceInfo and supplementary tools are partly available through the recently released Galaxy KaruBioNet platform (http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html). Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04809-5.
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Affiliation(s)
- Vincent Moco
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Damien Cazenave
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Maëlle Garnier
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Matthieu Pot
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Isabel Marcelino
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Antoine Talarmin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Stéphanie Guyomard-Rabenirina
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France.,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France.,Centre d'Investigation Clinique Antilles Guyane, Inserm CIC 1424, Pointe-à-Pitre, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Alexis Dereeper
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - David Couvin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France.
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Gruel G, Couvin D, Guyomard-Rabenirina S, Arlet G, Bambou JC, Pot M, Roy X, Talarmin A, Tressieres B, Ferdinand S, Breurec S. High Prevalence of bla CTXM-1/IncI1-Iγ/ST3 Plasmids in Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Collected From Domestic Animals in Guadeloupe (French West Indies). Front Microbiol 2022; 13:882422. [PMID: 35651489 PMCID: PMC9149308 DOI: 10.3389/fmicb.2022.882422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/23/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) have been classified in the group of resistant bacteria of highest priority. We determined the prevalence of ESBL-E collected in feces from household and shelter pets in Guadeloupe (French West Indies). A single rectal swab was taken from 125 dogs and 60 cats between June and September 2019. The prevalence of fecal carriage of ESBL-E was 7.6% (14/185, 95% CI: 4.2-12.4), within the range observed worldwide. The only risk factor associated with a higher prevalence of ESBL-E rectal carriage was a stay in a shelter, suggesting that refuges could be hotspots for their acquisition. All but one (Klebsiella pneumoniae from a cat) were Escherichia coli. We noted the presence of a bla CTX-M-1/IncI1-Iγ/sequence type (ST3) plasmid in 11 ESBL-producing E. coli isolates belonging to ST328 (n = 6), ST155 (n = 4) and ST953 (n = 1). A bla CTX-M-15 gene was identified in the three remaining ESBL-E isolates. The bla CTX-M-1 and most of the antimicrobial resistance genes were present in a well-conserved large conjugative IncI1-Iγ/ST3 plasmid characterized by two accessory regions containing antibiotic resistance genes. The plasmid has been detected worldwide in E. coli isolates from humans and several animal species, such as food-producing animals, wild birds and pets, and from the environment. This study shows the potential role of pets as a reservoir of antimicrobial-resistant bacteria or genes for humans and underlines the importance of basic hygiene measures by owners of companion animals.
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Affiliation(s)
- Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | | | | | - Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Benoit Tressieres
- INSERM 1424, Center for Clinical Investigation, University Hospital Center of Guadeloupe, Pointe-à-Pitre, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France.,INSERM 1424, Center for Clinical Investigation, University Hospital Center of Guadeloupe, Pointe-à-Pitre, France.,Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
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Couvin D, Dereeper A, Meyer DF, Noroy C, Gaete S, Bhakkan B, Poullet N, Gaspard S, Bezault E, Marcelino I, Pruneau L, Segretier W, Stattner E, Cazenave D, Garnier M, Pot M, Tressières B, Deloumeaux J, Breurec S, Ferdinand S, Gonzalez-Rizzo S, Reynaud Y. KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies). Bioinform Adv 2022; 2:vbac010. [PMID: 36699379 PMCID: PMC9710593 DOI: 10.1093/bioadv/vbac010] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/28/2023]
Abstract
Summary Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact dcouvin@pasteur-guadeloupe.fr. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- David Couvin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,To whom correspondence should be addressed
| | - Alexis Dereeper
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Damien F Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe 97170, France,ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier 34000, France
| | - Christophe Noroy
- Développement, Analyse, Transfert et Application (DATA), Lamentin, Guadeloupe 97129, France
| | - Stanie Gaete
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Bernard Bhakkan
- Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Nausicaa Poullet
- URZ Recherches Zootechniques, INRAE, Petit-Bourg, Guadeloupe 97170, France
| | - Sarra Gaspard
- Laboratoire COVACHIMM2E EA3592, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Etienne Bezault
- UMR BOREA (MNHN, CNRS-7208, IRD-207, Sorbonne Université, UCN, UA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Isabel Marcelino
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Ludovic Pruneau
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Damien Cazenave
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Maëlle Garnier
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Matthieu Pot
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Benoît Tressières
- Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Jacqueline Deloumeaux
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France,Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Silvina Gonzalez-Rizzo
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
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Pot M, Reynaud Y, Couvin D, Ducat C, Ferdinand S, Gravey F, Gruel G, Guérin F, Malpote E, Breurec S, Talarmin A, Guyomard-Rabenirina S. Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies). Front Microbiol 2021; 12:628058. [PMID: 34248862 PMCID: PMC8268024 DOI: 10.3389/fmicb.2021.628058] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 11/25/2022] Open
Abstract
Species belonging to Enterobacter cloacae complex have been isolated in numerous environments and samples of various origins. They are also involved in opportunistic infections in plants, animals, and humans. Previous prospection in Guadeloupe (French West Indies) indicated a high frequency of E. cloacae complex strains resistant to third-generation cephalosporins (3GCs) in a local lizard population (Anolis marmoratus), but knowledge of the distribution and resistance of these strains in humans and the environment is limited. The aim of this study was to compare the distribution and antibiotic susceptibility pattern of E. cloacae complex members from different sources in a “one health” approach and to find possible explanations for the high level of resistance in non-human samples. E. cloacae complex strains were collected between January 2017 and the end of 2018 from anoles, farm animals, local fresh produce, water, and clinical human samples. Isolates were characterized by the heat-shock protein 60 gene-fragment typing method, and whole-genome sequencing was conducted on the most frequent clusters (i.e., C-VI and C-VIII). The prevalence of resistance to 3GCs was relatively high (56/346, 16.2%) in non-human samples. The associated resistance mechanism was related to an AmpC overproduction; however, in human samples, most of the resistant strains (40/62) produced an extended-spectrum beta-lactamase. No relation was found between resistance in isolates from wild anoles (35/168) and human activities. Specific core-genome phylogenetic analysis highlighted an important diversity in this bacterial population and no wide circulation among the different compartments. In our setting, the mutations responsible for resistance to 3GCs, especially in ampD, were diverse and not compartment specific. In conclusion, high levels of resistance in non-human E. cloacae complex isolates are probably due to environmental factors that favor the selection of these resistant strains, and this will be explored further.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Célia Ducat
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Gravey
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Guérin
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France.,Department of Clinical Microbiology, Caen University Hospital, Caen, France
| | - Edith Malpote
- Laboratory of Clinical Microbiology, University Hospital of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France.,Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France.,Centre for Clinical Investigation 1424, INSERM, Pointe-à-Pitre/Les Abymes, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
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10
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Gruel G, Sellin A, Riveiro H, Pot M, Breurec S, Guyomard-Rabenirina S, Talarmin A, Ferdinand S. Antimicrobial use and resistance in Escherichia coli from healthy food-producing animals in Guadeloupe. BMC Vet Res 2021; 17:116. [PMID: 33685450 PMCID: PMC7938459 DOI: 10.1186/s12917-021-02810-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Selection pressure exerted by use of antibiotics in both human and veterinary medicine is responsible for increasing antimicrobial resistance (AMR). The objectives of this study were to better understand antimicrobial use in pigs, beef cattle, and poultry on farms on Guadeloupe, French West Indies, and to acquire data on AMR in Escherichia coli in these food-producing animals. A cross-sectional survey was conducted at 45 farms on Guadeloupe, and practical use of antimicrobials was documented in declarative interviews between March and July 2018. A total of 216 fecal samples were collected between January 2018 and May 2019, comprising 124 from pigs, 75 from beef cattle, and 17 from poultry litter. E. coli isolates were obtained for further testing by isolation and identification from field samples. Antimicrobial susceptibility testing and screening for blaCTX-M, blaTEM, tetA, and tetB resistance genes by polymerase chain reaction on extracted genomic DNA were performed. Results The study showed rational use of antimicrobials, consisting of occasional use for curative treatment by veterinary prescription. Tetracycline was the most commonly used antimicrobial, but its use was not correlated to E. coli resistance. Extended-spectrum β-lactamase (ESBL) E. coli isolates were detected in 7.3% of pigs, 14.7% of beef cattle, and 35.3% of poultry. blaCTX-M-1 was the predominant gene found in ESBL-E. coli isolates (68.8%), followed by blaCTX-M-15 (31.3%). Conclusion Despite rational use of antimicrobials, the rate of ESBL-E. coli in food-producing animals in Guadeloupe, although moderate, is a concern. Further studies are in progress to better define the genetic background of the ESBL-E. coli isolates. Graphical abstract ![]()
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Affiliation(s)
- Gaëlle Gruel
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Arantxa Sellin
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Hélène Riveiro
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Matthieu Pot
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Sébastien Breurec
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France.,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, Guadeloupe, France.,Centre d'Investigation Clinique, INSERM CIC 1424, Pointe-à-Pitre, Guadeloupe, France
| | - Stéphanie Guyomard-Rabenirina
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Antoine Talarmin
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France
| | - Séverine Ferdinand
- Laboratory of Microbial Ecosystems Interactions, Transmission Reservoir and Pathogens Diversity Unit, Institut Pasteur of Guadeloupe, Morne Joliviere - B.P. 484, 97183, Les Abymes Cedex, Guadeloupe, France.
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11
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Guyomard-Rabenirina S, Weill FX, Le Hello S, Bastian S, Berger F, Ferdinand S, Legreneur P, Loraux C, Malpote E, Muanza B, Richard V, Talarmin A, Breurec S. Reptiles in Guadeloupe (French West Indies) are a reservoir of major human Salmonella enterica serovars. PLoS One 2019; 14:e0220145. [PMID: 31323053 PMCID: PMC6641201 DOI: 10.1371/journal.pone.0220145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/01/2019] [Accepted: 07/09/2019] [Indexed: 12/18/2022] Open
Abstract
The epidemiology of human Salmonella enterica infections in Guadeloupe (French West Indies) appears to be specific, with a higher prevalence of the subspecies enterica serovars Panama and Arechavaleta (Panama and Arechavaleta) than in other regions. A study was performed in Guadeloupe to identify the reservoir of Salmonella serovars by comparing their distribution in warm- and cold-blooded animals and in humans living in Guadeloupe and mainland France. Furthermore, a case–control study was conducted in 2012–2013 to identify the main epidemiologic risk factors for S. enterica infection among children under 15 years of age. Between June 2011 and December 2014, feces from 426 reptiles (322 anoles, 69 iguanas and 35 geckos) and 50 frogs distributed throughout Guadeloupe and nearby islands were investigated. The frequency of S. enterica carriage was 15.0% (n = 64) in reptiles but varied by species. The only significant risk factor for S. enterica infection was a more frequent presence of frogs in the houses of cases than in those of controls (P = 0.042); however, isolates were not collected. Panama and Arechavaleta were the two serovars most often recovered between 2005 and 2014 from humans living in Guadeloupe (24.5% (n = 174) and 11.5% (n = 82), respectively), which is in contrast to the low prevalence in mainland France (0.4%). Their presence at low frequencies in wild reptiles (4.6% (n = 3) and 3.1% (n = 2), respectively) and pigs (7.5% (n = 5) and 1.5% (n = 1), respectively) suggests a broad host range, and humans may be infected by indirect or direct contact with animals. These serovars are probably poorly adapted to humans and therefore cause more severe infections. The unusual subspecies houtenae serovar 43:z4,z32:- was a major subspecies in wild reptiles (24.6%, n = 16) and humans (9.4%, n = 67) but was not recovered from warm-blooded animals, suggesting that reptiles plays a key role in human infection.
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Affiliation(s)
| | - François-Xavier Weill
- Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Sylvaine Bastian
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Franck Berger
- Service de Santé des Armées, Centre d'épidémiologie et de santé publique des armées, Marseille, France.,INSERM, IRD, Sciences Economiques et Sociales de la Santé et Traitement de l'Information Médicale, Université d'Aix Marseille, Marseille, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
| | | | - Cécile Loraux
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Edith Malpote
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Blandine Muanza
- Service de Pédiatrie, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Vincent Richard
- Institut Pasteur de Nouvelle-Calédonie, Nouméa, Nouvelle-Calédonie
| | - Antoine Talarmin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, France.,Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France.,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, France
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12
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Sadikalay S, Reynaud Y, Guyomard-Rabenirina S, Falord M, Ducat C, Fabre L, Le Hello S, Talarmin A, Ferdinand S. High genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses. Vet Microbiol 2018; 219:117-122. [PMID: 29778183 DOI: 10.1016/j.vetmic.2018.04.016] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/07/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days. All isolated E. coli strains were evaluated for antimicrobial resistance (AMR) and by whole-genome sequencing. Multi locus sequence typing, phylogrouping, resistance genes and plasmid content were extracted from genomic data. A phylogenetic analysis based on single nucleotide polymorphism (SNP) divergence was also performed on the core genome. We isolated 35 strains belonging to the A, B1 and C phylo-groups. All but one expressed SHV-12 enzymes and one expressed CTX-M-1. Intra- and inter-horse genetic diversity of E. coli strains was identified in the genome analysis and 10 AMR profiles. Two distinct EP E. coli-resistant populations (phylo-group B1: ST4164-AMR3 and ST155-AMR2) were found in one horse, and five other resistant populations were found in the second horse (phylo-group A: ST1250-AMR1; phylo-group B1: ST1250-AMR1, ST6981-AMR1 and phylo-group C: ST10-AMR4). Some persistent EP E. coli strains were detected at least 1 month after treatment. These results indicate that EP E. coli strains isolated from horse feces show intra- and inter-host genetic diversity, even in a region with low ESBL prevalence and in horses that are rarely treated with third-generation cephalosporins. These results also suggest that horizontal gene transfer and/or selection of resistance genes probably occurs in vivo within the horse gut microbiome. Follow-up of EP E. coli resistance profiles for at least 1 month after treatment is warranted to prevent persistence of EP E. coli.
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Affiliation(s)
- Syndia Sadikalay
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Yann Reynaud
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | | | - Mélanie Falord
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Célia Ducat
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Laetitia Fabre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Réfé.rence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Réfé.rence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Antoine Talarmin
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France
| | - Séverine Ferdinand
- Unité Environnement Santé, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe, France.
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Larifla L, Armand C, Bangou J, Blanchet-Deverly A, Numeric P, Fonteau C, Michel CT, Ferdinand S, Bourrhis V, Vélayoudom-Céphise FL. Association of APOE gene polymorphism with lipid profile and coronary artery disease in Afro-Caribbeans. PLoS One 2017; 12:e0181620. [PMID: 28727855 PMCID: PMC5519172 DOI: 10.1371/journal.pone.0181620] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/04/2017] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES Apolipoprotein E gene (APOE) polymorphism is associated with the lipid profile and cardio-vascular disease. However, these relationships vary between ethnic groups. We evaluated, for the first time in an Afro-Caribbean population, the distribution of APOE polymorphisms and their associations with coronary artery disease (CAD), the lipid profile and other cardio-metabolic risk factors. METHODS We studied 712 Afro-Caribbean subjects including 220 with documented CAD and 492 healthy subjects. TaqMan assays were performed to genotype rs7412 and rs429358, the two variants that determine the APOE alleles ε2, ε3 and ε4. The association between APOE genotype and the lipid profile was analysed by comparing ε2 carriers, ε3 homozygotes and ε4 carriers. RESULTS The frequencies of ε2, ε3 and ε4 in the overall sample were 8%, 70% and 22%, respectively. CAD was not associated with APOE polymorphism. The total cholesterol level was higher in ε4 carriers compared with ε2 carriers: 5.07 vs 4.59 mmol/L (P = 0.016). The LDL-cholesterol level was lower in APOE ε2 carriers compared with ε3 homozygotes and ε4 carriers: 2.65 vs 3.03 and 3.17 mmol/L, respectively (p = 0.002). The total cholesterol/HDL-cholesterol and LDL-cholesterol/HDL-cholesterol ratios were similar in the three allelic groups. APOE polymorphism was not associated with diabetes, hypertension, waist circumference or body mass index. CONCLUSIONS Our results indicate that APOE gene polymorphism is associated with the lipid profile but not with CAD in Afro-Caribbean people. This lack of association with CAD may be explained by the low atherogenic profile observed in ε4 carriers, which may warrant further investigation.
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Affiliation(s)
- Laurent Larifla
- Research Group Clinical Epidemiology and Medicine, ECM/L.A.M.I.A EA 4540, University of Antilles, Pointe-à-Pitre, France
- Department of Cardiology, University Hospital of Guadeloupe, Pointe-à-Pitre, France
- * E-mail: ,
| | - Christophe Armand
- Research Group Clinical Epidemiology and Medicine, ECM/L.A.M.I.A EA 4540, University of Antilles, Pointe-à-Pitre, France
- Department of Medical Information and Public Health, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Jacqueline Bangou
- Research Group Clinical Epidemiology and Medicine, ECM/L.A.M.I.A EA 4540, University of Antilles, Pointe-à-Pitre, France
- Biochemistry Unit, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Anne Blanchet-Deverly
- Research Group Clinical Epidemiology and Medicine, ECM/L.A.M.I.A EA 4540, University of Antilles, Pointe-à-Pitre, France
| | - Patrick Numeric
- Department of Internal Medicine Unit, University Hospital of Martinique, Fort-de France, France
| | - Christiane Fonteau
- Biochemistry Unit, University Hospital of Martinique, Fort-de France, France
| | - Carl-Thony Michel
- Department of Cardiology, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Séverine Ferdinand
- Department of Medical Information and Public Health, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Véronique Bourrhis
- Department of Medicine, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Fritz-Line Vélayoudom-Céphise
- Research Group Clinical Epidemiology and Medicine, ECM/L.A.M.I.A EA 4540, University of Antilles, Pointe-à-Pitre, France
- Department of Endocrinology and Diabetology, University Hospital of Guadeloupe, Pointe-à-Pitre, France
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Garnier Y, Ferdinand S, Connes P, Garnier M, Etienne-Julan M, Lemonne N, Romana M. Decrease of externalized phosphatidylserine density on red blood cell-derived microparticles in SCA patients treated with hydroxycarbamide. Br J Haematol 2017; 182:448-451. [DOI: 10.1111/bjh.14810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yohann Garnier
- Unité Biologie Intégrée du Globule Rouge; laboratoire d'Excellence GR-Ex; Université des Antilles; Inserm; Paris France
| | - Séverine Ferdinand
- Unité Biologie Intégrée du Globule Rouge; laboratoire d'Excellence GR-Ex; Université des Antilles; Inserm; Paris France
| | - Philippe Connes
- Unité Biologie Intégrée du Globule Rouge; laboratoire d'Excellence GR-Ex; Université des Antilles; Inserm; Paris France
- Laboratoire LIBM EA7424; Equipe “Biologie vasculaire et du globule rouge”; laboratoire d'Excellence GR-Ex; Université de Lyon; Lyon France
- Institut Universitaire de France; Paris France
| | - Marie Garnier
- Unité Biologie Intégrée du Globule Rouge; laboratoire d'Excellence GR-Ex; Université des Antilles; Inserm; Paris France
| | - Maryse Etienne-Julan
- Unité Transversale de la Drépanocytose; Hôpital Ricou; CHU de Pointe-à-Pitre Guadeloupe
| | - Nathalie Lemonne
- Unité Transversale de la Drépanocytose; Hôpital Ricou; CHU de Pointe-à-Pitre Guadeloupe
| | - Marc Romana
- Unité Biologie Intégrée du Globule Rouge; laboratoire d'Excellence GR-Ex; Université des Antilles; Inserm; Paris France
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Garnier Y, Ferdinand S, Etienne-Julan M, Elana G, Petras M, Doumdo L, Tressières B, Lalanne-Mistrih ML, Hardy-Dessources MD, Connes P, Romana M. Differences of microparticle patterns between sickle cell anemia and hemoglobin SC patients. PLoS One 2017; 12:e0177397. [PMID: 28489923 PMCID: PMC5425024 DOI: 10.1371/journal.pone.0177397] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
Sickle cell anemia (SCA) and hemoglobin SC (HbSC) disease are the two most common forms of sickle cell disease (SCD), a frequent hemoglobinopathy which exhibits a highly variable clinical course. Although high levels of microparticles (MPs) have been consistently reported in SCA and evidence of their harmful impact on the SCA complication occurrences have been provided, no data on MP pattern in HbSC patients has been reported so far. In this study, we determined and compared the MP patterns of 84 HbSC and 96 SCA children, all at steady-state, using flow cytometry. Most of circulating MPs were derived from platelets (PLTs) and red blood cells (RBCs) in the two SCD syndromes. Moreover, we showed that HbSC patients exhibited lower blood concentration of total MPs compared to SCA patients, resulting mainly from a decrease of MP levels originated from RBCs and to a lesser extent from PLTs. We did not detect any association between blood MP concentrations and the occurrence of painful vaso-occlusive crises, acute chest syndrome and pulmonary hypertension in both patient groups. We also demonstrated for the first time, that whatever the considered genotype, RBC-derived MPs exhibited higher externalized phosphatidylserine level and were larger than PLT-derived MPs.
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Affiliation(s)
- Yohann Garnier
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
| | - Séverine Ferdinand
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
| | - Maryse Etienne-Julan
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
- Unité Transversale de la Drépanocytose, CHU de Pointe-à-Pitre, Pointe-à-Pitre, Guadeloupe, France
| | - Gisèle Elana
- Pôle mère-enfant, CHU de Fort de France, Fort de France, Martinique
| | - Marie Petras
- Unité Transversale de la Drépanocytose, CHU de Pointe-à-Pitre, Pointe-à-Pitre, Guadeloupe, France
| | - Lydia Doumdo
- Unité Transversale de la Drépanocytose, CHU de Pointe-à-Pitre, Pointe-à-Pitre, Guadeloupe, France
| | - Benoit Tressières
- Centre d’Investigation Clinique Antilles Guyane, Inserm/DGOS CIC 1424, Pointe-à-Pitre, Guadeloupe, France
| | - Marie-Laure Lalanne-Mistrih
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
- Centre d’Investigation Clinique Antilles Guyane, Inserm/DGOS CIC 1424, Pointe-à-Pitre, Guadeloupe, France
| | | | - Philippe Connes
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
- Institut Universitaire de France, Paris, France
- Laboratoire LIBM EA7424, Equipe « Biologie Vasculaire et du Globule Rouge », laboratoire d’Excellence GR-Ex, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Marc Romana
- Unité Biologie Intégrée du Globule Rouge, Université des Antilles, Inserm 1134, laboratoire d’Excellence GR-Ex, Paris, France
- * E-mail:
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16
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Renoux C, Romana M, Joly P, Ferdinand S, Faes C, Lemonne N, Skinner S, Garnier N, Etienne-Julan M, Bertrand Y, Petras M, Cannas G, Divialle-Doumdo L, Nader E, Cuzzubbo D, Lamarre Y, Gauthier A, Waltz X, Kebaili K, Martin C, Hot A, Hardy-Dessources MD, Pialoux V, Connes P. Effect of Age on Blood Rheology in Sickle Cell Anaemia and Sickle Cell Haemoglobin C Disease: A Cross-Sectional Study. PLoS One 2016; 11:e0158182. [PMID: 27355589 PMCID: PMC4927160 DOI: 10.1371/journal.pone.0158182] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 03/09/2016] [Accepted: 06/10/2016] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Blood rheology plays a key role in the pathophysiology of sickle cell anaemia (SS) and sickle cell haemoglobin C disease (SC), but its evolution over the lifespan is unknown. MATERIALS AND METHODS Blood viscosity, red blood cell (RBC) deformability and aggregation, foetal haemoglobin (HbF) and haematocrit were measured in 114 healthy individuals (AA), 267 SS (161 children + 106 adults) and 138 SC (74 children + 64 adults) patients. RESULTS Our results showed that 1) RBC deformability is at its maximal value during the early years of life in SS and SC populations, mainly because HbF level is also at its peak, 2) during childhood and adulthood, hydroxycarbamide treatment, HbF level and gender modulated RBC deformability in SS patients, independently of age, 3) blood viscosity is higher in older SS and SC patients compared to younger ones and 4) haematocrit decreases as SS patients age. CONCLUSION The hemorheological changes detected in older patients could play a role in the progressive development of several chronic disorders in sickle cell disease, whose prevalence increases with age. Retarding these age-related haemorheological impairments, by using suitable drugs, may minimize the risks of vaso-occlusive events and chronic disorders.
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Affiliation(s)
- Céline Renoux
- Unité de Pathologie Moléculaire du Globule Rouge, Laboratoire de Biochimie et de Biologie Moléculaire, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Marc Romana
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Philippe Joly
- Unité de Pathologie Moléculaire du Globule Rouge, Laboratoire de Biochimie et de Biologie Moléculaire, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Séverine Ferdinand
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Camille Faes
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Nathalie Lemonne
- Unité Transversale de la Drépanocytose, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
| | - Sarah Skinner
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Nathalie Garnier
- Institut d’Hématologie et d’Oncologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | - Maryse Etienne-Julan
- Unité Transversale de la Drépanocytose, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
| | - Yves Bertrand
- Institut d’Hématologie et d’Oncologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | - Marie Petras
- Unité Transversale de la Drépanocytose, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
| | - Giovanna Cannas
- Service de Médecine Interne, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Lydia Divialle-Doumdo
- Unité Transversale de la Drépanocytose, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
| | - Elie Nader
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Daniela Cuzzubbo
- Institut d’Hématologie et d’Oncologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | - Yann Lamarre
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Alexandra Gauthier
- Institut d’Hématologie et d’Oncologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | - Xavier Waltz
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Kamila Kebaili
- Institut d’Hématologie et d’Oncologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | - Cyril Martin
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Arnaud Hot
- Service de Médecine Interne, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | - Marie-Dominique Hardy-Dessources
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Vincent Pialoux
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- Service de Médecine Interne, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
| | - Philippe Connes
- Laboratoire Interuniversitaire de Biologie de la Motricité, Equipe “Vascular Biology and Red Blood Cell”, Université Claude Bernard Lyon 1, Lyon, France
- UMR Inserm U1134, Université des Antilles et de la Guyane, Hôpital de Pointe-à-Pitre, Hôpital Ricou, 97159 Pointe-à-Pitre Cedex, Guadeloupe, France
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne, Paris, France
- Institut Universitaire de France (IUF), Paris, France
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Cita KC, Brureau L, Lemonne N, Billaud M, Connes P, Ferdinand S, Tressières B, Tarer V, Etienne-Julan M, Blanchet P, Elion J, Romana M. Men with Sickle Cell Anemia and Priapism Exhibit Increased Hemolytic Rate, Decreased Red Blood Cell Deformability and Increased Red Blood Cell Aggregate Strength. PLoS One 2016; 11:e0154866. [PMID: 27145183 PMCID: PMC4856257 DOI: 10.1371/journal.pone.0154866] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/20/2016] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES To investigate the association between priapism in men with sickle cell anemia (SCA) and hemorheological and hemolytical parameters. MATERIALS AND METHODS Fifty-eight men with SCA (median age: 38 years) were included; 28 who had experienced priapism at least once during their life (priapism group) and 30 who never experienced this complication (control group). Twenty-two patients were treated with hydroxycarbamide, 11 in each group. All patients were at steady state at the time of inclusion. Hematological and biochemical parameters were obtained through routine procedures. The Laser-assisted Optical Rotational Cell Analyzer was used to measure red blood cell (RBC) deformability at 30 Pa (ektacytometry) and RBC aggregation properties (laser backscatter versus time). Blood viscosity was measured at a shear rate of 225 s-1 using a cone/plate viscometer. A principal component analysis was performed on 4 hemolytic markers (i.e., lactate dehydrogenase (LDH), aspartate aminotransferase (ASAT), total bilirubin (BIL) levels and reticulocyte (RET) percentage) to calculate a hemolytic index. RESULTS Compared to the control group, patients with priapism exhibited higher ASAT (p = 0.01), LDH (p = 0.03), RET (p = 0.03) levels and hemolytic indices (p = 0.02). Higher RBC aggregates strength (p = 0.01) and lower RBC deformability (p = 0.005) were observed in patients with priapism compared to controls. After removing the hydroxycarbamide-treated patients, RBC deformability (p = 0.01) and RBC aggregate strength (p = 0.03) were still different between the two groups, and patients with priapism exhibited significantly higher hemolytic indices (p = 0.01) than controls. CONCLUSION Our results confirm that priapism in SCA is associated with higher hemolytic rates and show for the first time that this complication is also associated with higher RBC aggregate strength and lower RBC deformability.
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Affiliation(s)
- Kizzy-Clara Cita
- Inserm UMR 1134, Université des Antilles, Pointe à Pitre, Guadeloupe
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), COMUE Sorbonne Paris Cité, Paris, France
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Service d’Urologie, Pointe-à-Pitre, Guadeloupe
- Inserm, U1085—IRSET, Pointe-à-Pitre, Guadeloupe, France
| | - Nathalie Lemonne
- CHU de Pointe-à-Pitre, Unité Transversale de la Drépanocytose, Centre de référence maladies rares de la drépanocytose aux Antilles-Guyane, Pointe-à-Pitre, Guadeloupe
| | - Marie Billaud
- CHU de Pointe-à-Pitre, Unité Transversale de la Drépanocytose, Centre de référence maladies rares de la drépanocytose aux Antilles-Guyane, Pointe-à-Pitre, Guadeloupe
| | - Philippe Connes
- Inserm UMR 1134, Université des Antilles, Pointe à Pitre, Guadeloupe
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), COMUE Sorbonne Paris Cité, Paris, France
- Institut Universitaire de France, Paris, France
- Université Claude Bernard Lyon 1, COMUE Lyon, Laboratoire LIBM EA 7424, Team “Vascular Biology and red blood cell”, Lyon, France
| | - Séverine Ferdinand
- Inserm UMR 1134, Université des Antilles, Pointe à Pitre, Guadeloupe
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), COMUE Sorbonne Paris Cité, Paris, France
| | - Benoit Tressières
- Inserm, CHU de Pointe-à-Pitre, Centre d’Investigation Clinique Antilles Guyane CIC 14–24, Guadeloupe, France
| | - Vanessa Tarer
- CHU de Pointe-à-Pitre, Unité Transversale de la Drépanocytose, Centre de référence maladies rares de la drépanocytose aux Antilles-Guyane, Pointe-à-Pitre, Guadeloupe
| | - Maryse Etienne-Julan
- CHU de Pointe-à-Pitre, Unité Transversale de la Drépanocytose, Centre de référence maladies rares de la drépanocytose aux Antilles-Guyane, Pointe-à-Pitre, Guadeloupe
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Service d’Urologie, Pointe-à-Pitre, Guadeloupe
- Inserm, U1085—IRSET, Pointe-à-Pitre, Guadeloupe, France
| | - Jacques Elion
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), COMUE Sorbonne Paris Cité, Paris, France
- Inserm U 1134, Paris, France
| | - Marc Romana
- Inserm UMR 1134, Université des Antilles, Pointe à Pitre, Guadeloupe
- Laboratoire d’Excellence du Globule Rouge (LABEX GR-Ex), COMUE Sorbonne Paris Cité, Paris, France
- * E-mail:
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Cita KC, Ferdinand S, Connes P, Brudey L, Tressières B, Etienne-Julan M, Lemonne N, Tarer V, Elion J, Romana M. Association of adenylyl cyclase 6 rs3730070 polymorphism and hemolytic level in patients with sickle cell anemia. Blood Cells Mol Dis 2016; 58:21-5. [PMID: 27067484 DOI: 10.1016/j.bcmd.2016.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/17/2022]
Abstract
A recent study suggested that adenosine signaling pathway could promote hemolysis in patients with sickle cell anemia (SCA). This signaling pathway involves several gene coding enzymes for which variants have been described. In this study, we analyzed the genotype-phenotype relationships between functional polymorphisms or polymorphisms associated with altered expression of adenosine pathway genes, namely adenosine deaminase (ada; rs73598374), adenosine A2b receptor (adora2b; rs7208480), adenylyl cyclase6 (adcy6; rs3730071, rs3730070, rs7300155), and hemolytic rate in SCA patients. One hundred and fifty SCA patients were genotyped for adcy6, ada, and adora2b variants as well as alpha-globin gene, a genetic factor known to modulate hemolytic rate. Hematological and biochemical data were obtained at steady-state. Lactate dehydrogenase, aspartate aminotransferase, reticulocytes and total bilirubin were used to calculate a hemolytic index. Genotype-phenotype relationships were investigated using parametric tests and multivariate analysis. SCA patients carrying at least one allele of adcy6 rs3730070-G exhibited lower hemolytic rate than non-carriers in univariate analysis (p=0.006). The presence of adcy6 rs3730070-G variant was associated with a decreased hemolytic rate in adjusted model for age and alpha-thalassemia (p=0.032). Our results support a protective effect of adcy6 rs3730070-G variant on hemolysis in SCA patients.
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Affiliation(s)
- Kizzy-Clara Cita
- Inserm UMR 1134, Hôpital Ricou, CHU de Pointe-à-Pitre, F-97157 Guadeloupe, France; Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France
| | - Séverine Ferdinand
- Inserm UMR 1134, Hôpital Ricou, CHU de Pointe-à-Pitre, F-97157 Guadeloupe, France; Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France
| | - Philippe Connes
- Inserm UMR 1134, Hôpital Ricou, CHU de Pointe-à-Pitre, F-97157 Guadeloupe, France; Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France; Institut Universitaire de France, F-75006 Paris, France; Laboratoire CRIS EA647, Equipe "Biologie Vasculaire et du Globule Rouge", Université Lyon 1, F-69100 Villeurbanne, France
| | - Laura Brudey
- Inserm UMR 1134, Hôpital Ricou, CHU de Pointe-à-Pitre, F-97157 Guadeloupe, France; Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France
| | - Benoit Tressières
- Centre d'Investigation Clinique Antilles Guyane CIC 14-24 Inserm, CHU de Pointe-à-Pitre, Guadeloupe, France
| | - Maryse Etienne-Julan
- Unité Transversale de la Drépanocytose, Centre de référence maladies rares pour la drépanocytose aux Antilles-Guyane, CHU de Pointe-à-Pitre, F-97157 Pointe-à-Pitre, Guadeloupe, France
| | - Nathalie Lemonne
- Unité Transversale de la Drépanocytose, Centre de référence maladies rares pour la drépanocytose aux Antilles-Guyane, CHU de Pointe-à-Pitre, F-97157 Pointe-à-Pitre, Guadeloupe, France
| | - Vanessa Tarer
- Unité Transversale de la Drépanocytose, Centre de référence maladies rares pour la drépanocytose aux Antilles-Guyane, CHU de Pointe-à-Pitre, F-97157 Pointe-à-Pitre, Guadeloupe, France
| | - Jacques Elion
- Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France; Inserm UMR 1134, F-75739 Paris, France
| | - Marc Romana
- Inserm UMR 1134, Hôpital Ricou, CHU de Pointe-à-Pitre, F-97157 Guadeloupe, France; Laboratoire d'Excellence du Globule Rouge (LABEX GR-Ex), PRES Sorbonne Paris Cité, F-a, Paris, France.
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Brureau L, Moningo D, Emeville E, Ferdinand S, Punga A, Lufuma S, Blanchet P, Romana M, Multigner L. Polymorphisms of Estrogen Metabolism-Related Genes and Prostate Cancer Risk in Two Populations of African Ancestry. PLoS One 2016; 11:e0153609. [PMID: 27074016 PMCID: PMC4830606 DOI: 10.1371/journal.pone.0153609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/31/2016] [Indexed: 11/30/2022] Open
Abstract
Background Estrogens are thought to play a critical role in prostate carcinogenesis. It has been suggested that polymorphisms of genes encoding enzymes involved in estrogen metabolism are risk factors for prostate cancer. However, few studies have been performed on populations of African ancestry, which are known to have a high risk of prostate cancer. Objective We investigated whether functional polymorphisms of CYP17, CYP19, CYP1B1, COMT and UGT1A1 affected the risk of prostate cancer in two different populations of African ancestry. Methods In Guadeloupe (French West Indies), we compared 498 prostate cancer patients and 565 control subjects. In Kinshasa (Democratic Republic of Congo), 162 prostate cancer patients were compared with 144 controls. Gene polymorphisms were determined by the SNaPshot technique or short tandem repeat PCR analysis. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Results The AA genotype and the A allele of rs4680 (COMT) appeared to be inversely associated with the risk of prostate cancer in adjusted models for both Afro-Caribbean and native African men. For the A allele, a significant inverse association was observed among cases with low-grade Gleason scores and localized clinical stage, in both populations. Conclusions These preliminary results support the hypothesis that polymorphisms of genes encoding enzymes involved in estrogen metabolism may modulate the risk of prostate cancer in populations of African ancestry.
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Affiliation(s)
- Laurent Brureau
- Inserm, U1085 - IRSET, Pointe-à-Pitre, Guadeloupe, France
- Service d’Urologie, CHU de Pointe à Pitre, Pointe à Pitre, Guadeloupe, France
- Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Dieudonné Moningo
- Service d’Urologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Elise Emeville
- Inserm, U1085 - IRSET, Pointe-à-Pitre, Guadeloupe, France
- Université de Rennes 1, Rennes, France
| | - Séverine Ferdinand
- Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
- Inserm, U1134, Pointe-à-Pitre, Guadeloupe, France
| | - Augustin Punga
- Service d’Urologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Simon Lufuma
- Service d’Urologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Pascal Blanchet
- Inserm, U1085 - IRSET, Pointe-à-Pitre, Guadeloupe, France
- Service d’Urologie, CHU de Pointe à Pitre, Pointe à Pitre, Guadeloupe, France
- Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
| | - Marc Romana
- Université des Antilles, Pointe-à-Pitre, Guadeloupe, France
- Inserm, U1134, Pointe-à-Pitre, Guadeloupe, France
| | - Luc Multigner
- Inserm, U1085 - IRSET, Pointe-à-Pitre, Guadeloupe, France
- Université de Rennes 1, Rennes, France
- * E-mail:
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Brureau L, Emeville E, Ferdinand S, Thome J, Romana M, Blanchet P, Multigner L. Exposition au chlordécone et cancer de la prostate. Interactions avec les gènes codants pour les œstrogènes. Prog Urol 2015; 25:755. [DOI: 10.1016/j.purol.2015.08.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Brureau L, Moningo D, Emeville E, Ferdinand S, Romana M, Blanchet P, Multigner L. Polymorphismes de gènes liés au métabolisme des œstrogènes et le risque de cancer de la prostate dans deux populations d’ascendance africaine. Prog Urol 2015; 25:755. [DOI: 10.1016/j.purol.2015.08.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ferdinand S, Connes P, Brudey L, Cita KC, Tressières B, Lemonne N, Hardy-Dessources MD, Lamarre Y, Waltz X, Etienne-Julan M, Romana M. Impact of eNOS polymorphisms on red blood cell aggregation in sickle cell disease. Blood Cells Mol Dis 2015; 55:151-3. [DOI: 10.1016/j.bcmd.2015.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 05/25/2015] [Indexed: 11/27/2022]
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Ferdinand S, Peters S, Mulligan H, Robinson B. Development and piloting of an exercise program for prostate cancer survivors using stakeholder engagement. Physiotherapy 2015. [DOI: 10.1016/j.physio.2015.03.599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Emeville E, Broquère C, Brureau L, Ferdinand S, Blanchet P, Multigner L, Romana M. Copy number variation of GSTT1 and GSTM1 and the risk of prostate cancer in a Caribbean population of African descent. PLoS One 2014; 9:e107275. [PMID: 25198353 PMCID: PMC4157893 DOI: 10.1371/journal.pone.0107275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 06/23/2014] [Accepted: 08/09/2014] [Indexed: 11/24/2022] Open
Abstract
Background Deletions of the glutathione S-transferase genes M1 and T1 (GSTM1 and GSTT1) have been studied as potential risk factors for prostate cancer. Conflicting results have been obtained. Moreover, most such studies could not discriminate heterozygous from homozygous carriers of the non-deleted alleles. Objective We investigated whether copy number variation (CNV) of the GSTM1 and/or GSTT1 genes contribute to the risk of prostate cancer in the Caribbean population of African descent of Guadeloupe. Methods In a population-based case-control study, we compared 629 prostate cancer patients and 622 control subjects. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Exact copy numbers of GSTM1 and GSTT1 were determined by real-time PCR. Results A higher copy number of GSTM1 was marginally associated with prostate cancer risk. Men with 2 and 3 or more GSTT1 genes were at higher risk of prostate cancer (OR: 1.55, 95% CI: 1.11–2.16 and OR: 4.89, 95% CI: 1.71–13.99, respectively; Ptrend<0.001). Men with 3, 4 and 5 or more copies of both GSTM1 and GSTT1 genes were at higher risk of prostate cancer (OR: 2.18, 95% CI: 1.21–3.91, OR: 3.24, 95% CI: 1.63–6.46, and OR: 5.77, 95% CI: 1.40–23.84, respectively; Ptrend<0.001). Conclusions Copy number of GSTT1 and combined GSTM1/GSTT1 appear to be associated with prostate cancer risk in our population study with gene dose relationship. Our results support the hypothesis that variations in copy number of GSTT1 modulate the risk of prostate cancer.
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Affiliation(s)
- Elise Emeville
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1085, Institut de Recherche sur la Santé, l’Environnement et le Travail (IRSET), Pointe-à-Pitre, Guadeloupe, France
- Université de Rennes 1, Rennes, France
| | - Cédric Broquère
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1134, Pointe-à-Pitre, Guadeloupe, France
- Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France
| | - Laurent Brureau
- Service d’Urologie, Centre Hospitalier Universitaire de Pointe à Pitre, Pointe à Pitre, Guadeloupe, France
| | - Séverine Ferdinand
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1134, Pointe-à-Pitre, Guadeloupe, France
- Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France
| | - Pascal Blanchet
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1085, Institut de Recherche sur la Santé, l’Environnement et le Travail (IRSET), Pointe-à-Pitre, Guadeloupe, France
- Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France
- Service d’Urologie, Centre Hospitalier Universitaire de Pointe à Pitre, Pointe à Pitre, Guadeloupe, France
| | - Luc Multigner
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1085, Institut de Recherche sur la Santé, l’Environnement et le Travail (IRSET), Pointe-à-Pitre, Guadeloupe, France
- Université de Rennes 1, Rennes, France
- * E-mail:
| | - Marc Romana
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1134, Pointe-à-Pitre, Guadeloupe, France
- Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France
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Blanchet P, Romana M, Emeville E, Broquere C, Brureau L, Ferdinand S, Multigner L. Polymorphismes du nombre de copies des gènes GSTT1 et M1 et risque de survenue du cancer de la prostate dans une population afrocaribéenne. Prog Urol 2013. [DOI: 10.1016/j.purol.2013.08.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rasolofo Razanamparany V, Quirin R, Rapaoliarijaona A, Rakotoaritahina H, Vololonirina EJ, Rasolonavalona T, Ferdinand S, Sola C, Rastogi N, Ramarokoto H, Chanteau S. Usefulness of restriction fragment length polymorphism and spoligotyping for epidemiological studies of Mycobacterium bovis in Madagascar: Description of new genotypes. Vet Microbiol 2006; 114:115-22. [PMID: 16384662 DOI: 10.1016/j.vetmic.2005.11.057] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2005] [Revised: 11/09/2005] [Accepted: 11/09/2005] [Indexed: 11/21/2022]
Abstract
Tuberculosis is highly prevalent in cattle in Madagascar. An epidemiological study based on genotyping of Mycobacterium bovis and its transmission to humans was carried out. The restriction fragment length polymorphism (IS6110 and DR markers) and spoligotyping were used to assess the genetic diversity of strains from different regions of Madagascar. One of these strains was isolated from goat, the other strains were isolated from zebu cattle. Nine IS6110 profiles, 20 DR profiles and 12 spoligotypes were obtained. About 90% of all isolates gave a single IS6110 band at about 1.8 kb. Most strains had the same spoligotype. M. bovis strains commonly lack spacers 39-43, and all Malagasy strains also lacked spacers 3-5, 8-10 and 16. This pattern has not been reported elsewhere. DR was the most discriminatory of the three markers. The patterns obtained with the three markers were combined to identify 34 different genotypes, one of which was found in 35% of the strains. No region-specific M. bovis genotype was identified, but the genotyping of 18 M. bovis strains isolated from patients showed that the human and bovine strains were identical, suggesting possible human contamination from zebu cattle.
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Brudey K, Filliol I, Ferdinand S, Guernier V, Duval P, Maubert B, Sola C, Rastogi N. Long-term population-based genotyping study of Mycobacterium tuberculosis complex isolates in the French departments of the Americas. J Clin Microbiol 2006; 44:183-91. [PMID: 16390968 PMCID: PMC1351934 DOI: 10.1128/jcm.44.1.183-191.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three French overseas departments of the Americas are characterized both by insular (Guadeloupe and Martinique) and continental (French Guiana) settings with a tuberculosis case detection rate that varies from less than 10 per 100,000 per year in insular areas to an estimated incidence of more than 55 per 100,000 in French Guiana. Under a long-term genotyping program, more than three-fourths of all the Mycobacterium tuberculosis isolates (n = 744) received from the three settings were fingerprinted over a 10-year period (1994 to 2003) by spoligotyping and variable number of tandem DNA repeats (VNTRs) in order to understand the current trends in their detection rates, drug resistance, and groups and subpopulations at risk of contracting the disease and to pinpoint the circulating phylogeographical clades of the bacilli. The major difference in the study populations was the nationality of the patients, with a high percentage of immigrants from high-incidence neighboring countries in French Guiana and a low but increasing percentage in the French Caribbean. The rate of recent transmission was calculated to be 49.3% in French Guiana, compared to 27.2% and 16.9% in Guadeloupe and Martinique, respectively. At the phylogeographic level, 77.9% of the isolates studied belonged to four major clades (Haarlem, Latin-American and Mediterranean, T, and X) which are already reported from neighboring Caribbean islands in an international database and may underline potential interregional transmission events.
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Affiliation(s)
- Karine Brudey
- Unité de la tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, French Guiana
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Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, de Viedma DG, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ly HM, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006; 6:23. [PMID: 16519816 PMCID: PMC1468417 DOI: 10.1186/1471-2180-6-23] [Citation(s) in RCA: 777] [Impact Index Per Article: 43.2] [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: 11/08/2005] [Accepted: 03/06/2006] [Indexed: 12/04/2022] Open
Abstract
Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
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Affiliation(s)
- Karine Brudey
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | | | - Leen Rigouts
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Wolfgang M Prodinger
- Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Andrea Gori
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Sahal A Al-Hajoj
- Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
| | - Liselotte Aristimuño
- Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
| | - Jyoti Arora
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Lothar Binder
- Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
| | | | - Angel Cataldi
- Instituto de Biotecnologia INTA, Castelar, Argentina
| | - Soonfatt Cheong
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Roland Diel
- University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
| | | | - Jason T Evans
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | | | - Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Dario Garcia de Viedma
- Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
| | - Carlo Garzelli
- Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
| | - Lidia Gazzola
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Harrison M Gomes
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Peter M Hawkey
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | - Paul D van Helden
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Gurujaj V Kadival
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | | | - Kristin Kremer
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Milan Kubin
- Municipal Institute of Hygiene, Prague, Czech Republic
| | - Savita P Kulkarni
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | - Benjamin Liens
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Troels Lillebaek
- Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
| | - Ho Minh Ly
- Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Christian Martin
- Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
| | - Igor Mokrousov
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Olga Narvskaïa
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Yun Fong Ngeow
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Ludmilla Naumann
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Stefan Niemann
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Ida Parwati
- Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
| | - Zeaur Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | | | | | | | - Sabine Rüsch-Gerdes
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Anna Sajduda
- Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
| | - Sofia Samper
- Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Igor G Shemyakin
- State Research Center for Applied Microbiology, Obolensk, Russian Federation
| | | | - Akos Somoskovi
- Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
| | - Robin A Skuce
- Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
| | - Dick van Soolingen
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Streicher
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Philip N Suffys
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Enrico Tortoli
- Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
| | | | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Tommie C Victor
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Robin M Warren
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Sook Fan Yap
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Khadiza Zaman
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | - Françoise Portaels
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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Ferdinand S, Sola C, Chanteau S, Ramarokoto H, Rasolonavalona T, Rasolofo-Razanamparany V, Rastogi N. A study of spoligotyping-defined Mycobacterium tuberculosis clades in relation to the origin of peopling and the demographic history in Madagascar. Infect Genet Evol 2005; 5:340-8. [PMID: 16168940 DOI: 10.1016/j.meegid.2004.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 10/08/2004] [Accepted: 10/12/2004] [Indexed: 11/28/2022]
Abstract
Despite well-developed tuberculosis (TB) control policies in Madagascar, the incidence of TB remains high and is estimated at about 100 new cases per 100000 inhabitants. This paper describes genetic characteristics of TB bacilli in Madagascar. Using an international spoligotyping database, SpolDB4, we also attempted to identify the origin of strains circulating in Madagascar. DNA polymorphism of 333 Mycobacterium tuberculosis complex isolates was assessed. A total of 301 isolates belonging to 60 spoligotyping-defined clusters were found, whereas 32 isolates harbored orphan patterns. By comparison with the international database, we identified a new genetic group of closely genetically related M. tuberculosis strains which we suggested to be specific from Madagascar. Most of them belonging to the East-African-Indian (EAI) superfamily of strains that are responsible for 14% of total TB cases (shared types ST1514-1525). These strains are closely related to the most prevalent shared type ST109, whose distribution is mainly confined to Madagascar. The observed distribution of genotypes shows that principal genetic group 1 strains (EAI, Beijing, CAS, Afri, "Manu") is high (35.4%) suggesting an ancient evolutionary history of tuberculosis in Madagascar, in relation to the origin of peopling and the demographic history.
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Affiliation(s)
- Séverine Ferdinand
- Unité de la Tuberculose and des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Joliviere, Pointe-à-Pitre, France
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Ferdinand S, Legrand E, Goh KS, Berchel M, Mazzarelli G, Sola C, Tortoli E, Rastogi N. Taxonomic and phylogenetic status of non-tuberculous mycobacteria in a Caribbean setting. Mol Cell Probes 2005; 18:399-408. [PMID: 15488380 DOI: 10.1016/j.mcp.2004.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 06/21/2004] [Indexed: 11/22/2022]
Abstract
This report describes detailed taxonomic and phylogenetic analysis of 15 non-tuberculous mycobacteria (NTMs) isolated from human pathological specimens in a Caribbean setting (12 slow-growers and three rapid-growers) that were not identified by cultural and biochemical tests and drug-susceptibility results. These isolates were further studied using PCR restriction fragment length polymorphism analysis (PRA) of a 441bp hsp65 fragment, as well as the sequencing of 16S rDNA and hsp65 DNA, and HPLC of the mycolic acids. Our results showed that taxonomic position of well-defined NTMs was resolved by PRA and sequencing of hsp65, nonetheless, it was not suitable to investigate rarely observed or new strains that required 16S rDNA sequencing and HPLC for a definite response. Unrooted neighbor-joining phylogenetic trees were drawn based upon the 16S rDNA and hsp65 sequences of the 15 NTMs compared with those from described species (73 for 16S rDNA and 45 for hsp65). For most of the NTMs not showing an exactly matching sequence with either hsp65 or 16S rDNA in the GenBank, the phylogenetic tree was able to provide with useful indications about their relatedness to known species. In such a case, a concording HPLC pattern with the sequence data and the place of the strain within the tree could lead to a potential identification. We also identified three identical isolates that define a new mycobacterial species within the group of M. simiae-related mycobacteria. The isolation and characterization of mycobacteria from new settings may lead to identify potential pathogens that may propogate in future because of increased human migration, travels, and climatic and ecological changes of the modern world.
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Affiliation(s)
- Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière, BP 484, F-97165 Pointe-à-Pitre Cedex, Guadeloupe France
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Sola C, Ferdinand S, Sechi LA, Zanetti S, Martial D, Mammina C, Nastasi A, Fadda G, Rastogi N. Mycobacterium tuberculosis molecular evolution in western Mediterranean Islands of Sicily and Sardinia. Infection, Genetics and Evolution 2005; 5:145-56. [PMID: 15639747 DOI: 10.1016/j.meegid.2004.08.003] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 08/17/2004] [Accepted: 08/24/2004] [Indexed: 11/22/2022]
Abstract
In this study, a total of 204 Mycobacterium tuberculosis DNAs from Sicily (n = 144) and Sardinia (n = 60) were studied by three genotyping methods. Results were analyzed both within and across islands, to define the phylogeographical specificities of the genotypes, look for their diversity and infer a molecular evolutionary scenario. A strong link between geography and tuberculosis genotypes was observed in Sardinia. The results were also matched against a world-wide genetic diversity database to compare the population structure of the tubercle bacilli in the islands. Eight common genotypes between Sicily, Sardinia and continental Italy were found which underlines the influences of the Italian mainland on the population structure on the islands and vice versa. A unified evolutionary scenario of M. tuberculosis evolution was built using numerical taxonomy and maximum parsimony (MP) methods. The finding of multiple families of M. tuberculosis strains (S, T, LAM, Haarlem), their presumed links with the major genetic groups (MGG) of M. tuberculosis complex, supports the view of independent introduction of several ancestral genotypes in Sicily and in Sardinia. We conclude that the two PCR-based genotyping combination (spoligotyping-VNTR) is an excellent tool to reconstruct M. tuberculosis phylogeny, that may be used to construct global and local evolutionary scenarios of the M. tuberculosis complex. The results obtained are paradigmatic of the complex interplay that exists between epidemic dynamics and evolutionary genetics of M. tuberculosis.
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Affiliation(s)
- Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière, BP 484, F97165 Pointe-à-Pitre, Guadeloupe, France.
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Ferdinand S, Valétudie G, Sola C, Rastogi N. Data mining of Mycobacterium tuberculosis complex genotyping results using mycobacterial interspersed repetitive units validates the clonal structure of spoligotyping-defined families. Res Microbiol 2004; 155:647-54. [PMID: 15380552 DOI: 10.1016/j.resmic.2004.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 04/22/2004] [Indexed: 11/17/2022]
Abstract
Recently, a combination of spoligotyping and bioinformatics was proposed as a potential tool for defining major circulating clades of tuberculosis bacilli. In the present study, we attempted to validate the above mentioned classification using a new high-throughput marker, named mycobacterial interspersed repetitive units (MIRUs). Using 12 MIRU loci and spoligotyping, we performed data mining of results on clinical isolates of the Mycobacterium tuberculosis complex representative of global mycobacterial allelic diversity. Knowledge rules permitting automatic labeling of major M. tuberculosis families were defined. Using this strategy, MIRU 24 appeared to be most appropriate for classifying our dataset. The Bovis family was shown to be perfectly classified by a maximum of 3 MIRUs, followed by Africanum and East African Indian (EAI) families by 4 MIRUs, the Beijing family by 6 MIRUs, Haarlem and X families by 8 MIRUs, the T family by 9, and the Latin-American and Mediterranean (LAM) family by 10 MIRUs. Considering the hierarchy of family divergence, our results corroborate a recent suggestion that EAI is the ancestral family followed by Africanum and Bovis. On the other hand, T, X, LAM and Haarlem families appear to be of more recent evolution. These results indicate that data mining of MIRUs is a valuable new tool for analyzing the evolutionary dynamics of the M. tuberculosis complex, and for monitoring an infectious disease such as tuberculosis.
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Affiliation(s)
- Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière BP 484, 97 165 Pointe-à-Pitre Cedex, Guadeloupe
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Duchêne V, Ferdinand S, Filliol I, Guégan JF, Rastogi N, Sola C. Phylogenetic reconstruction of Mycobacterium tuberculosis within four settings of the Caribbean region: tree comparative analyse and first appraisal on their phylogeography. Infect Genet Evol 2004; 4:5-14. [PMID: 15019584 DOI: 10.1016/j.meegid.2003.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2003] [Revised: 08/28/2003] [Accepted: 09/01/2003] [Indexed: 11/15/2022]
Abstract
In order to compare phylogenetic methods and to reconstruct the evolutionary history of the tubercle bacilli, a set of macro-array-based genotyping data of Mycobacterium tuberculosis clinical isolates (called spoligotyping for spacer oligonucleotide typing, which assays the variability of the Direct Repeat -DR- locus), was analyzed in four settings of the Caribbean region (Guadeloupe, Martinique, Cuba and Haiti). A set of 47 alleles, split into 26 shared and 21 unique alleles) representative of 321 individual M. tuberculosis clinical isolates from patients residing in the above regions was studied. The following methods (and software in brackets) were investigated: numerical taxonomy distance methods (TAXOTRON), maximum parsimony procedure (PAUP), median-joining networks (NETWORK), and nested clade analysis (GEODIS). Results using these methods were analyzed, compared and discussed. The latter method (GEODIS) was investigated in detail by introducing geographical data together with genetic variability results to detect a link between population structure and population history, and to test the null hypothesis of no association between geography and genotypes. Irrespective of the methods used, our findings demonstrate that a core structure of four families (or clades) of M. tuberculosis strains is highly prevalent within the islands studied, indirectly reflecting passed colonization history of these different settings. Specificity of M. tuberculosis genotypes in each of the islands is discussed in the light of their respective colonial and contemporary histories.
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Affiliation(s)
- Véronique Duchêne
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, BP 484, F-97165 Pointe à Pitre Cedex, Guadeloupe, France
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Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Dang DA, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Kassa-Kelembho E, Ho ML, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol 2003; 41:1963-70. [PMID: 12734235 PMCID: PMC154710 DOI: 10.1128/jcm.41.5.1963-1970.2003] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present update on the global distribution of Mycobacterium tuberculosis complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for M. tuberculosis complex, including Mycobacterium bovis, from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, a number of major and minor visual rules were also defined. A total of six major rules (A to F) with the precise description of the extra missing spacers (minor rules) were used to define 36 major clades (or families) of M. tuberculosis. Some major clades identified were the East African-Indian (EAI) clade, the Beijing clade, the Haarlem clade, the Latin American and Mediterranean (LAM) clade, the Central Asian (CAS) clade, a European clade of IS6110 low banders (X; highly prevalent in the United States and United Kingdom), and a widespread yet poorly defined clade (T). When the visual rules defined above were used for an automated labeling of the 813 shared types to define nine superfamilies of strains (Mycobacterium africanum, Beijing, M. bovis, EAI, CAS, T, Haarlem, X, and LAM), 96.9% of the shared types received a label, showing the potential for automated labeling of M. tuberculosis families in well-defined phylogeographical families. Intercontinental matches of shared types among eight continents and subcontinents (Africa, North America, Central America, South America, Europe, the Middle East and Central Asia, and the Far East) are analyzed and discussed.
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Affiliation(s)
- Ingrid Filliol
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe
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Ferdinand S, Sola C, Verdol B, Legrand E, Goh KS, Berchel M, Aubéry A, Timothée M, Joseph P, Pape JW, Rastogi N. Molecular characterization and drug resistance patterns of strains of Mycobacterium tuberculosis isolated from patients in an AIDS counseling center in Port-au-Prince, Haiti: a 1-year study. J Clin Microbiol 2003; 41:694-702. [PMID: 12574269 PMCID: PMC149692 DOI: 10.1128/jcm.41.2.694-702.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [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: 07/16/2002] [Revised: 10/23/2002] [Accepted: 11/17/2002] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) is one of the most common opportunistic diseases that appear among human immunodeficiency virus (HIV)-positive patients in Haiti. In this context the probable emergence of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis is of great epidemiological concern. However, as routine culture of M. tuberculosis and drug susceptibility testing are not performed in Haiti, it has not been possible so far to evaluate the rate of drug resistance among M. tuberculosis isolates from circulating TB cases. This report describes the first study on the molecular typing and drug resistance of M. tuberculosis isolates from patients with culture-positive pulmonary tuberculosis monitored at the GHESKIO Centers in Haiti during the year 2000. Clinical, epidemiological, and drug susceptibility testing results were available for 157 patients with confirmed cases of TB, with a total of 8.9% of patients harboring MDR M. tuberculosis. A significant association between the occurrence of resistance and previous TB treatment was observed (P < 0.001), suggesting that a previous history of TB treatment was a risk factor associated with MDR TB in Haiti. The DNAs of individual isolates from 106 samples were available and were typed by spoligotyping and determination of the variable number of tandem DNA repeats. Both typing methods provided interpretable results for 96 isolates, and the clusters observed were further confirmed by ligation-mediated PCR to define potential cases of active transmission. Thirty-three (34%) of the isolates were found to be grouped into 11 clusters with two or more identical patterns. However, an assessment of risk factors (sex, HIV positivity, previous treatment, drug resistance) showed that none was significantly associated with the active transmission of TB. These observations suggest that acquired MDR TB is prevalent in Haiti and may be associated with compliance issues during TB treatment since prior TB therapy is the strongest risk factor associated with MDR TB. Prevention of TB transmission in Haiti should target active case investigation, routine detection of drug resistance, and adequate treatment of patients. The use of directly observed short-course therapy should be enforced throughout the country; and relapses, reactivations, or newly acquired infections should be discriminated by genotyping methods.
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Affiliation(s)
- Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, F97165 Pointe-à-Pitre Cédex, Guadeloupe
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Filliol I, Driscoll JR, van Soolingen D, Kreiswirth BN, Kremer K, Valétudie G, Anh DD, Barlow R, Banerjee D, Bifani PJ, Brudey K, Cataldi A, Cooksey RC, Cousins DV, Dale JW, Dellagostin OA, Drobniewski F, Engelmann G, Ferdinand S, Gascoyne-Binzi D, Gordon M, Gutierrez MC, Haas WH, Heersma H, Källenius G, Kassa-Kelembho E, Koivula T, Ly HM, Makristathis A, Mammina C, Martin G, Moström P, Mokrousov I, Narbonne V, Narvskaya O, Nastasi A, Niobe-Eyangoh SN, Pape JW, Rasolofo-Razanamparany V, Ridell M, Rossetti ML, Stauffer F, Suffys PN, Takiff H, Texier-Maugein J, Vincent V, de Waard JH, Sola C, Rastogi N. Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg Infect Dis 2002; 8:1347-9. [PMID: 12453368 PMCID: PMC2738532 DOI: 10.3201/eid0811.020125] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We present a short summary of recent observations on the global distribution of the major clades of the Mycobacterium tuberculosis complex, the causative agent of tuberculosis. This global distribution was defined by data-mining of an international spoligotyping database, SpolDB3. This database contains 11708 patterns from as many clinical isolates originating from more than 90 countries. The 11708 spoligotypes were clustered into 813 shared types. A total of 1300 orphan patterns (clinical isolates showing a unique spoligotype) were also detected.
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Affiliation(s)
- Ingrid Filliol
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | - Dick van Soolingen
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Kristin Kremer
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | | | - Karin Brudey
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | | | - Debby V. Cousins
- Australian Reference Laboratory for Bovine Tuberculosis, Department of Agriculture, South Perth, Australia
| | | | | | | | | | | | | | - Max Gordon
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | | | | | - Herre Heersma
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | | | | | - Tuija Koivula
- Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Ho Minh Ly
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Gerald Martin
- Bundesinstitut für gesundheitlichenVerbraucherschutz und Veterinärmedizin, Jena, Germany
| | - Peter Moström
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | - Igor Mokrousov
- Pasteur Institute of Saint Petersburg, Saint Petersburg, Russia
| | | | - Olga Narvskaya
- Pasteur Institute of Saint Petersburg, Saint Petersburg, Russia
| | | | | | - Jean W Pape
- Les Centres Gheskio, Institut National de Laboratoire et de Recherche, Port-au- Prince, Haïti
- Cornell University, Ithaca, New York, USA
| | | | | | | | - Fritz Stauffer
- Bundesstaatliche bakteriologisch-serologische Untersuchungsanstalt Wien, Austria
| | | | | | | | | | | | - Christophe Sola
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
| | - Nalin Rastogi
- Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies
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Filliol I, Ferdinand S, Sola C, Thonnon J, Rastogi N. Spoligotyping and IS6110-RFLP typing of Mycobacterium tuberculosis from French Guiana: a comparison of results with international databases underlines interregional transmission from neighboring countries. Res Microbiol 2002; 153:81-8. [PMID: 11900267 DOI: 10.1016/s0923-2508(01)01292-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this investigation, 94 clinical isolates of Mycobacterium tuberculosis obtained over a 3-year period (1996-1998) from French Guiana were characterized by spoligotyping and IS6110-RFLP and the patterns obtained were compared with genotypes representing the worldwide diversity in an international spoligotyping database (n = 4269) and a IS6110-RFLP database (n = 4189). All the clustered isolates giving < or = 6 copies of IS6110 were further typed using the double-repetitive element (DRE)-PCR. The results obtained underlined the highly diverse nature of the M. tuberculosis population in French Guiana with potential links to neighboring countries within the Americas. It may be hypothesized that the genetic heterogeneity of tubercle bacilli in French Guiana is linked to the high number of imported cases of tuberculosis, that may account for as high as 68% of all tuberculosis cases. Although an epidemiological investigation based on direct interrogation of patients was not performed, available medical records suggested that the clustering of isolates was mostly linked to the following risk factors: pulmonary tuberculosis, smear-positive samples, foreign-born nationals and/or immigrants, and a high rate of HIV-TB coinfection. Thus the persisting foci of endemic disease and increased active transmission due to high population flux and HIV coinfection may be largely responsible for the relatively high incidence of tuberculosis in French Guiana.
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Affiliation(s)
- Ingrid Filliol
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière, Pointe à Pitre
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Sola C, Ferdinand S, Mammina C, Nastasi A, Rastogi N. Genetic diversity of Mycobacterium tuberculosis in Sicily based on spoligotyping and variable number of tandem DNA repeats and comparison with a spoligotyping database for population-based analysis. J Clin Microbiol 2001; 39:1559-65. [PMID: 11283087 PMCID: PMC87970 DOI: 10.1128/jcm.39.4.1559-1565.2001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study, we proposed to associate spoligotyping and typing with the variable number of tandem DNA repeats (VNTR) as an alternative strategy to IS6110-restriction fragment length polymorphism (RFLP) for molecular epidemiological studies on tuberculosis. The aim of the present study was to further evaluate this PCR-based typing strategy and to describe the population structure of Mycobacterium tuberculosis in another insular setting, Sicily. A collection of 106 DNA samples from M. tuberculosis patient isolates was characterized by spoligotyping and VNTR typing. All isolates were independently genotyped by the standard IS6110-RFLP method, and clustering results between the three methods were compared. The totals for the clustered isolates were, respectively, 15, 60, and 82% by IS6110-RFLP, spoligotyping, and VNTR typing. The most frequent spoligotype included type 42 that missed spacers 21 to 24 and spacers 33 to 36 and derived types 33, 213, and 273 that, together represented as much as 26% of all isolates, whereas the Haarlem clade of strains (types 47 and 50, VNTR allele 32333) accounted for 9% of the total strains. The combination of spoligotyping and VNTR typing results reduced the number of clusters to 43% but remained superior to the level of IS6110-RFLP clustering (ca. 15%). All but one IS6110-defined cluster were identified by the combination of spoligotyping and VNTR clustering results, whereas 9 of 15 spoligotyping-defined clusters could be further subdivided by IS6110-RFLP. Reinterpretation of previous IS6110-RFLP results in the light of spoligotyping-VNTR typing results allowed us to detect an additional cluster that was previously missed. Although less discriminative than IS6110-RFLP, our results suggest that the use of the combination of spoligotyping and VNTR typing is a good screening strategy for detecting epidemiological links for the study of tuberculosis epidemiology at the molecular level.
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Affiliation(s)
- C Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur, F-97165 Pointe-à-Pitre Cedex, Guadeloupe.
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Filliol I, Ferdinand S, Negroni L, Sola C, Rastogi N. Molecular typing of Mycobacterium tuberculosis based on variable number of tandem DNA repeats used alone and in association with spoligotyping. J Clin Microbiol 2000; 38:2520-4. [PMID: 10878036 PMCID: PMC86957 DOI: 10.1128/jcm.38.7.2520-2524.2000] [Citation(s) in RCA: 47] [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] [Indexed: 11/20/2022] Open
Abstract
Fingerprinting based on variable numbers of tandem DNA repeats (VNTR), a recently described methodology, was evaluated for molecular typing of Mycobacterium tuberculosis in an insular setting. In this study, VNTR fingerprinting was used alone or as a second-line test in association with spoligotyping, double-repetitive-element PCR (DRE-PCR), and IS6110 restriction fragment length polymorphism (RFLP) analysis, and the discriminatory power for each method or the combination of methods was compared by calculating the Hunter-Gaston discriminative index (HGI). The results obtained showed that in 6 out of 12 (50%) cases, VNTR-defined clusters were further subdivided by spoligotyping, compared to 7 out of 18 (39%) cases where spoligotyping-defined clusters were further subdivided by VNTR. When used alone, VNTR was the least discriminatory method (HGI = 0.863). Although VNTR was significantly more discriminatory when used in association with spoligotyping (HGI = 0.982), the combination of spoligotyping and DRE-PCR (HGI = 0.992) was still the most efficient among rapid, PCR-based methodologies, giving results comparable to IS6110 RFLP analysis. Nonetheless, VNTR typing may provide additional phylogenetical information that may be helpful to trace the molecular evolution of tubercle bacilli.
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Affiliation(s)
- I Filliol
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur, F-97165 Pointe-à-Pitre Cedex, Guadeloupe
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Lashley PM, Ramesh J, Ferdinand S. Spontaneous rupture of the spleen. W INDIAN MED J 1998; 47:172-3. [PMID: 10097671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
A 10 year old boy presented to the surgical service of the Queen Elizabeth Hospital with spontaneous rupture of the spleen and was later discovered to have chronic myeloid leukaemia. He has been in haematological remission for five years followed splenectomy and alpha-interferon therapy.
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Affiliation(s)
- P M Lashley
- Department of Child Health, Queen Elizabeth Hospital, Barbados
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