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Savin C, Le Guern AS, Chereau F, Guglielmini J, Heuzé G, Demeure C, Pizarro-Cerdá J. First Description of a Yersinia pseudotuberculosis Clonal Outbreak in France, Confirmed Using a New Core Genome Multilocus Sequence Typing Method. Microbiol Spectr 2022; 10:e0114522. [PMID: 35863020 PMCID: PMC9431522 DOI: 10.1128/spectrum.01145-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/18/2022] [Indexed: 12/04/2022] Open
Abstract
Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis in children and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We report for the first time a Y. pseudotuberculosis clonal outbreak in France, that occurred in 2020. An epidemiological investigation based on food queries pointed toward the consumption of tomatoes as the suspected source of infection. The Yersinia National Reference Laboratory (YNRL) developed a new cgMLST scheme with 1,921 genes specific to Y. pseudotuberculosis that identified the clustering of isolates associated with the outbreak and allowed to perform molecular typing in real time. In addition, this method allowed to retrospectively identify isolates belonging to this cluster from earlier in 2020. This method, which does not require specific bioinformatic skills, is now used systematically at the YNRL and proves to display an excellent discriminatory power and is available to the scientific community. IMPORTANCE We describe in here a novel core-genome MLST method that allowed to identify in real time, and for the first time in France, a Y. pseudotuberculosis clonal outbreak that took place during the summer 2020 in Corsica. Our method allows to support epidemiological and microbiological investigations to establish a link between patients infected with closely associated Y. pseudotuberculosis isolates, and to identify the potential source of infection. In addition, we made this method available for the scientific community.
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Affiliation(s)
- Cyril Savin
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université de Paris Cité, Yersinia National Reference Laboratory, Paris, France
- Institut Pasteur, Université de Paris Cité, WHO Collaborating Research & Reference Centre for Yersinia FRA-140, Paris, France
| | - Anne-Sophie Le Guern
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université de Paris Cité, Yersinia National Reference Laboratory, Paris, France
- Institut Pasteur, Université de Paris Cité, WHO Collaborating Research & Reference Centre for Yersinia FRA-140, Paris, France
| | - Fanny Chereau
- French National Public Health Agency, Department of Infectious Diseases, Saint-Maurice, France
| | - Julien Guglielmini
- Institut Pasteur, Université de Paris Cité, Hub de Bioinformatique et Biostatistique, Paris, France
| | | | - Christian Demeure
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université de Paris Cité, WHO Collaborating Research & Reference Centre for Yersinia FRA-140, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université de Paris Cité, Yersinia National Reference Laboratory, Paris, France
- Institut Pasteur, Université de Paris Cité, WHO Collaborating Research & Reference Centre for Yersinia FRA-140, Paris, France
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Valeix N, Costa D, Basmaciyan L, Valot S, Vincent A, Razakandrainibe R, Robert-Gangneux F, Nourrisson C, Pereira B, Fréalle E, Poirier P, Favennec L, Dalle F. Multicenter Comparative Study of Six Cryptosporidium parvum DNA Extraction Protocols Including Mechanical Pretreatment from Stool Samples. Microorganisms 2020; 8:E1450. [PMID: 32971858 PMCID: PMC7564494 DOI: 10.3390/microorganisms8091450] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Nowadays, many commercial kits allow the detection of Cryptosporidium sp. in stool samples after deoxyribonucleic acid (DNA) extraction. Protocols of stool pretreatment have been proposed to optimize oocysts' DNA extraction. Among them, mechanical grinding was reported to improve the performance of Cryptosporidium oocysts' DNA extraction. METHODS A multicenter comparative study was conducted within the framework of the French National Reference Center-Expert Laboratory for Cryptosporidiosis. Six extraction systems (i.e., manual or automated) associated with various mechanical pretreatment protocols, were compared for the Cryptosporidium parvum oocyst' DNA extraction, before amplification using the same real-time PCR method targeting. RESULTS The sensitivity of real-time PCR assay was unequally impacted by the pretreatment/extraction protocol. We observed significant differences for the lowest concentrations of C. parvum oocysts (i.e., 0-94.4% and 33.3-100% respectively for 10 and 50 oocysts/mL). All in all, the protocol using Quick DNA Fecal/Soil Microbe-Miniprep® manual kit showed the best performances. In addition, optimal performances of mechanical pretreatment were obtained by combining a grinding duration of 60 s with a speed of 4 m/s using Fastprep24® with Lysing Matrix E®. CONCLUSIONS Sample pretreatment, as well as the extraction method, needs to be properly adapted to improve the diagnostic performances of the C. parvum DNA amplification methods.
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Affiliation(s)
- Nicolas Valeix
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Damien Costa
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Louise Basmaciyan
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
- UMR PAM, University Bourgogne Franche-Comté-AgroSup Dijon-Equipe Vin, Aliment, Microbiologie, Stress, CEDEX, 21078 Dijon, France
| | - Stéphane Valot
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Anne Vincent
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
| | - Romy Razakandrainibe
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Florence Robert-Gangneux
- Univ. Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé Environnement Travail), UMR_S 1085, 35000 Rennes, France;
| | - Céline Nourrisson
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Bruno Pereira
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Emilie Fréalle
- CHU Lille, Laboratoire de Parasitologie-Mycologie, F-59000 Lille, France;
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019–UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Philippe Poirier
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire de Clermont-Ferrand, 63000 Clermont-Ferrand, France; (C.N.); (B.P.); (P.P.)
| | - Loic Favennec
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France; (D.C.); (R.R.); (L.F.)
- Centre National de Référence–Laboratoire Expert des Cryptosporidioses, Institut de Biologie Clinique, Centre Hospitalo-Universitaire C. Nicolle de Rouen, 76000 Rouen, France
| | - Frederic Dalle
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire, 2 rue A. Ducoudray, BP 37013, CEDEX, 21070 Dijon, France; (N.V.); (L.B.); (S.V.); (A.V.)
- UMR PAM, University Bourgogne Franche-Comté-AgroSup Dijon-Equipe Vin, Aliment, Microbiologie, Stress, CEDEX, 21078 Dijon, France
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