title: Multilocus sequence typing scheme for the Mycobacterium abscessus complex.
abstract: We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in France, Germany, Switzerland and Brazil. We identified 100 different sequence types (STs), which were distributed into three groups on the tree obtained by concatenating the sequences of the seven housekeeping gene fragments (3576bp): the M. abscessus sensu stricto group (44 STs), the "M. massiliense" group (31 STs) and the "M. bolletii" group (25 STs). SplitTree analysis showed a degree of intergroup lateral transfers. There was also evidence of lateral transfer events involving rpoB. The most prevalent STs in our collection were ST1 (CC5; 20 isolates) and ST23 (CC3; 31 isolates). Both STs were found in Europe and Brazil, and the latter was implicated in a large post-surgical procedure outbreak in Brazil. Respiratory isolates from patients with cystic fibrosis belonged to a large variety of STs; however, ST2 was predominant in this group of patients. Our MLST scheme, publicly available at www.pasteur.fr/mlst, offers investigators a valuable typing tool for M. abscessus sensu lato in future epidemiological studies throughout the world.
authors.affiliation: APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France. Electronic address: macheras_edouard@yahoo.fr.
authors.forename: Edouard
authors.initials: E
authors.lastname: Macheras
authors.affiliation: EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France. Electronic address: julie.konjek@ens.uvsq.fr.
authors.forename: Julie
authors.initials: J
authors.lastname: Konjek
authors.affiliation: APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France. Electronic address: anne-laure.roux@rpc.aphp.fr.
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Roux
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France. Electronic address: jean-michel.thiberge@pasteur.fr.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Thiberge
authors.affiliation: Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France. Electronic address: sylvaine.bastian@bch.aphp.fr.
authors.forename: Sylvaine
authors.initials: S
authors.lastname: Bastian
authors.affiliation: Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu, 862, Vila Clementino, São Paulo SP CEP 04023-062, Brazil. Electronic address: sylvia.leao@unifesp.br.
authors.forename: Sylvia Cardoso
authors.initials: SC
authors.lastname: Leão
authors.affiliation: Nucleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari, 514, Goiabeiras Vitória - ES, CEP 29075-910, Brazil. Electronic address: mpalaci@ndi.ufes.br.
authors.forename: Moises
authors.initials: M
authors.lastname: Palaci
authors.affiliation: APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France. Electronic address: valerie.sivadon-tardy@apr.aphp.fr.
authors.forename: Valérie
authors.initials: V
authors.lastname: Sivadon-Tardy
authors.affiliation: Caribbean Public Health Agency (CARPHA), 16-18 Jamaica Boulevard, Federation Park, Port of Spain, Trinidad and Tobago. Electronic address: crisgupe1@gmail.com.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gutierrez
authors.affiliation: National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany. Electronic address: erichter@fz-borstel.de.
authors.forename: Elvira
authors.initials: E
authors.lastname: Richter
authors.affiliation: National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany. Electronic address: srueschg@fz-borstel.de.
authors.forename: Sabine
authors.initials: S
authors.lastname: Rüsch-Gerdes
authors.affiliation: Institut für Medizinische Mikrobiologie, Zentrum für LaborMedizin, Luzerner Kantonsspital, Spitalstrasse, 6004 Luzern, Switzerland. Electronic address: gaby.pfyffer@luks.ch.
authors.forename: Gaby E
authors.initials: GE
authors.lastname: Pfyffer
authors.affiliation: Institut für Infektionskrankheiten, Universität Bern, Hochschulstrasse 4, 3010 Bern, Switzerland. Electronic address: thomas.bodmer@risch.ch.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bodmer
authors.affiliation: Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France. Electronic address: vincent.jarlier@psl.aphp.fr.
authors.forename: Vincent
authors.initials: V
authors.lastname: Jarlier
authors.affiliation: APHP, Groupe hospitalier Lariboisière-Fernand Widal, Laboratoire de Microbiologie, 2 rue Ambroise Paré, 75010 Paris, France. Electronic address: emmanuelle.cambau@lrb.aphp.fr.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Cambau
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France. Electronic address: sylvain.brisse@pasteur.fr.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
authors.affiliation: Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France. Electronic address: valerie.caro@pasteur.fr.
authors.forename: Valérie
authors.initials: V
authors.lastname: Caro
authors.affiliation: Institut Pasteur, Laboratoire de Recherche et de Référence sur la Tuberculose et les Mycobactéries, BP 484 Morne Jolivière, Les Abymes 97183 Cedex, Guadeloupe, France. Electronic address: nrastogi@pasteur-guadeloupe.fr.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
authors.affiliation: APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France. Electronic address: jean-louis.gaillard@apr.aphp.fr.
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Gaillard
authors.affiliation: APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France. Electronic address: beate.heym@apr.aphp.fr.
authors.forename: Beate
authors.initials: B
authors.lastname: Heym
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D020043:Genes, Essential; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058885:Multilocus Sequence Typing / Q000379:methods*; D009161:Mycobacterium / Q000145:classification* / Q000235:genetics*; D009165:Mycobacterium Infections, Nontuberculous / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial
keywords: Cystic fibrosis; Molecular identification; Molecular typing; Multilocus sequence typing; Mycobacterium abscessus complex; Non-tuberculous mycobacteria; Opportunistic mycobacteria; Phylogenetic analysis; rpoB