André Birgy1,2, Fouad Madhi3,4,5, Camille Jung3,5, Corinne Levy4,6,7, Aurélie Cointe1,2, Philippe Bidet1,2, Claire Amaris Hobson1, Stéphane Bechet6, Elsa Sobral6, Hoang Vuthien8, Agnès Ferroni9, Saïd Aberrane10, Gaëlle Cuzon11,12,13,14, Laetitia Beraud15, Vincent Gajdos16,17, Elise Launay18, Didier Pinquier19, Hervé Haas20, Marie Desmarest21, Marie-Aliette Dommergues4,22, Robert Cohen4,5,6,7,23, Stéphane Bonacorsi1,2. 1. Université de Paris, IAME, INSERM, F-75018, Paris, France. 2. AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France. 3. Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, France. 4. Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France. 5. Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France. 6. Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France. 7. Université Paris Est, IMRB-GRC GEMINI, ACTIV, 94000, Créteil, France. 8. AP-HP, HU-Est Parisien site Trousseau, Service de Bactériologie, F-75012, Paris, France. 9. AP-HP, Hopital Necker, Service de Microbiologie, University Paris Descartes, Paris, France. 10. Microbiology Laboratory, Créteil Hospital, Créteil, France. 11. Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France. 12. Université Paris Sud, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France. 13. Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France. 14. Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur, APHP-Université Paris Sud, Paris, France. 15. Centre National de Référence des Légionelles, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France. 16. Service de Pédiatrie, Antoine Béclère University Hospital, Assistance Publique-Hôpitaux de Paris, Clamart, France. 17. Centre for Research in Epidemiology and Population Health, Villejuif, France. 18. Service de Pédiatrie Générale et Infectiologie Pédiatrique, Hôpital Femme-Enfant-Adolescent, Centre Hospitalier Universitaire de Nantes, Nantes, France. 19. Unité de Pneumologie et Allergologie pédiatriques & CRCM mixte, Pédiatrie Médicale, CHU Charles Nicolle, Rouen, France. 20. Hôpitaux pédiatriques CHU Lenval, Nice, France. 21. Service d'Accueil des Urgences Pédiatriques, AP-HP, Hôpital Robert Debré, Paris, France. 22. Service de pédiatrie, centre hospitalier de Versailles, Le Chesnay, France. 23. Unité Court Séjour, Petits Nourrisson, Service de Néonatologie, Centre Hospitalier Intercommunal de Créteil, France.
Abstract
BACKGROUND: The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E). OBJECTIVES: To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E. METHODS: A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined. RESULTS: E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs. cgMLST enabled discrimination of clusters within the main STs. CONCLUSIONS: The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.
BACKGROUND: The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E). OBJECTIVES: To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E. METHODS: A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined. RESULTS:E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs. cgMLST enabled discrimination of clusters within the main STs. CONCLUSIONS: The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.
Authors: Michael Biggel; Basil B Xavier; James R Johnson; Karen L Nielsen; Niels Frimodt-Møller; Veerle Matheeussen; Herman Goossens; Pieter Moons; Sandra Van Puyvelde Journal: Nat Commun Date: 2020-11-24 Impact factor: 14.919
Authors: Lorena Patrícia Gaviria; Lourdes Montsant; Carlos Azuaje; Aida González-Díaz; Juan P Horcajada; Enric Limón; Miguel Viñas; Paula Espinal; Ester Fusté Journal: Microorganisms Date: 2022-02-22