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1. Populations of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: a multicentre European study

Author

Martak, Daniel, Guther, Julia, Verschuuren, Tess, Valot, Benoit, Conzelmann, Nadine, Bunk, Stefanie, Riccio, M Eugenia, Salamanca, Elena, Meunier, Alexandre, Henriot, Charles, Brossier, Caroline Pressacco, Bertrand, Xavier, Cooper, Ben, Harbarth, Stephan, Tacconelli, Evelina, Fluit, Ad, Rodriguez-Baño, Jesús, Kluytmans, Jan, Peter, Silke, Hocquet, Didier, Riccio, M. Eugenia, Kluytmans, Jan A.J.W., Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Cherkaoui, Abdessalam, and Renzi, Gesuele

Subjects
Microbiology (medical), Veterinary medicine, Klebsiella pneumoniae, Escherichia coli, K. pneumoniae, ESBL, food, environment, Biology, Environment, Polluted environment, medicine.disease_cause, beta-Lactamases, K. pneumoniae, 03 medical and health sciences, Food chain, Plasmid, Data sequences, Extended-spectrum β-lactamase, medicine, polycyclic compounds, Escherichia coli, Humans, Escherichia coli Infections, 030304 developmental biology, ddc:616, 0303 health sciences, 030306 microbiology, K pneumoniae, General Medicine, Sequence types, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, 3. Good health, Anti-Bacterial Agents, Klebsiella Infections, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ESBL, Food, bacteria, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Plasmids
Abstract

Objectives To assess the extent to which food items are a source of extended-spectrum β-lactamase (ESBL) -producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities. Methods We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination) and 714 food items in Besancon (France), Geneva (Switzerland), Sevilla (Spain), Tubingen (Germany) and Utrecht (The Netherlands). A total of 254 ESBL-Ec and 39 ESBL-Kp isolates were cultured. All genomes were fully sequenced to compare their sequence types (ST) and core genomes, along with the distribution of blaESBL genes and their genetic supports (i.e. chromosome or plasmid). Results Sequence data revealed that ESBL-Ec and ESBL-Kp isolates from hp-environments were genetically different from those contaminating food items. ESBL-Ec ST131 was widespread in the hp-environment (21.5% of the isolates) but absent from the food items tested. ESBL-Ec ST10 was in similar proportions in hp-environments and food items (15 and 10 isolates, respectively) but mostly carried reservoir-specific blaESBL. blaCTX-M-1 and blaSHV-12 predominated in food-related E. coli isolates (32% and 34% of the isolates, respectively), whereas blaCTX-M-15 and blaCTX-M-27 predominated in isolates from hp-environments (52% and 15% of the isolates, respectively). Conclusions We found a very limited connection between ESBL-Ec and ESBL-Kp populations retrieved in food items and from hp-environments and blaESBL. This suggests that human-to-human contamination, rather than the food chain, is possibly the most frequent route of ESBL-Ec and ESBL-Kp transmission in high-income countries.

Published
2021
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2. Emergence of New Non–Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae Isolates, France

Author

Adriana Chiarelli, Philippe Glaser, Laurent Dortet, Agnès B Jousset, Rémy A. Bonnin, Cécile Emeraud, Thierry Naas, Institut Pasteur [Paris] (IP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Sud - Paris 11 (UP11), Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Université Paris-Saclay, French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae [Le Kremlin-Bicêtre], AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), This work was funded in part by the University Paris-Sud, France. L.D., T.N., and R.A.B. are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics, which is supported by a grant from France’s National Research Agency (grant no. ANR-10-LABX-33)., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), and Institut Pasteur [Paris]

Subjects
Microbiology (medical), clone (Java method), Klebsiella pneumoniae, 030231 tropical medicine, lcsh:Medicine, Biology, beta-Lactamases, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, carbapenemase, 0302 clinical medicine, Antibiotic resistance, Bacterial Proteins, polycyclic compounds, nosocomial infections, Humans, lcsh:RC109-216, 030212 general & internal medicine, antimicrobial resistance, bacteria, Whole genome sequencing, Portugal, Research, lcsh:R, K pneumoniae, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Carbapenemase producing, Sequence types, biology.organism_classification, bacterial infections and mycoses, ST147, 3. Good health, Anti-Bacterial Agents, Clone Cells, Klebsiella Infections, Europe, KPC, Infectious Diseases, Emergence of New Non–Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae Isolates, France, bacterial infections, whole-genome sequencing, Western europe, ST307, epidemiology, France, Multilocus Sequence Typing
Abstract

International audience; The worldwide spread of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) isolates was reported to be caused by dissemination of 1 clonal complex (i.e., clonal group [CG] 258, which includes sequence types [STs] 258 and 512). We conducted whole-genome sequencing and epidemiologic analysis of all KPC-Kp isolates in France in 2018 and found that new successful high-risk clones of ST147, ST307, ST231, and ST383 are now the main drivers of blaKPC genes. The blaKPC genes were mostly carried by Tn4401a and Tn4401d structures and a new non-Tn4401 element. Our epidemiologic investigations showed that the emergence of these non-CG258 KPC-Kp isolates in France was linked to dissemination of these clones from Portugal. Thus, KPC-Kp epidemiology has changed in Europe, at least in several non-KPC-endemic countries of western Europe, such as France and Portugal, where CG258 is not the most prevalent clone.

Published
2020
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3. Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings

Author

Jean-Louis Herrmann, Thomas Obadia, Laura Temime, Audrey Duval, Pierre-Yves Boëlle, Lulla Opatowski, Eric Fleury, Didier Guillemot, Bodescot, Myriam, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Biostatistique, Biomathématique, Pharmacoépidémiologie et Maladies Infectieuses (B2PHI), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Malaria : parasites et hôtes - Malaria : parasites and hosts, Institut Pasteur [Paris] (IP), Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Laboratoire de l'Informatique du Parallélisme (LIP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Dynamic Networks : Temporal and Structural Capture Approach (DANTE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de l'Informatique du Parallélisme (LIP), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut Rhône-Alpin des systèmes complexes (IXXI), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Service de Microbiologie [Garches], Hôpital Raymond Poincaré [AP-HP], Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), This study was supported by the European Commission under the Life Science Health Priority of the 6th Framework Program (MOSAR network contract LSHP-CT-2007-037941), funding was also received from the French Government through the National Clinical Research Program and the Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant no. ANR-10-LABX-62-IBEID, http://www.agencenationale-recherche.fr/ProjetIA-10-LABX-0062) to DG and from the Ecole des Hautes Etudes en Santé Publique (EHESP, https://www.ehesp.fr/) to AD., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Centre National de la Recherche Scientifique (CNRS)-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut Rhône-Alpin des systèmes complexes (IXXI)

Subjects
0301 basic medicine, Male, Species Delimitation, Klebsiella pneumoniae, Nosocomial Infections, Speciation, Health Care Providers, Nurses, Pathology and Laboratory Medicine, law.invention, Klebsiella Pneumoniae, 0302 clinical medicine, law, Antibiotics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Klebsiella, Epidemiology, Medicine and Health Sciences, polycyclic compounds, Infection control, Public and Occupational Health, 030212 general & internal medicine, Medical Personnel, Biology (General), Escherichia coli Infections, 0303 health sciences, Cross Infection, Ecology, biology, Antimicrobials, K pneumoniae, Drugs, Drug Resistance, Microbial, Hygiene, Middle Aged, Hospitals, 3. Good health, Care facility, Anti-Bacterial Agents, Bacterial Pathogens, Professions, Transmission (mechanics), Infectious Diseases, Computational Theory and Mathematics, Medical Microbiology, Modeling and Simulation, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Pathogens, Wireless Technology, Research Article, Adult, medicine.medical_specialty, Evolutionary Processes, QH301-705.5, Microbiology, beta-Lactamases, Cellular and Molecular Neuroscience, 03 medical and health sciences, Antibiotic resistance, Enterobacteriaceae, Environmental health, Microbial Control, Drug Resistance, Bacterial, Genetics, medicine, Disease Transmission, Infectious, Escherichia coli, Humans, Molecular Biology, Microbial Pathogens, Ecology, Evolution, Behavior and Systematics, Aged, Pharmacology, Infection Control, Evolutionary Biology, Bacteria, 030306 microbiology, Organisms, Biology and Life Sciences, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, Health Care, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Antibiotic Resistance, Healthcare settings, People and Places, bacteria, Population Groupings, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Antimicrobial Resistance, 030217 neurology & neurosurgery
Abstract

Antibiotic-resistance of hospital-acquired infections is a major public health issue. The worldwide emergence and diffusion of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, including Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP), is of particular concern. Preventing their nosocomial spread requires understanding their transmission. Using Close Proximity Interactions (CPIs), measured by wearable sensors, and weekly ESBL-EC–and ESBL-KP–carriage data, we traced their possible transmission paths among 329 patients in a 200-bed long-term care facility over 4 months. Based on phenotypically defined resistance profiles to 12 antibiotics only, new bacterial acquisitions were tracked. Extending a previously proposed statistical method, the CPI network’s ability to support observed incident-colonization episodes of ESBL-EC and ESBL-KP was tested. Finally, mathematical modeling based on our findings assessed the effect of several infection-control measures. A potential infector was identified in the CPI network for 80% (16/20) of ESBL-KP acquisition episodes. The lengths of CPI paths between ESBL-KP incident cases and their potential infectors were shorter than predicted by chance (P = 0.02), indicating that CPI-network relationships were consistent with dissemination. Potential ESBL-EC infectors were identified for 54% (19/35) of the acquisitions, with longer-than-expected lengths of CPI paths. These contrasting results yielded differing impacts of infection control scenarios, with contact reduction interventions proving less effective for ESBL-EC than for ESBL-KP. These results highlight the widely variable transmission patterns among ESBL-producing Enterobacteriaceae species. CPI networks supported ESBL-KP, but not ESBL-EC spread. These outcomes could help design more specific surveillance and control strategies to prevent in-hospital Enterobacteriaceae dissemination., Author summary Tracing extended-spectrum β-lactamase (ESBL) dissemination in hospitals is an important step in the fight against the spread of multi-drug resistant bacteria. Indeed, understanding ESBL spreading dynamics will help identify efficient control interventions. In the i-Bird study, patients and hospital staff from a French long-term care facility carried a wearable sensor to capture their interactions at less than 1.5 meters, every 30 seconds over a 4-month period. Every week, patients were also swabbed to detect carriage of ESBL-producing Enterobacteriaceae. Based on the analysis of these longitudinal data, this study shows that ESBL-producing Klebsiella pneumoniae (ESBL-KP) mostly spreads during close-proximity interactions between individuals, while this is not the case for ESBL-producing Escherichia coli (ESBL-EC), suggesting that ESBL-KP but not ESBL-EC may be controlled by contact reduction interventions.

Published
2019
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4. Primary osteomyelitis caused by an NDM-1-producing K. pneumoniae strain of the highly virulent sequence type 23

Author

Isabelle Podglajen, Nathalie Genel, Astrid Ramahefasolo, Fabrice Compain, Marie Gominet, Dominique Decré, David Lebeaux, Alexis Vandenberghe, Structures bactériennes impliquées dans la modulation de la résistance aux antibiotiques, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR58-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Université Paris Descartes - Paris 5 (UPD5), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), HAL-UPMC, Gestionnaire, Service de microbiologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR58-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Université Paris Descartes - Paris 5 ( UPD5 ), Centre d'Immunologie et de Maladies Infectieuses ( CIMI ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), and Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Saint-Antoine [APHP]

Subjects
0301 basic medicine, Epidemiology, 030106 microbiology, Immunology, Virulence, Biology, Microbiology, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Drug Discovery, medicine, Letter to the Editor, Sequence (medicine), [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Strain (chemistry), Osteomyelitis, K pneumoniae, General Medicine, medicine.disease, 3. Good health, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious Diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Parasitology
Abstract

International audience; Hypervirulent variant of Klebsiella pneumoniae (hvKP) is characterized by its hypermucoviscosity and its capacity to cause invasive community-acquired infections in previously healthy young individuals. The most common clinical presentation is a pyogenic liver abscess with metastatic spread, while various other invasive infections have been reported. Strains of hvKP belong predominantly to the capsular serotypes K1 and K22 and their genetic background seems to differ from that of multidrug-resistant (MDR) isolates. The most commonly encountered sequence types (STs) among hvKP include ST23 (associated with serotype K1), ST25, ST65, ST86, ST375 and the recently emerging ST380.

Published
2017
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