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Pineros N, Tenaillon K, Marin J, Berry V, Jaureguy F, Ghelfenstein-Ferreira T, Carbonnelle E, Lescat M. Using gamification to improve engagement and learning outcomes in medical microbiology: the case study of "BacteriaGame". FEMS Microbiol Lett 2023; 370:7136151. [PMID: 37086092 DOI: 10.1093/femsle/fnad034] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/22/2023] [Accepted: 04/20/2023] [Indexed: 04/23/2023] Open
Abstract
The fight against antibiotic resistance has become a true global public health challenge of gargantuan proportions. Amongst the myriad of approaches being explored to tackle this predicament, one strategy involves enhancing prescriber knowledge and in particular their basic knowledge of medical bacteriology. Yet, as we well know in medical microbiology teachings, traditional lectures can be arduous, attempting to cram in a vast array of information in a limited time. An alternative solution to improve student engagement and enhance learning outcomes is to utilize educational games in complementary approach. Such games are an effective means of inspiring students to learn, encouraging self-assessment, and injecting diversity into the teaching process. To this end, we have developed and evaluated an educational card game, the 'BacteriaGame,' aimed at our medical students in medical bacteriology. Designed for students at the basic level, it serves as activity at the end of their apprenticeship to their bacteriology education. Additionally, it can also be used as a review tool by more advanced students, with teachers able to impart additional knowledge as the game progresses. We also use it in continuous training of medical laboratory staff. In this study, we evaluated the game at various stages of medical education, collecting feedback and analyzing its impact on knowledge acquisition, comparing it to traditional lectures. Feedback from the majority of students revealed that the rules were clear, the game was enjoyable, and not too lengthy nor too challenging. The integration of 'BacteriaGame' into their future training piqued their interest. In terms of learning outcomes, we discovered a significant increase in knowledge acquisition among those who used the game (p < 0.05). 'BacteriaGame' is now published by the French Society of Microbiology (SFM) and distributed in all medical and pharmacy schools thanks to a funding of the French Health Ministry. An English edition of the game is also available for international use as a physical copy to be purchased from the SFM. This will allow a large-scale distribution to colleagues who would like to use this game in their teaching.
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Affiliation(s)
| | | | - Julie Marin
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Vincent Berry
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
| | - Françoise Jaureguy
- Laboratoire de Microbiologie clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis Assistance publique-Hôpitaux de Paris (AP-HP), Bobigny, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Théo Ghelfenstein-Ferreira
- Laboratoire de Microbiologie clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis Assistance publique-Hôpitaux de Paris (AP-HP), Bobigny, France
| | - Etienne Carbonnelle
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
- Laboratoire de Microbiologie clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis Assistance publique-Hôpitaux de Paris (AP-HP), Bobigny, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Mathilde Lescat
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
- Laboratoire de Microbiologie clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis Assistance publique-Hôpitaux de Paris (AP-HP), Bobigny, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Ghelfenstein-Ferreira T, Beaumont AL, Dellière S, Peiffer-Smadja N, Pineros N, Carbonnelle E, Greub G, Abbara S, Luong Nguyen LB, Lescat M. An Educational Game Evening for Medical Residents: A Proof of Concept to Evaluate the Impact on Learning of the Use of Games. J Microbiol Biol Educ 2021; 22:00119-21. [PMID: 34594443 PMCID: PMC8442010 DOI: 10.1128/jmbe.00119-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Insufficient knowledge of bacteria and antimicrobials leads to the emergence of multidrug-resistant-bacterium infections. Diversification of the teaching forms, such as the use of games, could be a solution. We organized an event around 3 games (Bacteria Game, KROBS, and Dawaa) to collect student feedback on the evening and assess their knowledge before and after the evening using multiple-choice questions. The preliminary results suggest a positive effect of this event, but due to the low number of participants, we see this report more as a proof of concept to assess the impact of games on the learning.
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Affiliation(s)
- Théo Ghelfenstein-Ferreira
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine-Saint-Denis Assistance Publique–Hôpitaux de Paris (AP-HP), Bobigny, France
| | - Anne-Lise Beaumont
- Service de Maladies Infectieuses, Hôpital Saint Louis, AP-HP, Paris, France
| | - Sarah Dellière
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, AP-HP, Paris, France
- Université de Paris, Paris, France
| | - Nathan Peiffer-Smadja
- Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude-Bernard, AP-HP, Paris, France
- Université de Paris, Paris, France
- INSERM, IAME, Paris, France
| | | | - Etienne Carbonnelle
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine-Saint-Denis Assistance Publique–Hôpitaux de Paris (AP-HP), Bobigny, France
- Université de Paris, Paris, France
- INSERM, IAME, Paris, France
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
| | - Gilbert Greub
- Institut de Microbiologie, Département des Laboratoires, Université de Lausanne, CHUV, Lausanne, Switzerland
| | - Salam Abbara
- Institut Pasteur, U1018 Inserm, UVSQ, Paris, France
| | - Liem Binh Luong Nguyen
- Université de Paris, Paris, France
- INSERM, IAME, Paris, France
- Centre d’Investigation Clinique, Hôpital Cochin, AP-HP, Paris, France
| | - Mathilde Lescat
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine-Saint-Denis Assistance Publique–Hôpitaux de Paris (AP-HP), Bobigny, France
- Université de Paris, Paris, France
- INSERM, IAME, Paris, France
- Université Sorbonne Paris Nord, Epinay Villetaneuse, France
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Saliba R, Zahar JR, El Allaoui F, Carbonnelle E, Lescat M. Impact of freeze/thaw cycles and single freezing at -80 °C on the viability of aerobic bacteria from rectal swabs performed with the ESwab TM system. Diagn Microbiol Infect Dis 2019; 96:114895. [PMID: 31864757 DOI: 10.1016/j.diagmicrobio.2019.114895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
The testing of bacterial preservation should be included in preliminary studies to epidemiological studies. In the case of multidrug-resistant organism (MDRO) studies, quantifications of the bacteria make it possible to understand their emergence. The purpose of this preliminary study was to evaluate the performance of ESwabTM on survival of Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis, based on the number of freezing and thawing (F/T) cycles at -80 °C and freezing time. A first experiment with 9 samples showed that multiple F/T cycles drastically affected Enterobacteriaceae viabilities and less E. faecalis one. A single freezing maintained the three species viabilities during three weeks. A second experiment showed that E. coli survival was maintained with a 3-month single freezing. This study which used a limited number of bacterial isolates is however a proof of concept establishing the utility of ESwabTM samples when frozen once in quantitative studies of bacteria.
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Affiliation(s)
- Rindala Saliba
- APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, Bondy, France
| | - Jean Ralph Zahar
- APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, Bondy, France; Université Paris 13, Université Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Fatma El Allaoui
- APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, Bondy, France
| | - Etienne Carbonnelle
- APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, Bondy, France; Université Paris 13, Université Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France
| | - Mathilde Lescat
- APHP, Hôpitaux Universitaires de Paris Seine Saint-Denis, Bondy, France; Université Paris 13, Université Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.
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Ghalayini M, Magnan M, Dion S, Zatout O, Bourguignon L, Tenaillon O, Lescat M. Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon. Mol Ecol 2019; 28:4470-4485. [PMID: 31482587 DOI: 10.1111/mec.15232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/24/2019] [Indexed: 02/02/2023]
Abstract
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin-treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother-to-offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated into two different diets: a regular one (chow diet, CD) and high-fat and high-sugar one (Western Diet, WD). Genome sequences revealed an early and rapid selection during the breastfeeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD; however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
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Affiliation(s)
- Mohamed Ghalayini
- IAME, INSERM, Université Paris 13, Bobigny, France.,Service de Réanimation Médico-Chirurgicale, Hôpital Avicenne, AP - HP, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Melanie Magnan
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Sara Dion
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | | | - Lucie Bourguignon
- IAME, INSERM, Université de Paris, Paris, France.,École de l'Inserm Liliane Bettencourt, Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Mathilde Lescat
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France.,Service de Microbiologie, Hôpital Avicenne, AP - HP, Bobigny, France
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Lescat M, Poirel L, Jayol A, Nordmann P. Performances of the Rapid Polymyxin Acinetobacter and Pseudomonas Tests for Colistin Susceptibility Testing. Microb Drug Resist 2019; 25:520-523. [DOI: 10.1089/mdr.2018.0153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Mathilde Lescat
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA, IAME), Paris France
- Université Paris Nord, Sorbonne Paris Cité, Paris, France
- AP-HP, Hôpitaux Universitaires Paris Seine Saint-Denis, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA, IAME), Paris France
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Aurélie Jayol
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA, IAME), Paris France
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA, IAME), Paris France
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
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Tashk P, Lecronier M, Clermont O, Renvoisé A, Aubry A, Barrou B, Hertig A, Lescat M, Tenaillon O, Denamur E, Tourret J. [Molecular epidemiology and kinetics of early Escherichia coli urinary tract infections in kidney transplant recipients]. Nephrol Ther 2017; 13:236-244. [PMID: 28576434 DOI: 10.1016/j.nephro.2016.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 10/12/2016] [Indexed: 10/19/2022]
Abstract
BACKGROUND Escherichia coli strains causing Urinary Tract Infections (UTI) have a fecal origin. METHODS A fecal sample was collected before Kidney Transplantation (KT) and concomitantly with urine at each of the 15 E. coli UTIs which occurred in 11 KT recipients. Unique E. coli strains were identified among 25 isolates per feces and 5 isolates per urinary sample by random amplification of polymorphic DNA. Phylogenetic group (which is correlated to virulence in the E. coli species) was determined for each E. coli strain by a PCR based method. RESULTS Forty-three unique fecal strains and 14 unique urinary strains were identified among 650 fecal isolates and 75 urinary isolates. Urinary strains frequently (55% of the cases) belonged to a phylogroup usually not linked to virulence. They were detected in the feces collected concomitantly in 60% of the cases. Urinary strains belonging to a phylogroup usually linked to virulence were more frequently dominant in the feces (100%) than urinary strains belonging to a non-pathogenic phylogroup (42%; P<0.05). Vesical catheter was a facilitating factor only for urinary strains belonging to non-pathogenic phylogroups. Thirty-three percent of the fecal strains were persisting in two consecutive fecal samples and 62% were detected for the first time at the UTI. Numerous pathway lead to UTIs: from a unique, virulent and persisting strain to a non-virulent recently acquired strain facilitated by a vesical catheter. CONCLUSION Our work shows the diversity of host-microbial interactions which precede extra-intestinal virulence.
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Affiliation(s)
- Parvine Tashk
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Marie Lecronier
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Olivier Clermont
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Aurélie Renvoisé
- Service de bactériologie et d'hygiène, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France
| | - Alexandra Aubry
- Service de bactériologie et d'hygiène, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France; Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France
| | - Benoît Barrou
- Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Département d'urologie, néphrologie et transplantation, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France
| | - Alexandre Hertig
- Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Urgences néphrologiques et transplantation rénale, hôpital Tenon, AP-HP, 4, rue de la Chine, 75020 Paris, France
| | - Mathilde Lescat
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France; Laboratoire de microbiologie, hôpital Jean-Verdier, AP-HP, avenue, du 14-Juillet, 93140 Bondy, France
| | - Olivier Tenaillon
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Erick Denamur
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Jérôme Tourret
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France; Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Département d'urologie, néphrologie et transplantation, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France.
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Nahon P, Lescat M, Layese R, Bourcier V, Talmat N, Allam S, Marcellin P, Guyader D, Pol S, Larrey D, De Lédinghen V, Ouzan D, Zoulim F, Roulot D, Tran A, Bronowicki JP, Zarski JP, Goria O, Calès P, Péron JM, Alric L, Bourlière M, Mathurin P, Blanc JF, Abergel A, Serfaty L, Mallat A, Grangé JD, Attali P, Bacq Y, Wartelle C, Dao T, Benhamou Y, Pilette C, Silvain C, Christidis C, Capron D, Bernard-Chabert B, Hillaire S, Di Martino V, Trinchet JC, Moreau R, Roudot-Thoraval F. Bacterial infection in compensated viral cirrhosis impairs 5-year survival (ANRS CO12 CirVir prospective cohort). Gut 2017; 66:330-341. [PMID: 26511797 DOI: 10.1136/gutjnl-2015-310275] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/27/2015] [Accepted: 09/29/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To assess incidence and prognostic significance of bacterial infections (BIs) occurring in compensated viral cirrhosis. DESIGN This prospective study involved 35 French centres. Inclusion criteria were biopsy-proven HCV or HBV cirrhosis, Child-Pugh A and no previous hepatic complications. Cumulative incidence (CumI) of events was estimated in a competing risks framework. RESULTS 1672 patients were enrolled (HCV 1323, HBV 318, HCV-HBV 31). During a median follow-up of 43 months, 234 BIs occurred in 171 patients (5 year CumI: 12.9%), among whom 14.6% had septic shock. Main localisations included the urinary tract (27.4%), lung (25.2%) and peritoneum (10.7%) (other, 86 (36.7%)). Most BIs occurred as a first event prior to liver decompensation (n=140, 81.8%) and were community-acquired (CA, 84.2%). The risk of BI was higher in patients with HCV than in patients with HBV (5 year CumI: 15.2% vs 5.5%, p=0.0008). Digestive localisation, concomitant interferon-based treatment, isolation of resistant bacteria and non-CA BIs were associated with lowest probability of resolution. The occurrence of a first BI impaired survival in patients infected with HCV (5 year survival: 60.2% vs 90.4%, p<0.001) and patients infected with HBV (5 year survival: 69.2% vs 97.6%, p<0.001). BIs represented the third cause of death (14.1%) after liver failure and liver cancer. BI risk factors comprised older age, lower albumin, proton pump inhibitor intake and absence of virological eradication/control. CONCLUSION BI mostly occurs as a first complication and represents a turning point in the course of compensated viral cirrhosis. Its occurrence impacts long-term prognosis and may define a subgroup of patients in whom adaptation of management is warranted.
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Affiliation(s)
- Pierre Nahon
- AP-HP, Hôpital Jean Verdier, Service d'Hépatologie, Bondy, Université Paris 13, Bobigny et INSERM U1162, Université Paris 5, Paris, France
| | - Mathilde Lescat
- AP-HP, Hôpital Jean Verdier, Service de Microbiologie, Bondy, Université Paris 13, Bobigny, et INSERM UMR 1139, Paris, France
| | - Richard Layese
- AP-HP, Hôpital Henri Mondor, Département de Santé Publique, Créteil, France
| | - Valérie Bourcier
- AP-HP, Hôpital Jean Verdier, Service d'Hépatologie, Bondy, Université Paris 13, Bobigny et INSERM U1162, Université Paris 5, Paris, France
| | - Nabila Talmat
- AP-HP, Hôpital Jean Verdier, Service d'Hépatologie, Bondy, Université Paris 13, Bobigny et INSERM U1162, Université Paris 5, Paris, France
| | - Setty Allam
- Unit for Basic and Clinical research on Viral Hepatitis, ANRS (France REcherche Nord & sud Sida-HIV Hépatites-FRENSH), Paris, France
| | | | | | - Stanislas Pol
- AP-HP, Hôpital Cochin, Département d'Hépatologie et INSERM UMS20, Institut Pasteur, Université Paris Descartes, Paris, France
| | | | | | - Denis Ouzan
- Institut Arnaud Tzanck, Service d'Hépatologie, St Laurent du Var, France
| | - Fabien Zoulim
- Hôpital Hôtel Dieu, Service d'Hépatologie, Lyon, France
| | | | - Albert Tran
- CHU de Nice, Service d'Hépatologie, et INSERM U1065, Université de Nice-Sophia-Antipolis, Nice, France
| | | | | | - Odile Goria
- Hôpital Charles-Nicolle, Service d'Hépatologie, Rouen, France
| | - Paul Calès
- CHU d'Angers, Service d'Hépatologie, Angers, France
| | | | - Laurent Alric
- CHU Toulouse, Service de Médecine Interne-Pôle Digestif UMR 152, Toulouse, France
| | - Marc Bourlière
- Hôpital Saint Joseph, Service d'Hépatologie, Marseille, France
| | | | | | - Armand Abergel
- Hôpital Hôtel Dieu, Service d'Hépatologie, Clermont-Ferrand, France
| | - Lawrence Serfaty
- AP-HP, Hôpital Saint-Antoine, Service d'Hépatologie, Paris, France
| | - Ariane Mallat
- AP-HP, Hôpital Henri Mondor, Service d'Hépatologie, Créteil, France
| | | | - Pierre Attali
- AP-HP, Hôpital Paul Brousse, Service d'Hépatologie, Villejuif, France
| | - Yannick Bacq
- Hôpital Trousseau, Unité d'Hépatologie, CHRU de Tours, Tours, France
| | - Claire Wartelle
- Hôpital d'Aix-En-Provence, Service d'Hépatologie, Aix-En-Provence, France
| | - Thông Dao
- Hôpital de la Côte de Nacre, Service d'Hépatologie, Caen, France
| | - Yves Benhamou
- AP-HP, Groupe Hospitalier de La Pitié-Salpêtrière, Service d'Hépatologie, Paris, France
| | | | | | | | | | | | | | | | - Jean-Claude Trinchet
- AP-HP, Hôpital Jean Verdier, Service d'Hépatologie, Bondy, Université Paris 13, Bobigny et INSERM U1162, Université Paris 5, Paris, France
| | - Richard Moreau
- AP-HP, Hôpital Beaujon, Service d'Hépatologie, Clichy, France
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Lescat M, Launay A, Ghalayini M, Magnan M, Glodt J, Pintard C, Dion S, Denamur E, Tenaillon O. Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut. Mol Ecol 2016; 26:1802-1817. [PMID: 27661780 DOI: 10.1111/mec.13851] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023]
Abstract
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
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Affiliation(s)
- Mathilde Lescat
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Paris, France
| | - Adrien Launay
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mohamed Ghalayini
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Nord, Sorbonne Paris Cité, Paris, France
| | - Mélanie Magnan
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Coralie Pintard
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,APHP, Hôpitaux Universitaires Paris Nord Val de Seine, Paris, France
| | - Olivier Tenaillon
- INSERM, IAME, UMR 1137, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateau C, Launay A, Ledda A, Cruvellier S, Tourret J, Tenaillon O. The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence. PLoS One 2014; 9:e108738. [PMID: 25268639 PMCID: PMC4182557 DOI: 10.1371/journal.pone.0108738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 01/03/2014] [Accepted: 09/04/2014] [Indexed: 02/03/2023] Open
Abstract
The Escherichia coli species is divided in phylogenetic groups that differ in their virulence and commensal distribution. Strains belonging to the B2 group are involved in extra-intestinal pathologies but also appear to be more prevalent as commensals among human occidental populations. To investigate the genetic specificities of B2 sub-group, we used 128 sequenced genomes and identified genes of the core genome that showed marked difference between B2 and non-B2 genomes. We focused on the gene and its surrounding region with the strongest divergence between B2 and non-B2, the antiporter gene nhaA. This gene is part of the nhaAR operon, which is in the core genome but flanked by mobile regions, and is involved in growth at high pH and high sodium concentrations. Consistently, we found that a panel of non-B2 strains grew faster than B2 at high pH and high sodium concentrations. However, we could not identify differences in expression of the nhaAR operon using fluorescence reporter plasmids. Furthermore, the operon deletion had no differential impact between B2 and non-B2 strains, and did not result in a fitness modification in a murine model of gut colonization. Nevertheless, sequence analysis and experiments in a murine model of septicemia revealed that recombination in nhaA among B2 strains was observed in strains with low virulence. Finally, nhaA and nhaAR operon deletions drastically decreased virulence in one B2 strain. This effect of nhaAR deletion appeared to be stronger than deletion of all pathogenicity islands. Thus, a population genetic approach allowed us to identify an operon in the core genome without strong effect in commensalism but with an important role in extra-intestinal virulence, a landmark of the B2 strains.
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Affiliation(s)
- Mathilde Lescat
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- Laboratoire de Microbiologie, Hôpital Jean Verdier, Assistance Publique-Hôpitaux de Paris, Bondy, France et Université Paris Nord, Sorbonne Paris Cité, Paris, France
- * E-mail:
| | - Florence Reibel
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Coralie Pintard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Sara Dion
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jérémy Glodt
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cecile Gateau
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Adrien Launay
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Alice Ledda
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
| | - Stephane Cruvellier
- Laboratoire de Génomique Comparative, Centre national de la Recherche Scientifique (CNRS) UMR 8030, Institut de Génomique, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope, Evry, France
| | - Jérôme Tourret
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
- Département d'Urologie, Néphrologie et Transplantation, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris et Université Pierre et Marie Curie, Paris, France
| | - Olivier Tenaillon
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1137, Paris, France
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Lescat M, Clermont O, Woerther PL, Glodt J, Dion S, Skurnik D, Djossou F, Dupont C, Perroz G, Picard B, Catzeflis F, Andremont A, Denamur E. Commensal Escherichia coli strains in Guiana reveal a high genetic diversity with host-dependant population structure. Environ Microbiol Rep 2013; 5:49-57. [PMID: 23757130 DOI: 10.1111/j.1758-2229.2012.00374.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/21/2012] [Indexed: 05/02/2023]
Abstract
We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an isolated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated and 198 wild animals were collected in the close proximity of the village. The prevalence of E. coli was decreasing from humans (100%) to human associated (64%) and wild (45%) animals. A clear genetic structure between these three E. coli populations was observed with human strains belonging very rarely to B2 phylogroup (3.7%), exhibiting few virulence genes and bacteriocins but being antibiotic resistant whereas wild animal strains were characterized by 46.1% of B2 phylogroup belonging, with very unique and infrequent sequence types, numerous extraintestinal genes and bacteriocins but no antibiotic resistance; the human-associated animal strains being intermediate. Furthermore, an unexpected genetic diversity was observed among the strains, as the housekeeping gene nucleotide diversity per site of the Trois-Sauts's strains was higher than the one of reference strains representative of the known species diversity. The existence of such E. coli structured phylogenetic diversity within various hosts of a single localization has never been reported.
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Matta M, Kernéis S, Day N, Lescat M, Hoi AB, Varon E, Gutmann L, Mainardi JL. Do clinicians consider the results of the BinaxNOW Streptococcus pneumoniae urinary antigen test when adapting antibiotic regimens for pneumonia patients? Clin Microbiol Infect 2011; 16:1389-93. [PMID: 19845695 DOI: 10.1111/j.1469-0691.2009.03088.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The BinaxNOW Streptococcus pneumoniae urinary antigen test is a rapid and reliable immunochromatographic test (ICT) for the identification of a pneumococcal aetiology of pneumonia. The aim of this study was to evaluate the attitude of clinicians in their everyday practice towards prescription of the ICT and the impact of its results on the adaptation of the antibiotic therapy when pneumonia is suspected. From October 2007 to March 2008, we prospectively evaluated 541 consecutive inpatients for whom the ICT was performed in our institution. Of the 541 patients evaluated, only 233 (43%) were suspected by the treating physicians to have a pneumonia, 58 of whom had a positive ICT result. Among these 58 patients, four (7%) and 26 (45%), respectively, were treated with amoxycillin monotherapy before and after the ICT result had been obtained (p <10(-4)). Although a positive ICT result led to a rise in the proportion of patients treated with amoxycillin alone, a large number continued to be treated with broader-spectrum antibiotics. These results suggest that prescription monitoring of the ICT should be implemented along with encouragement to adhere more strictly to treatment guidelines.
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Affiliation(s)
- M Matta
- AP-HP, Hôpital Européen Georges Pompidou, Service de Microbiologie, Université Paris Descartes et UPMC, Paris, France
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Ruimy R, Angebault C, Djossou F, Dupont C, Epelboin L, Jarraud S, Lefevre LA, Bes M, Lixandru BE, Bertine M, El Miniai A, Renard M, Bettinger RM, Lescat M, Clermont O, Peroz G, Lina G, Tavakol M, Vandenesch F, van Belkum A, Rousset F, Andremont A. Are host genetics the predominant determinant of persistent nasal Staphylococcus aureus carriage in humans? J Infect Dis 2010; 202:924-34. [PMID: 20677941 DOI: 10.1086/655901] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Staphylococcus aureus nasal carriage is influenced by multifactorial interactions which are difficult to study in open populations. Therefore, we concomitantly assessed the epidemiological, microbiological, and human-genetic carriage-related factors in a nearly closed population. METHODS In 2006 and 2008, we collected nasal S. aureus strains, human DNA, and epidemiological data from 154 adult Wayampi Amerindians living in an isolated village in the Amazonian forest. The genetics of the strains (multilocus sequence type, spa type, and toxin-content type), epidemiological risk factors, antibiotic exposure, and allelic polymorphism of human genes putatively involved in carriage of the persistent carriers were compared with those of other volunteers. RESULTS Overall carriage prevalence was 41.7% in 2006 and 57.8% in 2008, but the overall prevalence of persistent carriage was only 26%. The rare and phylogenetically distant multilocus sequence type ST1223 was present in 18.5% of the carriers in 2006 and 34.8% in 2008. No epidemiological factors or antibiotic exposure were significantly associated with persistent carriage, but single nucleotide polymorphism distribution in C-reactive proteins C2042T and C1184T and interleukin-4 C524T genes was significantly associated (P=.02, by global test). CONCLUSION Host genetic factors appeared to be the predominant determinant for S. aureus persistent nasal carriage in humans.
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Affiliation(s)
- Raymond Ruimy
- EA3964 Université Paris-Diderot and Centre National de Référence, Résistance bactérienne dans les flores commensales, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
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13
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Matta M, Kernéis S, Day N, Lescat M, Buu Hoi A, Varon E, Gutmann L, Mainardi JL. Do clinicians consider the results of the BinaxNOW Streptococcus pneumoniae urinary antigen test when adapting antibiotic regimens for pneumonia patients? Clin Microbiol Infect 2010. [DOI: 10.1111/j.1469-0691.2010.03088.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Woerther P, Angebault C, Lescat M, Ruppé E, Skurnik D, Mniai A, Clermont O, Jacquier H, Costa A, Renard M, Bettinger R, Epelboin L, Dupont C, Guillemot D, Rousset F, Arlet G, Denamur E, Djossou F, Andremont A. Emergence and Dissemination of Extended‐Spectrum β‐Lactamase–ProducingEscherichia coliin the Community: Lessons from the Study of a Remote and Controlled Population. J Infect Dis 2010; 202:515-23. [DOI: 10.1086/654883] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Lescat M, Hoede C, Clermont O, Garry L, Darlu P, Tuffery P, Denamur E, Picard B. aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species. BMC Microbiol 2009; 9:273. [PMID: 20040078 PMCID: PMC2805673 DOI: 10.1186/1471-2180-9-273] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 01/27/2009] [Accepted: 12/29/2009] [Indexed: 11/30/2022] Open
Abstract
Background Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2 variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1 variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene. Results We identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis of aes nucleotide sequences in a panel of 78 reference strains, including the E. coli reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from aes sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1 and B2 by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between aes and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of aes to be associated with virulence. Conclusion Our findings suggest that aes does not play a direct role in the virulence of E. coli extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.
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Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EPC, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5:e1000344. [PMID: 19165319 PMCID: PMC2617782 DOI: 10.1371/journal.pgen.1000344] [Citation(s) in RCA: 775] [Impact Index Per Article: 51.7] [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: 09/02/2008] [Accepted: 12/16/2008] [Indexed: 01/01/2023] Open
Abstract
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
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Affiliation(s)
- Marie Touchon
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
| | - Claire Hoede
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Olivier Tenaillon
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - Simon Baeriswyl
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Philippe Bidet
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Edouard Bingen
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Stéphane Bonacorsi
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | | | - Odile Bouvet
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Alexandra Calteau
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Hélène Chiapello
- UR1077 Mathématique, Informatique, et Génome, INRA, Jouy en Josas, France
| | - Olivier Clermont
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Stéphane Cruveiller
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - Médéric Diard
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Meriem El Karoui
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Eric Frapy
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Louis Garry
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Jean Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, CNRS URA2172, Paris, France
| | - Anne Marie Gilles
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - James Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Mathilde Lescat
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | | | - Ivan Matic
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Xavier Nassif
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Sophie Oztas
- Génoscope, Institut de Génomique, CEA, Evry, France
| | - Marie Agnès Petit
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Christophe Pichon
- Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France
| | - Zoé Rouy
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claude Saint Ruf
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Jérôme Tourret
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - David Vallenet
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claudine Médigue
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
- * E-mail: (CM); (EPCR); (ED)
| | - Eduardo P. C. Rocha
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
- * E-mail: (CM); (EPCR); (ED)
| | - Erick Denamur
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
- * E-mail: (CM); (EPCR); (ED)
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Lescat M, Dupeyron C, Faubert E, Mangeney N. Pulse-field gel electrophoresis typing of methicillin-resistant Staphylococcus aureus strains susceptible to aminoglycosides isolated from 1993 to 2002. J Hosp Infect 2004; 57:253-7. [PMID: 15236856 DOI: 10.1016/j.jhin.2004.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 10/14/2003] [Accepted: 02/20/2004] [Indexed: 11/25/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) susceptible strains to aminoglycosides (AS-MRSA) have been increasingly isolated in the Albert Cheneiver Hospital during the past 10 years. The aim of this study was first, to analyse the genotypes and the profiles of resistance to antibiotics and second to compare the AS-MRSA with the MRSA resistant to gentamicin (GR-MRSA) and with MRSA resistant to kanamycin and tobramycin, but susceptible to gentamicin (GS-MRSA), previously studied in our laboratory. All the AS-MRSA consecutively isolated from clinical samples (carriage isolates excluded) from 01/01/1993 to 31/12/2002 (33 isolates) were typed by DNA macrorestriction. Their susceptibilities to other anti-staphylococcal drugs (erythromycin, lincomycin, tetracycline, rifampicin, fusidic acid and fosfomycin) were studied by the French standard disk method. The 33 strains showed a heterogeneous resistance to oxacillin and fell into five phenotypes. The main phenotype (51.5% of the AS-MRSA strains) was susceptible to the six antibiotics studied. DNA macrorestriction defined 24 genotypes (percentage similarity <80%). Among them 16 genotypes contained only one strain each, and none contained more than three isolates. Conversely the comparison with GR-MRSA and GS-MRSA isolated during the same period showed that the strains were not closely linked. The diversity of our isolates showed that it was not an epidemic phenomenon, in contrast to the results of similar studies. Our findings may be explained by the patients coming mostly from different hospital units. This work indicates the need for further studies on the genome, to determine whether AS-MRSA have derived from strains that occurred before aminoglycosides came into clinical use.
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Affiliation(s)
- M Lescat
- Laboratoire de Microbiologie, Hôpital Albert Chenevier, 40 rue de Mesly, 94000 Creteil, France
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