Edouard Bingen

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

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 genomes 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.

Rapid-antigen detection tests for group a streptococcal pharyngitis: revisiting false-positive results using polymerase chain reaction testing.

We investigated mechanisms of the false-positive test results on rapid-antigen detection test (RADT) for group A Streptococcal (GAS) pharyngitis. Most RADT false-positives (76%) were associated with polymerase chain reaction-positive GAS results, suggesting that RADT specificity could be considered close to 100%. Finding that 61% of GAS culture-negative but RADT-positive cases were positive on both GAS polymerase chain reaction and Staphylococcus aureus testing, we posit bacterial inhibition as causative.

Infections néonatales tardives à entérobactéries multirésistantes

Resume Objectif: Determiner l’incidence des infections ou colonisations secondaires a enterobacteries multiresistantes chez les nouveau-nes hospitalises dans un service de reanimation et pediatrie neonatales. Methodes: Etude prospective entre le 1 er Janvier 2000 et le 31 decembre 2009 dans le service de Reanimation et Pediatrie Neonatales de l’Hopital Robert Debre avec recherche de beta-lactamase a spectre etendu (BLSE) dans l’ecouvillonnage rectal a l’admission puis tous les 10 jours et releve prospectif informatise de toutes les infections systemiques en collaboration avec le service de Microbiologie. Resultats et discussion: Entre 2000 et 2009, 46 nouveau-nes ont ete colonises a Enterobacteries BLSE (EBLSE) (58,7 % E coli , 10,8 % Enterobacter cloacae , 19,5 % Klebsiella pneumoniae , 6,5 % K. oxytoca , 4,5 % Citrobacter ), soit une incidence de 5,11 cas/ 1000 admissions. Trois ont developpe une infection a E.coli (sepsis, pneumopathie) et a E.cloacae (omphalite). Les enterobacteries multiresistantes (EBMR) sont representees principalement par Escherichia coli , Klebsiella pneumoniae et Enterobacter spp. Elles ont une responsabilite croissante dans les infections nosocomiales en periode neonatale. La presence de cas epidemiques d’infections nosocomiales a EBMR represente un des indicateurs les plus sensibles du controle des mesures de prevention contre les infections nosocomiales en neonatologie. En cas d’infections systemiques dues a ces germes, leur profil de resistance aux cephalosporines de 3 e generation impose l’utilisation d’antibiotiques specifiques, les carbapenemes dont l’experience chez le nouveau-ne est encore limitee mais qui semblent bien tolerees.

Effect of Partial Ureteral Obstruction and Bacterial Virulence on the Occurrence of Renal Scarring in a Mouse Model

OBJECTIVE To evaluate the effect of the infection and the obstruction of urinary tract on renal parenchyma, we developed a model of ascending urinary infection in mice with partial unilateral obstructive uropathy. METHODS Six week-old CBA/J mice were operated on to perform a right partial ureteral obstruction and challenged transurethrally with Escherichia coli CFT073 (high virulent strain) or E. coli Mez (low virulent strain). Level of infection of urine and kidneys, score of inflammation and fibrosis of kidneys, and kidney weight ratio (KWR) in the short and long term were studied. RESULTS At short-term (72 hours) experimentation, partial ureteral obstruction does not influence the level of kidney infection in terms of bacterial count, and the score of inflammation regardless of whether a virulent or low virulent strain was used. At long-term (42 days) experimentation, E. coli Mez was eliminated from all mice kidneys, but CFT073 persisted in almost all; obstruction did not influence the level of kidney infection with CFT073 but a significant difference of KWR and the inflammation and fibrosis score between obstructed and unobstructed kidneys was found (P = .0078; P = .036, respectively). Although the E. coli Mez strain did not persist in renal parenchyma, severe damage of the renal parenchyma was observed. CONCLUSION The proposed model is similar to the obstructive uropathy in children in which ureteral obstruction is present before the onset of infection. The association of obstruction and urinary infection impairs kidney growth and favors the occurrence of renal damage.

Mécanismes d’acquisition des infections nosocomiales en pédiatrie

Si les mecanismes d’acquisition des infections nosocomiales sont identiques a ceux decrits dans la population adulte, certaines particularites de la population pediatrique doivent etre connues et prises en compte dans la prevention de l’acquisition de ces infections : les pathogenes specifiques, absents ou tres minoritaires chez l’adulte ; la dependance du petit enfant pour tout ce qui concerne les tâches de la vie quotidienne, l’affect et le developpement intellectuel, source de contact rapproche avec de multiples intervenants, augmentant le risque de transmission de nombreux micro-organismes ; et les difficultes de maintenir des mesures d’isolement chez ces petits patients.

Apports des marqueurs moléculaires dans l’analyse des mécanismes d’acquisition et dans le suivi des infections nosocomiales

L’investigation des cas d’infections nosocomiales s’apparente a une enquete policiere, visant a retracer la diffusion d’une souche bacterienne epidemique au sein de l’environnement hospitalier. Le laboratoire joue un role important dans ces enquetes epidemiologiques grâce a l’analyse comparative des souches bacteriennes par differentes methodes de typage. Du fait des nombreux inconvenients des marqueurs phenotypiques (biotypie, antibiotypie, serotypage), des methodes de typage moleculaire, analysant l’ADN lui-meme, sont preferentiellement utilisees. Ces methodes de typage permettent de demontrer la transmission d’une meme souche de patients a patients, de distinguer les recidives des reinfections, d’identifier les voies de contaminations et de suivre la diffusion de clones au sein d’une population.