Prediction of the intestinal resistome by a three-dimensional structure-based method

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens

Apport de l'imagerie par résonance magnétique et de la ponction neurochirurgicale dans le diagnostic et la prise en charge des abcès cérébraux de l'adulte

Le diagnostic positif d abcès cérébral est souvent difficile et le traitement antibiotique reste le plus souvent empirique, expliquant en partie une morbimortalité élevée. L épidémiologie est marquée par l augmentation du nombre de patients immunodéprimés et la diminution des abcès secondaires à des infections ORL ou dentaires. L'obtention d'un diagnostic microbiologique rapide est donc primordial. Les nouvelles stratégies diagnostiques et thérapeutiques récemment développées: les séquences de diffusion en IRM, permettant de différencier abcès et tumeur, et la ponction neurochirurgicale à visée diagnostique pourraient permettre d'atteindre cet objectif. Nous avons évalué ces nouvelles stratégies de prise en charge dans une cohorte rétrospective de 21 patients. L IRM de diffusion a permis d affirmer le diagnostic d abcès chez 11/11 malades et leur prise en charge plus rapide. La ponction a permis le diagnostic microbiologique dans 19/19 cas, même chez les 5 malades déjà sous antibiotiques. Plus de 50% des malades, dont tous les immunodéprimés et la moitié des malades ayant une infection dentaire, étaient infectés avec des germes autres que ceux ciblés par l antibiothérapie empirique. Aucun sous-groupe de patients ne semble donc pouvoir être traité empiriquement au risque d échecs. Devant les changements épidémiologiques récents, un diagnostic positif rapide et le diagnostic microbiologique sont indispensables à la prise en charge des abcès cérébraux à pyogènes. La réalisation d une IRM de diffusion suivie d une ponction diagnostique systématique est une stratégie fiable et rentable pour obtenir un diagnostic bactériologique avant toute antibiothérapie.PARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Impact des fluoroquinolones sur l'emergence de la résistance bactérienne chez Escherichia coli dans le microbiote intestinal

PARIS-BIUP (751062107) / SudocSudocFranceF

Independent Behavior of Commensal Flora for Carriage of Fluoroquinolone-Resistant Bacteria in Patients at Admission▿

The important role of commensal flora as a natural reservoir of bacterial resistance is now well established. However, whether the behavior of each commensal flora is similar to that of other floras in terms of rates of carriage and risk factors for bacterial resistance is unknown. During a 6-month period, we prospectively investigated colonization with fluoroquinolone-resistant bacteria in the three main commensal floras from hospitalized patients at admission, targeting Escherichia coli in the fecal flora, coagulase-negative Staphylococcus (CNS) in the nasal flora, and α-hemolytic streptococci in the pharyngeal flora. Resistant strains were detected on quinolone-containing selective agar. Clinical and epidemiological data were collected. A total of 555 patients were included. Carriage rates of resistance were 8.0% in E. coli, 30.3% in CNS for ciprofloxacin, and 27.2% in streptococci for levofloxacin; 56% of the patients carried resistance in at least one flora but only 0.9% simultaneously in all floras, which is no more than random. Risk factors associated with the carriage of fluoroquinolone-resistant strains differed between fecal E. coli (i.e., colonization by multidrug-resistant bacteria) and nasal CNS (i.e., age, coming from a health care facility, and previous antibiotic treatment with a fluoroquinolone) while no risk factors were identified for pharyngeal streptococci. Despite high rates of colonization with fluoroquinolone-resistant bacteria, each commensal flora behaved independently since simultaneous carriage of resistance in the three distinct floras was uncommon, and risk factors differed. Consequences of environmental selective pressures vary in each commensal flora according to its local specificities (clinical trial NCT00520715 [http://clinicaltrials.gov/ct2/show/NCT00520715])

Clinical and microbiological characteristics of reflux cholangitis following bilio-enteric anastomosis

International audienceTwenty-five patients with reflux cholangitis (RC) defined as acute cholangitis (AC) with normal abdominal imaging occurring > 3 months after bilioenteric anastomosis were described and compared to 116 AC patients with biliary obstruction (tumoral, lithiasis). RC episodes occurred a median 4.5 months after surgery; 18 (72%) had recurrent RC (n >= 3). RC episodes were less severe than obstructive AC; the outcome was favorable with short antibiotic courses and no selection of antibiotic-resistance. However, multiple recurrent RC occurred in 20 patients (80%). Prophylactic or pre-emptive antibiotics were successful in 3 and 11 patients. Revision surgery for jejunal loop lengthening was successful in 2/4 patients

Ceftriaxone promotes the emergence of AmpC-overproducing Enterobacteriaceae in gut microbiota from hospitalized patients

International audienc