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1.  Multicenter Outbreak of Infections by Saprochaete clavata, an Unrecognized Opportunistic Fungal Pathogen 
Vaux, Sophie | Criscuolo, Alexis | Desnos-Ollivier, Marie | Diancourt, Laure | Tarnaud, Chloé | Vandenbogaert, Matthias | Brisse, Sylvain | Coignard, Bruno | Dromer, Françoise | Garcia-Hermoso, Dea | Blanc, Catherine | Hoinard, Damien | Lortholary, Olivier | Bretagne, Stéphane | Thiolet, Jean-Michel | de Valk, Henriette | Courbil, Rémi | Chabanel, Anne | Simonet, Marion | Maire, Francoise | Jbilou, Saadia | Tiberghien, Pierre | Blanchard, Hervé | Venier, Anne-Gaëlle | Bernet, Claude | Simon, Loïc | Sénéchal, Hélène | Pouchol, Elodie | Angot, Christiane | Ribaud, Patricia | Socié, G. | Flèche, M. | Brieu, Nathalie | Lagier, Evelyne | Chartier, Vanessa | Allegre, Thierry | Maulin, Laurence | Lanic, Hélène | Tilly, Hervé | Bouchara, Jean-Philippe | Pihet, Marc | Schmidt, Aline | Kouatchet, Achille | Vandamme, Yves-Marie | Ifrah, Norbert | Mercat, Alain | Accoceberry, Isabelle | Albert, Olivier | Leguay, Thibaut | Rogues, Anne-Marie | Bonhomme, Julie | Reman, Oumédaly | Lesteven, Claire | Poirier, Philippe | Chabrot, Cécile Molucon | Calvet, Laure | Baud, Olivier | Cambon, Monique | Farkas, Jean Chistophe | Lafon, Bruno | Dalle, Frédéric | Caillot, Denis | Lazzarotti, Aline | Aho, Serge | Combret, Sandrine | Facon, Thierry | Sendid, Boualem | Loridant, Séverine | Louis, Terriou | Cazin, Bruno | Grandbastien, Bruno | Bourgeois, Nathalie | Lotthé, Anne | Cartron, Guillaume | Ravel, Christophe | Colson, Pascal | Gaudard, Philippe | Bonmati, Caroline | Simon, Loic | Rabaud, Christian | Machouart, Marie | Poisson, Didier | Carp, Diana | Meunier, Jérôme | Gaschet, Anne | Miquel, Chantal | Sanhes, Laurence | Ferreyra, Milagros | Leibinger, Franck | Geudet, Philippe | Toubas, Dominique | Himberlin, Chantal | Bureau-Chalot, Florence | Delmer, Alain | Favennec, Loïc | Gargala, Gilles | Michot, Jean-Baptiste | Girault, Christophe | David, Marion | Leprêtre, Stéphane | Jardin, Fabrice | Honderlick, Pierre | Caille, Vincent | Cerf, Charles | Cassaing, Sophie | Recher, Christian | Picard, Muriel | Protin, Caroline | Huguet, Françoise | Huynh, Anne | Ruiz, Jean | Riu-Poulenc, Béatrice | Letocart, Philippe | Marchou, Bruno | Verdeil, Xavier | Cavalié, Laurent | Chauvin, Pamela | Iriart, Xavier | Valentin, Alexis | Bouvet, Emmanuelle | Delmas-Marsalet, Béatrice | Jeblaoui, Asma | Kassis-Chikhani, Najiby | Mühlethaler, Konrad | Zimmerli, Stefan | Zalar, Polona | Sánchez-Reus, Ferran | Gurgui, Merce
mBio  2014;5(6):e02309-14.
Rapidly fatal cases of invasive fungal infections due to a fungus later identified as Saprochaete clavata were reported in France in May 2012. The objectives of this study were to determine the clonal relatedness of the isolates and to investigate possible sources of contamination. A nationwide alert was launched to collect cases. Molecular identification methods, whole-genome sequencing (WGS), and clone-specific genotyping were used to analyze recent and historical isolates, and a case-case study was performed. Isolates from thirty cases (26 fungemias, 22 associated deaths at day 30) were collected between September 2011 and October 2012. Eighteen cases occurred within 8 weeks (outbreak) in 10 health care facilities, suggesting a common source of contamination, with potential secondary cases. Phylogenetic analysis identified one clade (clade A), which accounted for 16/18 outbreak cases. Results of microbiological investigations of environmental, drug, or food sources were negative. Analysis of exposures pointed to a medical device used for storage and infusion of blood products, but no fungal contamination was detected in the unused devices. Molecular identification of isolates from previous studies demonstrated that S. clavata can be found in dairy products and has already been involved in monocentric outbreaks in hematology wards. The possibility that S. clavata may transmit through contaminated medical devices or can be associated with dairy products as seen in previous European outbreaks is highly relevant for the management of future outbreaks due to this newly recognized pathogen. This report also underlines further the potential of WGS for investigation of outbreaks due to uncommon fungal pathogens.
Several cases of rapidly fatal infections due to the fungus Saprochaete clavata were reported in France within a short period of time in three health care facilities, suggesting a common source of contamination. A nationwide alert collected 30 cases over 1 year, including an outbreak of 18 cases over 8 weeks. Whole-genome sequencing (WGS) was used to analyze recent and historical isolates and to design a clade-specific genotyping method that uncovered a clone associated with the outbreak, thus allowing a case-case study to analyze the risk factors associated with infection by the clone. The possibility that S. clavata may transmit through contaminated medical devices or can be associated with dairy products as seen in previous European outbreaks is highly relevant for the management of future outbreaks due to this newly recognized pathogen.
PMCID: PMC4271555  PMID: 25516620
2.  Evolving epidemiology and antimicrobial resistance in spontaneous bacterial peritonitis: a two-year observational study 
BMC Infectious Diseases  2014;14:287.
Current recommendations for empirical antimicrobial therapy in spontaneous bacterial peritonitis (SBP) are based on quite old trials. Since microbial epidemiology and the management of patients have changed, whether these recommendations are still appropriate must be confirmed.
An observational study that exhaustively collected the clinical and biological data associated with positive ascitic fluid cultures was conducted in four French university hospitals in 2010–2011.
Two hundred and sixty-eight documented positive cultures were observed in 190 cirrhotic patients (median age 61.5 years, 58.5% Child score C). Of these, 57 were classified as confirmed SBP and 140 as confirmed bacterascites. The predominant flora was Gram-positive cocci, whatever the situation (SBP, bacterascites, nosocomial/health-care related or not). Enteroccocci (27.7% E. faecium) were isolated in 24% of the episodes, and in 48% from patients receiving quinolone prophylaxis. E. coli were susceptible to amoxicillin-clavulanate and to third-generation cephalosporins in 62.5% and 89.5% of cases, respectively. No single antibiotic allowed antimicrobial coverage of more than 60%. Only combinations such as amoxicillin + third-generation cephalosporin or cotrimoxazole allowed coverage close to 75-80% in non-nosocomial episodes. Combinations based on broader spectrum antibiotics should be considered for empirical therapy of nosocomial infections.
Our study confirmed the changing spectrum of pathogens in SBP and bacterascites, and the need for more complex antibiotic strategies than those previously recommended. Our findings also underline the need for new clinical trials conducted in the current epidemiological context.
PMCID: PMC4055793  PMID: 24884471
Bacterascites; Spontaneous bacterial peritonitis; Epidemiology; Antibiotic susceptibility; Resistance
3.  Characterization of a New blaOXA-48-Carrying Plasmid in Enterobacteriaceae 
In this work, we characterized a new, 160-kb, blaOXA-48-harboring IncL/M-type plasmid isolated from a Klebsiella pneumoniae strain from France. Moreover, we report the transfer of a 60-kb OXA-48-encoding plasmid from Klebsiella pneumoniae to other Enterobacteriaceae in two patients.
PMCID: PMC3719702  PMID: 23733457
4.  Is Universal HBV Vaccination of Healthcare Workers a Relevant Strategy in Developing Endemic Countries? The Case of a University Hospital in Niger 
PLoS ONE  2012;7(9):e44442.
Exposure to hepatitis B virus (HBV) remains a serious risk to healthcare workers (HCWs) in endemic developing countries owing to the strong prevalence of HBV in the general and hospital populations, and to the high rate of occupational blood exposure. Routine HBV vaccination programs targeted to high-risk groups and especially to HCWs are generally considered as a key element of prevention strategies. However, the high rate of natural immunization among adults in such countries where most infections occur perinatally or during early childhood must be taken into account.
Methodology/Principal Findings
We conducted a cross sectional study in 207 personnel of 4 occupational groups (medical, paramedical, cleaning staff, and administrative) in Niamey’s National Hospital, Niger, in order to assess the prevalence of HBV markers, to evaluate susceptibility to HBV infection, and to identify personnel who might benefit from vaccination. The proportion of those who declared a history of occupational blood exposure ranged from 18.9% in the administrative staff to 46.9% in paramedical staff. Only 7.2% had a history of vaccination against HBV with at least 3 injections. Ninety two percent were anti-HBc positive. When we focused on170 HCWs, only 12 (7.1%) showed no biological HBV contact. Twenty six were HBsAg positive (15,3%; 95% confidence interval: 9.9%–20.7%) of whom 8 (32%) had a viral load >2000 IU/ml.
The very small proportion of HCWs susceptible to HBV infection in our study and other studies suggests that in a global approach to prevent occupational infection by bloodborne pathogens, a universal hepatitis B vaccination of HCWs is not priority in these settings. The greatest impact on the risk will most likely be achieved by focusing efforts on primary prevention strategies to reduce occupational blood exposure. HBV screening in HCWs and treatment of those with chronic HBV infection should be however considered.
PMCID: PMC3436880  PMID: 22970218
6.  Gluconobacter as Well as Asaia Species, Newly Emerging Opportunistic Human Pathogens among Acetic Acid Bacteria ▿ †  
Journal of Clinical Microbiology  2010;48(11):3935-3942.
Acetic acid bacteria (AAB) are broadly used in industrial food processing. Among them, members of the genera Asaia, Acetobacter, and Granulibacter were recently reported to be human opportunistic pathogens. We isolated AAB from clinical samples from three patients and describe here the clinical and bacteriological features of these cases. We report for the first time (i) the isolation of a Gluconobacter sp. from human clinical samples; (ii) the successive isolation of different AAB, i.e., an Asaia sp. and two unrelated Gluconobacter spp., from a cystic fibrosis patient; and (iii) persistent colonization of the respiratory tract by a Gluconobacter sp. in this patient. We reviewed the main clinical features associated with AAB isolation identified in the 10 documented reports currently available in the literature. Albeit rare, infections as well as colonization with AAB are increasingly reported in patients with underlying chronic diseases and/or indwelling devices. Clinicians as well as medical microbiologists should be aware of these unusual opportunistic pathogens, which are difficult to detect during standard medical microbiological investigations and which are multiresistant to antimicrobial agents. Molecular methods are required for identification of genera of AAB, but the results may remain inconclusive for identification to the species level.
PMCID: PMC3020812  PMID: 20826638
7.  Probiotics and Intestinal Colonization by Vancomycin-Resistant Enterococci in Mice and Humans▿  
Journal of Clinical Microbiology  2010;48(7):2595-2598.
We investigated the impact of probiotics on the intestinal carriage of vancomycin-resistant enterococci (VRE). Administration of Lactobacillus rhamnosus Lcr35 but not Escherichia coli Nissle reduced, although not significantly, the density of VRE colonization in a murine model. No effect of Lcr35 was observed in a double-blind placebo randomized study, involving nine patients.
PMCID: PMC2897524  PMID: 20421444
8.  Laboratory Diagnosis of Clostridium difficile-Associated Diarrhea and Colitis: Usefulness of Premier Cytoclone A+B Enzyme Immunoassay for Combined Detection of Stool Toxins and Toxigenic C. difficile Strains 
Journal of Clinical Microbiology  2001;39(5):1996-1998.
Detection of Clostridium difficile toxins A and B in stools by Premier Cytoclone A+B enzyme immunoassay (EIA) was compared with detection by stool culture for C. difficile followed by detection of toxigenic isolates using the same EIA. Chart reviews were performed to evaluate the likelihood of C. difficile-associated diarrhea and colitis (CADC) for all patients with at least one positive toxin assay. While the toxins were detected in 58 of 85 consecutive CADC patients by both assays, CADC in 5 patients was detected only by stool toxin assay, and in 22 patients CADC was detected only by toxigenic culture. Our results suggest that for laboratories using a rapid toxin A+B EIA, direct toxin detection in stools should be combined with toxigenic culture in cases in which there is a negative stool toxin assay.
PMCID: PMC88068  PMID: 11326033

Results 1-8 (8)