We have searched for sulfate-reducing bacteria in the feces of 41 healthy individuals and 110 patients from a Hepato-Gastro-Enterology Unit using a specific liquid medium (Test-kit Labège, Compagnie Française de Géothermie, Orléans, France). The 110 patients were separated in 22 patients presenting with inflammatory bowel diseases and 88 patients hospitalized for other lower (n=30) or upper (n=58) digestive tract diseases. Sulfate-reducing bacteria were isolated from 10 healthy individuals (24%), 15 patients presenting with inflammatory bowel diseases (68%), and 33 patients with other symptoms (37%). A multiplex PCR was devised for the identification of Desulfovibrio piger (formerly Desulfomonas pigra), Desulfovibrio fairfieldensis and Desulfovibrio desulfuricans, and applied to the above isolates. The strains of sulfate-reducing bacteria consisted of D. piger (39 isolates), D. fairfieldensis (19 isolates) and D. desulfuricans (one isolate). The prevalence of D. piger was significantly higher in inflammatory bowel disease patients (55%) as compared to healthy individuals (12%) or patients with other symptoms (25%) (P<0.05).

Eight isolates of Desulfovibrio spp. have been obtained over 5 years from abdominal or brain abscesses or blood. In seven patients these strains were part of a mixed flora. One strain was isolated in pure culture from the blood of a patient with peritonitis of appendicular origin. According to the 16S rRNA gene sequences, this strain was close to Desulfovibrio fairfieldensis. The present report describes the fourth isolate of this recently described species to be isolated in pure culture or as a predominant part of the flora and to be associated with infectious processes. Thus, D. fairfieldensis may possess a higher pathogenic potential than other Desulfovibrio species.

Severe invasive group A streptococcal diseases have re-emerged during the past 10-20 years. In order to provide a better insight into the current epidemiological situation in France, we analysed the questionnaires regarding all invasive strains received at the National Reference Center for Streptococci (CNR-Strep) between 2006 and 2010 from patients aged ≥ 18 and characterized them by emm typing, spe gene detection and antibiotic resistance. Among the 1542 invasive GAS strains studied, 78% (n=1206) were from blood cultures, and a streptococcal toxic shock syndrome (STSS) was described in 22% (n=340) of cases, mainly associated with necrotizing fasciitis (NF) and pleuro-pulmonary infections (p<0.001). The in-hospital fatality rate was 15%. A total of 83 different emm types were recovered but the three predominant emm types, representing almost 60% of the isolates, were emm1 (24%), emm28 (17%) and emm89 (15%). The preponderance of each emm type varied according to the year, with a significant constant increase of emm28 strains, whereas emm1 strains, representing approximately 32% of GAS invasive isolates in 2007 and 2008, dropped to <15% in 2010 (p<0.001). The distribution of phage-associated superantigen genes (speA, speC and ssa) was linked to certain emm types. Between 2006 and 2010, the percentage that was macrolide-resistant decreased from 11% to 5%, confirming the trend observed in 2007. Fortunately, emm1 strains associated with the most life-threatening clinical manifestations remain susceptible to all anti-streptococcal antibiotics.

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Background: Improving timeliness of pathogen identification is crucial to allow early adaptation of antibiotic therapy and improve prognosis in patients with pneumonia. We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with communityacquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP). Methods: This retrospective multicenter study was conducted in four French university hospitals. Respiratory samples were obtained from patients with clinical and radiological signs of pneumonia and simultaneously tested using conventional microbiological methods and the rm-PCR. A committee composed of an intensivist, a microbiologist, and an infectious diseases specialist retrospectively assessed all medical files and agreed on the most appropriate antimicrobial therapy for each pneumonia episode, according to the results of rm-PCR and blinded to the culture results. The rm-PCR-guided antimicrobial regimen was compared to the empirical treatment routinely administered to the patient in standard care. Results: We included 159 pneumonia episodes. Most patients were hospitalized in intensive care units (n = 129, 81%), and episodes were HAP (n = 68, 43%), CAP (n = 54, 34%), and VAP (n = 37, 23%). Conventional culture isolated ≥ 1 microorganism(s) at significant level in 95 (60%) patients. The syndromic rm-PCR detected at least one bacteria in 132 (83%) episodes. Based on the results of the rm-PCR, the multidisciplinary committee proposed a modification of the empirical therapy in 123 (77%) pneumonia episodes. The modification was a de-escalation in 63 (40%), an escalation in 35 (22%), and undetermined in 25 (16%) patients. In microbiologically documented episodes (n = 95), the rm-PCR increased appropriateness of the empirical therapy to 83 (87%), as compared to 73 (77%) in routine care.

Objectives: To evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens. Methods: This prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods. Results: A total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/ 515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7% e96.5%) and 96.0% (95% CI 95.5%e96.4%), respectively, when compared with culture. Of FA-PP falsenegative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of 1 log 10 in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with 10 6 DNA copies/mL grew significantly in culture. Conclusions: FA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.

Fifty-three pharyngitis-related and invasive isolates of Streptococcus pyogenes that are resistant to bacitracin were collected. They were also resistant to streptomycin, kanamycin, macrolides, lincosamides, and streptogramin B. These multiresistant isolates were of emm type 28 and clonally related as shown by pulsed-field gel electrophoresis.

We characterized 182 Streptococcus dysgalactiae subsp. equisimilis isolates and analyzed the epidemiological data on the corresponding infections. stG6, stG485, and stG6792 were the 3 most prevalent invasive emm types among the 27 different emm types recovered. High rates of antimicrobial resistance were observed for macrolides (26.4%) and tetracycline (34.6%).