All organisms usually isolated in our laboratory are now routinely identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using the Andromas software. The aim of this study was to describe the use of this strategy in a routine clinical microbiology laboratory. The microorganisms identified included bacteria, mycobacteria, yeasts and Aspergillus spp. isolated on solid media or extracted directly from blood cultures. MALDI-TOF MS was performed on 2665 bacteria isolated on solid media, corresponding to all bacteria isolated during this period except Escherichia coli grown on chromogenic media. All acquisitions were performed without extraction. After a single acquisition, 93.1% of bacteria grown on solid media were correctly identified. When the first acquisition was not contributory, a second acquisition was performed either the same day or the next day. After two acquisitions, the rate of bacteria identified increased to 99.2%. The failures reported on 21 strains were due to an unknown profile attributed to new species (9) or an insufficient quality of the spectrum (12). MALDI-TOF MS has been applied to 162 positive blood cultures. The identification rate was 91.4%. All mycobacteria isolated during this period (22) were correctly identified by MALDI-TOF MS without any extraction. For 96.3% and 92.2% of yeasts and Aspergillus spp., respectively, the identification was obtained with a single acquisition. After a second acquisition, the overall identification rate was 98.8% for yeasts (160/162) and 98.4% (63/64) for Aspergillus spp. In conclusion, the MALDI-TOF MS strategy used in this work allows a rapid and efficient identification of all microorganisms isolated routinely.

Ceftriaxone has a higher biliary elimination than cefotaxime (40% versus 10%), which may result in a more pronounced impact on the intestinal microbiota. We performed a monocenter, randomized open-label clinical trial in 22 healthy volunteers treated by intravenous ceftriaxone (1 g/24 h) or cefotaxime (1 g/8 h) for 3 days. We collected fecal samples for phenotypic analyses, 16S rRNA gene profiling, and measurement of the antibiotic concentration and compared the groups for the evolution of microbial counts and indices of bacterial diversity over time. Plasma samples were drawn at day 3 for pharmacokinetic analysis. The emergence of 3rd-generation-cephalosporin-resistant Gram-negative enteric bacilli (Enterobacterales), Enterococcus spp., or noncommensal microorganisms was not significantly different between the groups. Both antibiotics reduced the counts of total Gram-negative enteric bacilli and decreased the bacterial diversity, but the differences between the groups were not significant. All but one volunteer from each group exhibited undetectable levels of antibiotic in feces. Plasma pharmacokinetic endpoints were not correlated to alteration of the bacterial diversity of the gut. Both antibiotics markedly impacted the intestinal microbiota, but no significant differences were detected when standard clinical doses were administered for 3 days. This might be related to the similar daily amounts of antibiotics excreted through the bile using a clinical regimen. (This study has been registered at ClinicalTrials.gov under identifier NCT02659033.)

TB in kidney transplant recipients is a rare and late event, but is associated with significantly reduced survival. Our results emphasize the need for systematic screening for LTBI, followed by IPT in high-risk patients.

Background: Cardiac implantable electronic devices (CIEDs) chronic infection diagnosis is challenging because the clinical presentation is frequently misleading and echocardiography may be inconclusive. The aim of this study was to evaluate the diagnostic value of 18 F-fluorodeoxyglucose positron emission tomography/computed tomography (CT) and radiolabeled white blood cells single photon emission CT/CT in a cohort of patients who underwent both scans for suspicion of CIED infection and inconclusive routine investigations. Methods: Forty-eight consecutive patients with suspicion of CIED infection who underwent both 18 F-fluorodeoxyglucose positron emission tomography/CT and white blood cell single photon emission CT/CT in a time span ≤30 days were retrospectively included. The final diagnosis of CIED infection by the endocarditis expert team was based on the modified Duke-Li classification at the end of follow-up. 18 F-Fluorodeoxyglucose positron emission tomography/CT and white blood cell single photon emission CT/CT scans were independently analyzed blinded to the patients’ medical record. Results: In the overall study population, the diagnostic sensitivity, specificity, positive predictive value, and negative predictive value were respectively 80%, 91%, 80%, and 91% for 18 F-fluorodeoxyglucose positron emission tomography/CT and 60%, 100%, 100%, and 85% for white blood cell single photon emission CT/CT. Addition of a positive nuclear imaging scan as a major criterion markedly improved the Duke-Li classification at admission. Semiquantitative parameters did not allow to discriminate between definite and rejected CIED infection. Prolonged antibiotic therapy before imaging tended to decrease the sensitivity for both techniques. Conclusions: Nuclear imaging can improve the diagnostic performances of the Duke-Li score at admission in a selected population of patients with suspected CIED infection, particularly when the infection was initially graded as possible. Whenever possible, imaging should be performed before or early after antibiotic initiation.

BackgroundDe-escalation is strongly recommended for antibiotic stewardship. No studies have addressed this issue in the context of health care-associated intra-abdominal infections (HCIAI). We analyzed the factors that could interfere with this process and their clinical consequences in intensive care unit (ICU) patients with HCIAI.MethodsAll consecutive patients admitted for the management of HCIAI who survived more than 3 days following their diagnosis, who remained in the ICU for more than 3 days, and who did not undergo early reoperation during the first 3 days were analyzed prospectively in an observational, single-center study in a tertiary care university hospital.ResultsOverall, 311 patients with HCIAI were admitted to the ICU. De-escalation was applied in 110 patients (53 %), and no de-escalation was reported in 96 patients (47 %) (escalation in 65 [32 %] and unchanged regimen in 31 [15 %]). Lower proportions of Enterococcus faecium, nonfermenting Gram-negative bacilli (NFGNB), and multidrug-resistant (MDR) strains were cultured in the de-escalation group. No clinical difference was observed at day 7 between patients who were de-escalated and those who were not. Determinants of de-escalation in multivariate analysis were adequate empiric therapy (OR 9.60, 95 % CI 4.02–22.97) and empiric use of vancomycin (OR 3.39, 95 % CI 1.46–7.87), carbapenems (OR 2.64, 95 % CI 1.01–6.91), and aminoglycosides (OR 2.31 95 % CI 1.08–4.94). The presence of NFGNB (OR 0.28, 95 % CI 0.09–0.89) and the presence of MDR bacteria (OR 0.21, 95 % CI 0.09–0.52) were risk factors for non-de-escalation. De-escalation did not change the overall duration of therapy. The risk factors for death at day 28 were presence of fungi (HR 2.64, 95 % CI 1.34–5.17), Sequential Organ Failure Assessment score on admission (HR 1.29, 95 % CI 1.16–1.42), and age (HR 1.03, 95 % CI 1.01–1.05). The survival rate expressed by a Kaplan-Meier curve was similar between groups (log-rank test p value 0.176).ConclusionsDe-escalation is a feasible option in patients with polymicrobial infections such as HCIAI, but MDR organisms and NFGNB limit its implementation.

Cefiderocol is a novel siderophore cephalosporin, which has proven in vitro activity against carbapenem-resistant (CR) Gram-negative pathogens and stability towards all carbapenemases. The aim of this study was to describe the first cases of prescriptions and the efficacy of cefiderocol for compassionate use in the 2 months following its access in France. We performed a national retrospective study of all patients who received at least one dose of cefiderocol from 2 November 2018 to 5 November 2019. We collected clinical characteristics and outcome through a standard questionnaire. Bacterial isolates from 12 patients were centralized and analyzed in the French National Reference Center for Antimicrobial Resistance, and sequenced using Illumina technology. Finally, 13 patients from 7 French university hospitals were included in the study. The main type of infection treated by cefiderocol was respiratory tract infections (RTI, n = 10). The targeted bacteria were Pseudomonas aeruginosa (n = 12), including carbapenemase-producing P. aeruginosa (n = 9), Acinetobacter baumannii (n = 2), Klebsiella pneumoniae (n = 1), and Enterobacter hormaechei (n = 1). Overall, of the 12 patients whose samples were analyzed, 5 P. aeruginosa strains were not susceptible to cefiderocol (4 categorized as resistant and 1 as intermediate) according to Clinical and Laboratory Standards Institute (CLSI) breakpoints. If considering susceptible strains, the cure rate was 6/7, while being 0/5 among not-susceptible strains. This study underlines the necessity to test strains in adequate conditions.

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Francisella tularensis is a highly infectious pathogen that infects animals and humans to cause the disease tularemia. The primary targets of this bacterium are macrophages, in which it replicates in the cytoplasm after escaping the initial phagosomal compartment. The ability to replicate within macrophages relies on the tightly regulated expression of a series of genes. One of the most commonly used means of coordinating the regulation of multiple genes in bacteria consists of the association of dedicated alternative sigma factors with the core of the RNA polymerase (RNAP). In silico analysis of the F. tularensis LVS genome led us to identify, in addition to the genes encoding the RNAP core (comprising the a1, a2, b, b9 and v subunits), one gene (designated rpoD) encoding the major sigma factor s 70 , and a unique gene (FTL_0851) encoding a putative alternative sigma factor homologue of the s 32 heat-shock family (designated rpoH). Hence, F. tularensis represents one of the minority of bacterial species that possess only one or no alternative sigma factor in addition to the main factor s 70 . In the present work, we show that FTL_0851 encodes a genuine s 32 factor. Transcriptomic analyses of the F. tularensis LVS heat-stress response allowed the identification of a series of orthologues of known heat-shock genes (including those for Hsp40, GroEL, GroES, DnaK, DnaJ, GrpE, ClpB and ClpP) and a number of genes implicated in Francisella virulence. A bioinformatic analysis was used to identify genes preceded by a putative s 32 -binding site, revealing both similarities to and differences from RpoH-mediated gene expression in Escherichia coli. Our results suggest that RpoH is an essential protein of F. tularensis, and positively regulates a subset of genes involved in the heat-shock response.