Data management and protection in occupational and environmental exposome research - A case study from the EU-funded EXIMIOUS project.

Within collaborative projects, such as the EU-funded Horizon 2020 EXIMIOUS project (Mapping Exposure-Induced Immune Effects: Connecting the Exposome and the Immunome), collection and analysis of large volumes of data pose challenges in the domain of data management, with regards to both ethical and legal aspects. However, researchers often lack the right tools and/or accurate understanding of the ethical/legal framework to independently address such challenges. With the guidance and support within and between the partner institutes (the researchers and the ethical and legal teams) in the EXIMIOUS project, we have been able to understand and solve most challenges during the first two project years. This has fed into the development of a Data Management Plan and the establishment of data management platforms in accordance with the ethical and legal framework laid down by the EU and the different national regulations of the partners involved. Through this elaborate exercise, we have acquired tools which allow us to make our research data FAIR (Findable, Accessible, Interoperable, and Reusable), while at the same time ensuring data privacy and security (GDPR compliant). Herein we share our experience of creating and managing the data workflow through an open research communication, with the aim of helping other researchers build their data management framework in their own projects. Based on the measures adopted in EXIMIOUS to ensure FAIR data management, we also put together a checklist "DMP CHECK" containing a series of recommendations based on our experience.

A Real-World Assessment of Clinical Outcomes and Safety of Eravacycline: A Novel Fluorocycline.

BACKGROUND: Eravacycline is a novel fluorocycline approved for treatment of intraabdominal infections, with a broad spectrum of activity against a range of pathogens including multidrug-resistant species, including ESBL- or KPC-producing isolates. It is approved for twice-daily dosing with no need for adjustment in renal dysfunction. In the concomitant administration with CYP 3A4-inducing drugs, eravacycline dosing should be modified. OBJECTIVE: To evaluate the efficacy and safety of eravacycline in a range of infections such as intraabdominal infections, pneumonia and diabetic foot infections in seriously ill patients. METHODS: A retrospective observational cohort study using electronic patient records of 50 consecutive patients administered eravacycline during inpatient acute care admission or as part of outpatient antibiotic therapy (OPAT). RESULTS: Therapy of 1.5 mg/kg q24h was initiated in the hospital in most patients, although some of the less sick were managed in the office or OPAT setting. All patients concluded their management outside of the hospital. Of the 50 patients, 47 (94%) achieved clinical resolution of their infection and 3 (6%) clinical failures occurred. Only three (6%) patients did not have comorbidities, three had a single comorbidity (6%), and the majority (88%) of patients had two or more comorbidities. Most common infections were intraabdominal (36%), pneumonia (18%), diabetic foot (12%), spontaneous bacterial peritonitis (8%) and empyema (8%). Almost half of infections had more than one pathogen isolated, and resistant isolates were frequent. The drug was well tolerated with only two reports of nausea, which did not result in treatment discontinuation, and in 30 days of post-eravacycline therapy only one case of Clostridiodes difficile. CONCLUSIONS: In this real-world setting, eravacycline demonstrated a similar high level of clinical efficacy as seen in clinical trials, 94%, in a variety of infections, including against multidrug-resistant bacteria, and was well tolerated.

Treatment of Acute Osteomyelitis with Once-Weekly Oritavancin: A Two-Year, Multicenter, Retrospective Study.

BACKGROUND: Acute osteomyelitis is typically caused by Gram-positive pathogens, commonly antibiotic-resistant Staphylococcus species. Standard antibiotic treatment is challenging due to required multiple daily doses, therapeutic drug monitoring, and parenteral administration for at least 4 weeks. Oritavancin is a long-acting lipoglycopeptide antibiotic approved as a single 1200 mg dose for the treatment of adult patients with acute bacterial skin and skin structure infections. OBJECTIVE: To characterize the real-world use, efficacy, and safety of oritavancin in adult patients with acute osteomyelitis. METHODS: This was a 2-year, multicenter, retrospective, descriptive study of patients treated for acute osteomyelitis with weekly doses of oritavancin. End of therapy evaluation (ETE) was defined as evaluation at 7-10 days after the last dose of oritavancin, and post-therapy assessment (PTE) was at 3 months and 6 months. At ETE and PTE, patients were interviewed via telephone for clinical outcomes, using a standard questionnaire. Electronic medical record review was also conducted. RESULTS: 134 patients were treated with oritavancin for acute osteomyelitis across 20 different Metro Infectious Disease Consultants infusion centers in six states. Of total positive cultures, 71.9% (92/128) were methicillin-resistant Staphylococcus aureus (MRSA) from deep wounds, bone, or joint culture; an additional nine (6.7%) of 134 patients presented with concomitant MRSA bacteremia. Oritavancin was administered via intravenous catheter; patients received an initial treatment of 1200 mg and then 800 mg weekly thereafter for a total number of doses of four (n = 118) or five (n = 16). 118 patients (88.1%) of the baseline 134 patients achieved clinical success at the ETE timepoint. 130 patients were available for PTE at 3 months and 6 months. Overall, relapse or persistent infection was diagnosed in 13/134 (9.7%) patients. Nine (6.7%) of 134 patients were admitted to the hospital during the follow-up period but none for osteomyelitis. Adverse events were reported in five (3.7%) patients including hypoglycemia-related symptoms (three patients), tachycardia (one patient), and tachycardia with chest pain (one patient). None of these patients were hospitalized due to adverse events, and all patients eventually finished their treatment regimens. CONCLUSION: This is the largest real-world clinical study of adult patients treated with oritavancin for acute osteomyelitis. Use of oritavancin for acute osteomyelitis infection resulted in a high rate of positive clinical outcomes and a low incidence of adverse events, thereby providing potential for a convenient, effective, and safe therapeutic option. Future prospective and comparative studies are needed to validate these findings.

Can an etiologic agent be identified in adults who are hospitalized for community-acquired pneumonia: results of a one-year study.

INTRODUCTION: Determining the cause of community-acquired pneumonia (CAP) remains problematic. In this observational study, we systematically applied currently approved diagnostic techniques in patients hospitalized for CAP in order to determine the proportion in which an etiological agent could be identified. METHODS: All patients admitted with findings consistent with CAP were included. Sputum and blood cultures, urine tests for pneumococcal and Legionella antigens, nasopharyngeal swab for viral PCR, and serum procalcitonin were obtained in nearly every case. Admission-related electronic medical records were reviewed in entirety. RESULTS: By final clinical diagnosis, 44 patients (17.0%) were uninfected. A causative bacterium was identified in only 60 (23.2%) cases. PCR identified a respiratory virus in 42 (16.2%), 12 with documented bacterial coinfection. In 119 (45.9%), no cause for CAP was found; 69 (26.6%) of these had a syndrome indistinguishable from bacterial pneumonia. Procalcitonin was elevated in patients with bacterial infection and low in uninfected patients or those with viral infection, but with substantial overlap. CONCLUSIONS: Only 23.2% of 259 patients admitted with a CAP syndrome had documented bacterial infection; another 26.6% had no identified bacterial etiology, but findings closely resembled those of bacterial infection. Nevertheless, all 259 received antibacterial therapy. Careful attention to the clinical picture may identify uninfected patients or those with viral infection, perhaps with reassurance by a non-elevated procalcitonin. Determining an etiologic diagnosis remains elusive. Better discriminators of bacterial infection are sorely needed.

Device-related infective endocarditis, with special consideration of implanted intravascular and cardiac devices in a predominantly male population.

BACKGROUND: The relationship between invasive medical devices and infective endocarditis (IE) has not been comprehensively assessed. We describe our experience of patients with IE, with particular attention to the role of pre-existing intravascular catheters and implanted cardiac devices in the pathogenesis. METHODS: We performed a retrospective review of hospital records over a 10-y period (1997-2007), and included patients with 'definite' or 'possible' IE as per the modified Duke criteria. The complete electronic medical record was reviewed for the presence of intravascular devices prior to the onset of IE, including intravascular catheters and implanted cardiac devices (defibrillators and pacemakers). RESULTS: We identified 155 patients with IE. Infection involved a native valve in 124 (80%) patients and a prosthetic valve in 15 (9.7%). In the remaining 16 (10.3%) patients, infection was attributed to an implanted cardiac device. The most commonly identified source of infection was a central venous catheter, accounting for 17.4% of patients, followed by an implanted cardiac device in 10.3% of patients. Staphylococcus aureus was the most commonly isolated organism in catheter-associated IE and cardiac device-associated IE (31.9% and 62.5%, respectively). Thirty-five (22.5%) patients died within 90 days. Mortality was 31.9% in patients with IE caused by methicillin-resistant S. aureus (MRSA). CONCLUSIONS: Intravascular catheters and cardiac implantable devices are common sources of infection leading to IE, and the intracardiac devices themselves often become infected, with MRSA as the predominant pathogen.

Severe pulmonary involvement in a case attributed to domestically acquired Seoul hantavirus in the United States.

Hantavirus is known to cause 2 distinct clinical syndromes: hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome. Seoul virus is an Old World hantavirus known to cause HFRS. We report a case attributed to domestically acquired Seoul hantavirus with prominent pulmonary involvement and a fatal outcome.