DNAGear: a free software for spa type identification in Staphylococcus aureus

Staphylococcus aureus is both human commensal and an important human pathogen, responsible for community-acquired and nosocomial infections ranging from superficial wound infections to invasive infections, such as osteomyelitis, bacteremia and endocarditis, pneumonia or toxin shock syndrome with a mortality rate up to 40%. S. aureus reveals a high genetic polymorphism and detecting the genotypes is extremely useful to manage and prevent possible outbreaks and to understand the route of infection. One of current and expanded typing method is based on the X region of the spa gene composed of a succession of repeats of 21 to 27 bp. More than 10000 types are known. Extracting the repeats is impossible by hand and needs a dedicated software. Unfortunately the only software on the market is a commercial program from Ridom. Findings This article presents DNAGear, a free and open source software with a user friendly interface written all in Java on top of NetBeans Platform to perform spa typing, detecting new repeats and new spa types and synchronizing automatically the files with the open access database. The installation is easy and the application is platform independent. In fact, the SPA identification is a formal regular expression matching problem and the results are 100% exact. As the program is using Java embedded modules written over string manipulation of well established algorithms, the exactitude of the solution is perfectly established. Conclusions DNAGear is able to identify the types of the S. aureus sequences and detect both new types and repeats. Comparing to manual processing, which is time consuming and error prone, this application saves a lot of time and effort and gives very reliable results. Additionally, the users do not need to prepare the forward-reverse sequences manually, or even by using additional tools. They can simply create them in DNAGear and perform the typing task. In short, researchers who do not have commercial software will benefit a lot from this application.Peer Reviewe

Pseudomonas aeruginosa bloodstream infections in patients with cancer: differences between patients with hematological malignancies and solid tumors

Objectives: To assess the clinical features and outcomes of Pseudomonas aeruginosa bloodstream infection (PA BSI) in neutropenic patients with hematological malignancies (HM) and with solid tumors (ST), and identify the risk factors for 30-day mortality. Methods: We performed a large multicenter, retrospective cohort study including onco-hematological neutropenic patients with PA BSI conducted across 34 centers in 12 countries (January 2006-May 2018). Episodes occurring in hematologic patients were compared to those developing in patients with ST. Risk factors associated with 30-day mortality were investigated in both groups. Results: Of 1217 episodes of PA BSI, 917 occurred in patients with HM and 300 in patients with ST. Hematological patients had more commonly profound neutropenia (0.1 × 109 cells/mm) (67% vs. 44.6%; p < 0.001), and a high risk Multinational Association for Supportive Care in Cancer (MASCC) index score (32.2% vs. 26.7%; p = 0.05). Catheter-infection (10.7% vs. 4.7%; p = 0.001), mucositis (2.4% vs. 0.7%; p = 0.042), and perianal infection (3.6% vs. 0.3%; p = 0.001) predominated as BSI sources in the hematological patients, whereas pneumonia (22.9% vs. 33.7%; p < 0.001) and other abdominal sites (2.8% vs. 6.3%; p = 0.006) were more common in patients with ST. Hematological patients had more frequent BSI due to multidrug-resistant P. aeruginosa (MDRPA) (23.2% vs. 7.7%; p < 0.001), and were more likely to receive inadequate initial antibiotic therapy (IEAT) (20.1% vs. 12%; p < 0.001). Patients with ST presented more frequently with septic shock (45.8% vs. 30%; p < 0.001), and presented worse outcomes, with increased 7-day (38% vs. 24.2%; p < 0.001) and 30-day (49% vs. 37.3%; p < 0.001) case-fatality rates. Risk factors for 30-day mortality in hematologic patients were high risk MASCC index score, IEAT, pneumonia, infection due to MDRPA, and septic shock. Risk factors for 30-day mortality in patients with ST were high risk MASCC index score, IEAT, persistent BSI, and septic shock. Therapy with granulocyte colony-stimulating factor was associated with survival in both groups. Conclusions: The clinical features and outcomes of PA BSI in neutropenic cancer patients showed some differences depending on the underlying malignancy. Considering these differences and the risk factors for mortality may be useful to optimize their therapeutic management. Among the risk factors associated with overall mortality, IEAT and the administration of granulocyte colony-stimulating factor were the only modifiable variables.Funding: This study was supported by the Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economía, Industria y Competitividad, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC) (CB21/13/00009; CB21/13/00079; CB21/13/00054; CB21/13/00086), Madrid, Spain. Acknowledgments: We thank the ESCMID Study Group for Bloodstream Infections, Endocarditis, and Sepsis (ESGBIES) and the ESCMID Study Group for Immunocompromised Hosts (ESGICH) for supporting the study. We thank the Centres de Recerca de Catalunya (CERCA) Program and Generalitat de Catalunya for the institutional support. We thank the Spanish Network for Research in Infectious Diseases and the Río Hortega program of the Instituto de Salud Carlos III for the financial support of pre-doctoral student J. Laporte-Amargós and A. Bergas

Pseudomonas aeruginosa Bloodstream Infections in Patients with Cancer: Differences between Patients with Hematological Malignancies and Solid Tumors

Objectives: To assess the clinical features and outcomes of Pseudomonas aeruginosa bloodstream infection (PA BSI) in neutropenic patients with hematological malignancies (HM) and with solid tumors (ST), and identify the risk factors for 30-day mortality. Methods: We performed a large multicenter, retrospective cohort study including onco-hematological neutropenic patients with PA BSI conducted across 34 centers in 12 countries (January 2006-May 2018). Episodes occurring in hematologic patients were compared to those developing in patients with ST. Risk factors associated with 30-day mortality were investigated in both groups. Results: Of 1217 episodes of PA BSI, 917 occurred in patients with HM and 300 in patients with ST. Hematological patients had more commonly profound neutropenia (0.1 x 10(9) cells/mm) (67% vs. 44.6%; p < 0.001), and a high risk Multinational Association for Supportive Care in Cancer (MASCC) index score (32.2% vs. 26.7%; p = 0.05). Catheter-infection (10.7% vs. 4.7%; p = 0.001), mucositis (2.4% vs. 0.7%; p = 0.042), and perianal infection (3.6% vs. 0.3%; p = 0.001) predominated as BSI sources in the hematological patients, whereas pneumonia (22.9% vs. 33.7%; p < 0.001) and other abdominal sites (2.8% vs. 6.3%; p = 0.006) were more common in patients with ST. Hematological patients had more frequent BSI due to multidrug-resistant P. aeruginosa (MDRPA) (23.2% vs. 7.7%; p < 0.001), and were more likely to receive inadequate initial antibiotic therapy (IEAT) (20.1% vs. 12%; p < 0.001). Patients with ST presented more frequently with septic shock (45.8% vs. 30%; p < 0.001), and presented worse outcomes, with increased 7-day (38% vs. 24.2%; p < 0.001) and 30-day (49% vs. 37.3%; p < 0.001) case-fatality rates. Risk factors for 30-day mortality in hematologic patients were high risk MASCC index score, IEAT, pneumonia, infection due to MDRPA, and septic shock. Risk factors for 30-day mortality in patients with ST were high risk MASCC index score, IEAT, persistent BSI, and septic shock. Therapy with granulocyte colony-stimulating factor was associated with survival in both groups. Conclusions: The clinical features and outcomes of PA BSI in neutropenic cancer patients showed some differences depending on the underlying malignancy. Considering these differences and the risk factors for mortality may be useful to optimize their therapeutic management. Among the risk factors associated with overall mortality, IEAT and the administration of granulocyte colony-stimulating factor were the only modifiable variables

Pseudomonas aeruginosa Bloodstream Infections Presenting with Septic Shock in Neutropenic Cancer Patients: Impact of Empirical Antibiotic Therapy

This large, multicenter, retrospective cohort study including onco-hematological neutropenic patients with Pseudomonas aeruginosa bloodstream infection (PABSI) found that among 1213 episodes, 411 (33%) presented with septic shock. The presence of solid tumors (33.3% vs. 20.2%, p < 0.001), a high-risk Multinational Association for Supportive Care in Cancer (MASCC) index score (92.6% vs. 57.4%; p < 0.001), pneumonia (38% vs. 19.2% p < 0.001), and infection due to multidrug-resistant P. aeruginosa (MDRPA) (33.8% vs. 21.1%, p < 0.001) were statistically significantly higher in patients with septic shock compared to those without. Patients with septic shock were more likely to receive inadequate empirical antibiotic therapy (IEAT) (21.7% vs. 16.2%, p = 0.020) and to present poorer outcomes, including a need for ICU admission (74% vs. 10.5%; p < 0.001), mechanical ventilation (49.1% vs. 5.6%; p < 0.001), and higher 7-day and 30-day case fatality rates (58.2% vs. 12%, p < 0.001, and 74% vs. 23.1%, p < 0.001, respectively). Risk factors for 30-day case fatality rate in patients with septic shock were orotracheal intubation, IEAT, infection due to MDRPA, and persistent PABSI. Therapy with granulocyte colony-stimulating factor and BSI from the urinary tract were associated with improved survival. Carbapenems were the most frequent IEAT in patients with septic shock, and the use of empirical combination therapy showed a tendency towards improved survival. Our findings emphasize the need for tailored management strategies in this high-risk population

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Infections à Bartonella henselae chez l enfant. A propos de 28 cas pédiatriques diagnostiqués entre 2007 et 2012 au CHU de Reims

REIMS-BU Santé (514542104) / SudocSudocFranceF

Ostéites pelviennes secondaires aux escarres de décubitus (prise en charge standardisée et évolution de 38 patients au CHU de Montpellier)

Contexte : Aucun consensus n'existe sur la stratégie diagnostique et thérapeutique des escarres compliquées d'ostéite. Les objectifs de notre étude étaient d'évaluer l'impact d'une stratégie standardisée sur la guérison des escarres pelviennes, la concordance microbiologique entre les écouvillons superficiels et biopsies osseuses, et d'identifier les facteurs associés à cette guérison. Méthodes: Etude de cohorte rétrospective, incluant 38 patients avec 54 escarres suspectes d'ostéite biopsiées entre 2005 et 2011 au CHU de Montpellier. Les critères de jugement étaient le taux de guérison et récidive des escarres. Résultats: 81,6% étaient des hommes, 94,8% traumatisés médullaires, un âge moyen de 49,8 ans, et 31,6% avaient plusieurs escarres. Parmi 54 escarres, 50% étaient ischiatiques et 90,7% de stade IV. La positivité des biopsies était de 96,3%, polymicrobiennes, avec 61,1 % de bacilles Gram négatif et 59,3% d'anaérobies. La sensibilité dè l'imagerie par résonance magnétique (IRM) était de 91,9%. Une antibothérapie a été instaurée pour 51 des 5Z ostéites, 53,8% avaient une reconstruction par lambeau(x), et 71,1 % un traitement par pression négative (TPN). Les taux de guérison et de récidive étaient de 36,5% et 18,2% respectivement. La concordance entre écouvillons superficiels et biopsies osseuses n'était pas satisfaisante. Aucun facteur pertinent n'était associé à une guérison plus fréquente. Conclusion: Le taux de guérison reste médiocre mais comparable à celui d'autres études. Le diagnostic d'ostéite nécessite des biopsies osseuses guidées par l'IRM. L'association d'un traitement chirurgical, d'un TPN et d'une antibiothérapie ciblée semble indispensable.MONTPELLIER-BU Médecine UPM (341722108) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Theater practice and interpersonal synchronization behaviors: a pilot study comparing actors and non-actors

Recent studies in the field of theater studies no longer view theater as an object, but rather as a dynamic relationship between actors and spectators. In an embodied and situated perspective of cognition, imagination emerges as a product of this dynamic. This study aims to investigate whether acting practice enhances someone's abilities to set up an effective relationship with others and allows the individual to better manage not only the relationship itself, but also her/his own feelings and those of her/his partner. Eighty two healthy Italian adults, with no communication disorders, including 43 actors (Mage = 25.4; S.D. = 3.64) and 39 non-actors (Mage = 24.1 = S.D. = 4.17) completed a joint verbal production task named Random Sequence Generation (RSG) task. Initially, participants performed the task individually. Subsequently, in a second phase, they worked in pairs with another participant, taking turns to contribute to a shared sequence. Pairings were predetermined to ensure a balanced mix of actors and non-actors, and to prevent participants from having prior relationships. Following the task, subjects were queried about their sense of presence, and, their perception of entitativity with their partner. We observed a replication of previous studies, showing higher RSG scores and reduced repetition in the paired condition, indicative of coupling and synchronization behavior. Within pairs, the level of the sense of presence of both partners was positively correlated. Furthermore, an interaction effect between the sense of presence and acting experience on the perception of entitativity was observed. Specifically, actors described perceived entitativity with their partners when their sense of presence was heightened, whereas non-actors experienced a decrease in perceived entitativity with their partners under similar circumstances. We discuss the results and limitations of the study, suggesting the effect of artistic practice on the development of a sort of dual-task ability which enables actors to organize their sensations and actions while sustaining a meaningful connection with others. This research represents an interdisciplinary collaboration between theater studies and cognitive sciences, highlighting the value of a multidisciplinary approach to research

Characteristics of patients consulted for suspected Lyme neuroborreliosis in an endemic area

Introduction: Some patients with unexplained neurological symptoms sought care for presumed Lyme neuroborreliosis (LNB). We aimed to compare patients’ characteristics with and without LNB. Material and methods: All patients consulting for LNB suspicion and having a lumbar puncture between 2014 and 2020 in a high endemic area of Lyme borreliosis were included in the study. Results: One hundred fifty-five patients were included. Forty-five patients (29 %) had LNB (mean age: 57.6 years, 28.9 % of women) including 17 with isolated intrathecal synthesis. One hundred and ten patients had no LNB (mainly neurological (29 %) and rheumatological diseases (19 %)).Non-neurological symptoms were similar in patients with LNB and patients with no LNB (asthenia, 31 % vs. 46 %, p = 0.14, arthralgia 20 % vs. 31 %, p = 0.14) with the exception of myalgia, which was less frequent in patients with LNB (4.4 % vs. 19.1 % p = 0.02). In multivariable analysis, factors associated with LNB were presence of facial nerve palsy (OR = 5.7), radiculopathy (OR = 11.3), positive Lyme serology (OR = 5.4) and duration of symptoms less than 3 months (OR = 4.48). Patients with isolated intrathecal synthesis had a longer duration of symptoms (3 vs 1 months) than patients with pleocytosis. Asthenia (5.9 % vs. 32.1 %), headaches (0 % vs. 39.3 %) neuropathic pain (17.6 % vs. 50 %) and facial palsy (11.8 % vs. 39.3 %) were less frequent in patients with isolated intrathecal synthesis than patients with pleocytosis. The presence of isolated subjective neurological symptoms (paresthesia, memory disorders, insomnia, irritability, asthenia, headaches) was reported in 7/17 (41 %) of patients with isolated intrathecal synthesis, 2/28 (7.1 %) in patients with pleocytosis and 75/110 (68 %) in patients without LNB (p < 0.001). Conclusion: More than one quarter of patients consulted for suspected LNB had non-neurologic symptoms, whether or not they have a LNB. Concerning patients with isolated intrathecal synthesis, the question of presence of sequelae with a spontaneously cured disease or an active Lyme borreliosis requiring antibiotic remain