Core genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting.

PURPOSE: Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission. METHODS: We analyzed retrospectively all toxigenic C. difficile-positive stool samples stored at the Lausanne University Hospital over 6 consecutive months. All isolates were initially typed and classified using a modified double-locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering were subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for spatiotemporal epidemiological links supporting hospital transmission. A comparative descriptive analysis between genomic and epidemiological data was then performed. RESULTS: From January to June 2021, 86 C. difficile isolates were recovered from thawed samples of 71 patients. Thirteen different DLST types were shared by > 1 patient, and 13 were observed in single patients. A genomic cluster was defined as a set of isolates from different patients with ≤ 3 locus differences, determined by cgMLST. Seven genomic clusters were identified, among which plausible epidemiological links were identified in only 4/7 clusters. CONCLUSION: Among clusters determined by cgMLST analysis, roughly 40% included unexplained HA-CDI acquisitions, which may be explained by unidentified epidemiological links, asymptomatic colonization, and/or shared common community reservoirs. The use of DLST, followed by whole genome sequencing analysis, is a promising and cost-effective stepwise approach for the investigation of CDI transmission in the hospital setting.

[Methicillin-resistant Staphylococcus aureus: 15 years of molecular epidemiology in Western Switzerland]. / Staphylococcus aureus résistant à la méticilline : 15 ans de surveillance moléculaire en Suisse romande.

Since the introduction of antibiotics, successive waves of Staphylococcus aureus clones occurred, each one having characteristic susceptibility pattern to antibiotics and virulence factors. We report here the results of a molecular epidemiological surveillance of methicillin-resistant S. aureus (MRSA) in French-speaking Switzerland between 2006 and 2020 showing the emergence and disappearance of clones known for their international dissemination, and the sporadic appearance of other international clones. Since 2012, a marked decrease in the incidence of cases attributable to the biology of the clones and to the control measures taken in the hospitals has been observed. These results highlight the importance of continuous surveillance in order to better assess the burden of this multi-resistant pathogen in our region.

Depuis l'introduction des antibiotiques, des vagues successives de clones de Staphylococcus aureus sont apparues, chacun avec un profil de susceptibilité aux antibiotiques et de virulence caractéristique. Nous rapportons ici les résultats d'une surveillance épidémiologique moléculaire de S. aureus résistant à la méticilline (MRSA) en Suisse romande entre 2006 et 2020 montrant l'émergence et la disparition de clones connus pour leur dissémination internationale, ainsi que l'apparition sporadique d'autres clones internationaux. Depuis 2012, une diminution marquée de l'incidence des cas attribuable à la biologie des clones et aux mesures de contrôle prises dans les hôpitaux est observée. Ces résultats nous montrent l'importance d'une surveillance continue afin de mieux évaluer le fardeau que représente ce germe multirésistant dans notre région.

Increasing morbidity and mortality of candidemia over one decade in a Swiss university hospital.

BACKGROUND: The epidemiology of candidemia is evolving with raising concern about the emergence of intrinsically resistant non-albicans Candida species and acquisition of antifungal resistance. In addition to microbiological surveys, epidemiological studies including clinical data are needed to assess the impact of candidemia on morbidity and mortality. OBJECTIVES: To assess the clinical and microbiological trends of candidemia in a Swiss university hospital. PATIENTS/METHODS: This single-centre retrospective study compared the incidence of candidemia, Candida species distribution, antifungal resistance profiles, clinical characteristics and outcomes between two periods separated by one decade. RESULTS: A total of 170 candidemic episodes were included (68 from period 1, 2004-2006, and 102 from period 2, 2014-2017). Incidence of candidemia (0.85 to 0.97 episode/10,000 patient-days), species distribution (55%-57% C albicans) and antifungal susceptibilities remained unchanged. During period 2, candidemia was more frequently observed in intensive care units (ICU, 38% vs 19% in period 1, P = .01) and amongst older patients (median age 68 vs 59 years old, P < .01) with more immunosuppressive conditions (24% vs 9%, P = .01). Candidemia in period 2 was more frequently followed by septic shock (23% vs 7% in period 1, P = .01) and ICU admission (42% vs 12%, P < .01) and was associated with higher mortality (34% vs 18%, P = .03). Overall, factors associated with mortality in multivariate analyses included cirrhosis, solid malignancies and ICU stay at the time of candidemia. CONCLUSIONS: Despite stable incidence, species distribution and antifungal resistance of candidemia, an epidemiological shift of the disease towards older and more critically ill patients was observed, with higher mortality rates.

[SARS-CoV-2, a point in the storm]. / SARS-CoV-2, un point dans la tourmente.

Since its emergence in December 2019, scientific knowledge about the SARS-CoV-2 virus has evolved rapidly but, due to the complexity and novelty of this infection and its political and economic stakes, much remains to be clarified. Thousands of studies have already been published and scientific research is constantly evolving. In this multitude of information, we offer an update of the knowledge currently available. A limitation of the propagation, the understanding of the functioning of the virus and its clinical manifestations, the administration of specific treatments, rapid and reliable diagnostic tools are the basis of the fight against this germ, which is still little known today.

Depuis son apparition en Décembre 2019, les connaissances scientifiques concernant le virus SARS-CoV-2 ont rapidement évolués mais, en raison de la complexité et nouveauté de cette infection et de ses enjeux politiques et économiques, encore beaucoup reste à clarifier. Des milliers d'études ont déjà été publiés et la recherche scientifique est en constante évolution. Dans cette multitude d'informations, nous proposons une mise à jour des connaissances actuellement disponibles. Une limitation de la propagation, la compréhension du fonctionnement du virus et de ses manifestations cliniques, l'administration de traitements spécifiques et des outils diagnostiques rapides et fiables, sont à la base de la lutte contre ce germe à présent encore méconnu.

Early clindamycin for bacterial vaginosis in pregnancy (PREMEVA): a multicentre, double-blind, randomised controlled trial.

BACKGROUND: Preterm delivery during pregnancy (<37 weeks' gestation) is a leading cause of perinatal mortality and morbidity. Treating bacterial vaginosis during pregnancy can reduce poor outcomes, such as preterm birth. We aimed to investigate whether treatment of bacterial vaginosis decreases late miscarriages or spontaneous very preterm birth. METHODS: PREMEVA was a double-blind randomised controlled trial done in 40 French centres. Women aged 18 years or older with bacterial vaginosis and low-risk pregnancy were eligible for inclusion and were randomly assigned (2:1) to three parallel groups: single-course or triple-course 300 mg clindamycin twice-daily for 4 days, or placebo. Women with high-risk pregnancy outcomes were eligible for inclusion in a high-risk subtrial and were randomly assigned (1:1) to either single-course or triple-course clindamycin. The primary outcome was a composite of late miscarriage (16-21 weeks) or spontaneous very preterm birth (22-32 weeks), which we assessed in all patients with delivery data (modified intention to treat). Adverse events were systematically reported. This study is registered with ClinicalTrials.gov, number NCT00642980. FINDINGS: Between April 1, 2006, and June 30, 2011, we screened 84 530 pregnant women before 14 weeks' gestation. 5630 had bacterial vaginosis, of whom 3105 were randomly assigned to groups in the low-risk trial (n=943 to receive single-course clindamycin, n=968 to receive triple-course clindamycin, and n=958 to receive placebo) or high-risk subtrial (n=122 to receive single-course clindamycin and n=114 to receive triple-course clindamycin). In 2869 low-risk pregnancies, the primary outcome occurred in 22 (1·2%) of 1904 participants receiving clindamycin and 10 (1·0%) of 956 participants receiving placebo (relative risk [RR] 1·10, 95% CI 0·53-2·32; p=0·82). In 236 high-risk pregnancies, the primary outcome occurred in 5 (4·4%) participants in the triple-course clindamycin group and 8 (6·0%) participants in the single-course clindamycin group (RR 0·67, 95% CI 0·23-2·00; p=0·47). In the low-risk trial, adverse events were more common in the clindamycin groups than in the placebo group (58 [3·0%] of 1904 vs 12 [1·3%] of 956; p=0·0035). The most commonly reported adverse event was diarrhoea (30 [1·6%] in the clindamycin groups vs 4 [0·4%] in the placebo group; p=0·0071); abdominal pain was also observed in the clindamycin groups (9 [0·6%] participants) versus none in the placebo group (p=0·034). No severe adverse event was reported in any group. Adverse fetal and neonatal outcomes did not differ significantly between groups in the high-risk subtrial. INTERPRETATION: Systematic screening and subsequent treatment for bacterial vaginosis in women with low-risk pregnancies shows no evidence of risk reduction of late miscarriage or spontaneous very preterm birth. Use of antibiotics to prevent preterm delivery in this patient population should be reconsidered. FUNDING: French Ministry of Health.

Fidaxomicin for treatment of Clostridium difficile infection in clinical practice: a prospective cohort study in a French University Hospital.

PURPOSE: Two randomized controlled trials (RCTs) showed the non-inferiority of fidaxomicin compared with vancomycin for Clostridium difficile infection (CDI) treatment and its superiority regarding recurrence rate. The aim of this study was to evaluate fidaxomicin's efficacy in clinical practice. METHODS: This single-center prospective cohort study included hospitalized patients treated with fidaxomicin for CDI. Demographic, clinical and biological data were collected. Primary outcome was efficacy of fidaxomicin (clinical cure, recurrence and global cure) at 10 weeks. Secondary outcome was efficacy among different subgroups. RESULTS: Ninety-nine patients were included: 42 severe CDI, 16 complicated CDI and 41 recurrent CDI. Rates of clinical cure, recurrence and global cure were 87, 15 and 59%, respectively. Subgroup analysis showed a higher recurrence rate for patients with recurrent CDI compared with first episode (8 vs. 26%; p = 0.04). Binary toxin was associated with severe/complicated CDI (80 vs. 50%; p < 0.01) and recurrence (32 vs. 7%; p < 0.01). Fidaxomicin was used as a first line for 83% of the patients with recurrence and for only 52% of first episodes even though 86% had recurrence's risk factors. CONCLUSION: Compared with RCTs, fidaxomicin in real world is used for patients with more severe and recurrent CDI, but clinical cure and recurrence rates were similar. Comparative studies are needed in these specific subgroups. Our data also illustrate clinicians' difficulty to define a "patient at risk for recurrence" among the first episodes. Finally, we showed that binary toxin could be important in the screening for severity and recurrence risks.

Can the Pediatric Logistic Organ Dysfunction-2 Score on Day 1 Be Used in Clinical Criteria for Sepsis in Children?

OBJECTIVE: A recent task force has proposed the use of Sequential Organ Failure Assessment in clinical criteria for sepsis in adults. We sought to evaluate the predictive validity for PICU mortality of the Pediatric Logistic Organ Dysfunction-2 and of the "quick" Pediatric Logistic Organ Dysfunction-2 scores on day 1 in children with suspected infection. DESIGN: Secondary analysis of the database used for the development and validation of the Pediatric Logistic Organ Dysfunction-2. SETTINGS: Nine university-affiliated PICUs in Europe. PATIENTS: Only children with hypotension-low systolic blood pressure or low mean blood pressure using age-adapted cutoffs-and lactatemia greater than 2 mmol/L were considered in shock. MEASUREMENTS AND MAIN RESULTS: We developed the quick Pediatric Logistic Organ Dysfunction-2 score on day 1 including tachycardia, hypotension, and altered mentation (Glasgow < 11): one point for each variable (range, 0-3). Outcome was mortality at PICU discharge. Discrimination (Area under receiver operating characteristic curve-95% CI) and calibration (goodness of fit test) of the scores were studied. This study included 862 children with suspected infection (median age: 12.3 mo; mortality: n = 60 [7.0%]). Area under the curve of the Pediatric Logistic Organ Dysfunction-2 score on day 1 was 0.91 (0.86-0.96) in children with suspected infection, 0.88 (0.79-0.96) in those with low systolic blood pressure and hyperlactatemia, and 0.91 (0.85-0.97) in those with low mean blood pressure and hyperlactatemia; calibration p value was 0.03, 0.36, and 0.49, respectively. A Pediatric Logistic Organ Dysfunction-2 score on day 1 greater than or equal to 8 reflected an overall risk of mortality greater than or equal to 9.3% in children with suspected infection. Area under the curve of the quick Pediatric Logistic Organ Dysfunction-2 score on day 1 was 0.82 (0.76-0.87) with systolic blood pressure or mean blood pressure; calibration p value was 0.89 and 0.72, respectively. A score greater than or equal to 2 reflected a mortality risk greater than or equal to 19.8% with systolic blood pressure and greater than or equal to 15.9% with mean blood pressure. CONCLUSION: Among children admitted to PICU with suspected infection, Pediatric Logistic Organ Dysfunction-2 score on day 1 was highly predictive of PICU mortality suggesting its use to standardize definitions and diagnostic criteria of pediatric sepsis. Further studies are needed to determine the usefulness of the quick Pediatric Logistic Organ Dysfunction-2 score on day 1 outside of the PICU.

[Risk of infection and hygiene in paediatric intensive care]. / Risque infectieux et hygiène en réanimation pédiatrique.

The risk of infection in intensive care requires the implementation of adapted organisational measures and nuring techniques on a daily basis when caring for children in these sectors. Recommendations have evolved over recent years and the framework is now clearly defined.

Successful control of an environmental reservoir of NDM-producing Klebsiella pneumoniae associated with nosocomial transmissions in a low-incidence setting.

BACKGROUND: The hospital wastewater system has been reported as a source of nosocomial acquisition of carbapenemase producing Enterobacteriaceae (CPE) in various settings. Cleaning and disinfection protocols or replacement of contaminated equipment often fail to eradicate these environmental reservoirs, which can lead to long-term transmission of CPE. We report a successful multimodal approach to control a New Delhi metallo-beta-lactamase positive Klebsiella pneumoniae (NDM-KP) nosocomial outbreak implicating contamination of sink traps in a low-incidence setting. METHODS: Following the incidental identification of NDM-KP in a urine culture of an inpatient, we performed an epidemiological investigation, including patient and environmental CPE screening, and whole genome sequencing (WGS) of strains. We also implemented multimodal infection prevention and control (IPC) measures, namely the isolation of cases, waterless patient care, replacement of contaminated P-traps and connecting pieces, and bleach and steam disinfection of sinks for 6 months, followed by patient and environmental screenings for eradication. RESULTS: Between February and May 2022, five NDM-KP cases were identified in an eight-bed neurosurgical intermediate care unit. Among the eight sink traps of the unit, three were positive for NDM-KP. Patient and environmental isolates belonged to multilocus sequence typing ST-268. All isolate genomes were genetically very similar suggesting cross-transmission and a potential role of the environment as the source of transmissions. Following the introduction of combined IPC measures, no new case was subsequently detected and sink traps remained negative for NDM-KP within 6 months after the intervention. CONCLUSION: The implementation of multimodal IPC measures, including waterless patient care combined with the replacement and disinfection of P-traps and connecting pieces, was successful in the control of NDM-KP after eight months. In a low-incidence setting, this approach has made it possible to pursue the objective of zero transmission of carbapenemase-producing Enterobacteriaceae (CPE).

Investigations of an increased incidence of non-Aspergillus invasive mould infections in an onco-haematology unit.

AIMS OF THE STUDY: Invasive mould infections are life-threatening complications in patients with haematologic cancer and chemotherapy-induced neutropenia. While invasive aspergillosis represents the main cause of invasive mould infections, non-Aspergillus mould infections, such as mucormycosis, are increasingly reported. Consequently, their local epidemiology should be closely monitored. The aim of this study was to investigate the causes of an increased incidence of non-Aspergillus mould infections in the onco-haematology unit of a Swiss tertiary care hospital. METHODS: All cases of proven and probable invasive mould infections were retrospectively identified via a local registry for the period 2007-2021 and their incidence was calculated per 10,000 patient-days per year. The relative proportion of invasive aspergillosis and non-Aspergillus mould infections was assessed. Factors that may affect invasive mould infections' incidence, such as antifungal drug consumption, environmental contamination and changes in diagnostic approaches, were investigated. RESULTS: A significant increase of the incidence of non-Aspergillus mould infections (mainly mucormycosis) was observed from 2017 onwards (Mann and Kendall test p = 0.0053), peaking in 2020 (8.62 episodes per 10,000 patient-days). The incidence of invasive aspergillosis remained stable across the period of observation. The proportion of non-Aspergillus mould infections increased significantly from 2017 (33% vs 16.8% for the periods 2017-2021 and 2007-2016, respectively, p = 0.02). Building projects on the hospital site were identified as possible contributors of this increase in non-Aspergillus mould infections. However, novel diagnostic procedures may have improved their detection. CONCLUSIONS: We report a significant increase in non-Aspergillus mould infections, and mainly in mucormycosis infections, since 2017. There seems to be a multifactorial origin to this increase. Epidemiological trends of invasive mould infections should be carefully monitored in onco-haematology units in order to implement potential corrective measures.

Systematic scoping review of automated systems for the surveillance of healthcare-associated bloodstream infections related to intravascular catheters.

INTRODUCTION: Intravascular catheters are crucial devices in medical practice that increase the risk of healthcare-associated infections (HAIs), and related health-economic adverse outcomes. This scoping review aims to provide a comprehensive overview of published automated algorithms for surveillance of catheter-related bloodstream infections (CRBSI) and central line-associated bloodstream infections (CLABSI). METHODS: We performed a scoping review based on a systematic search of the literature in PubMed and EMBASE from 1 January 2000 to 31 December 2021. Studies were included if they evaluated predictive performance of automated surveillance algorithms for CLABSI/CRBSI detection and used manually collected surveillance data as reference. We assessed the design of the automated systems, including the definitions used to develop algorithms (CLABSI versus CRBSI), the datasets and denominators used, and the algorithms evaluated in each of the studies. RESULTS: We screened 586 studies based on title and abstract, and 99 were assessed based on full text. Nine studies were included in the scoping review. Most studies were monocentric (n = 5), and they identified CLABSI (n = 7) as an outcome. The majority of the studies used administrative and microbiological data (n = 9) and five studies included the presence of a vascular central line in their automated system. Six studies explained the denominator they selected, five of which chose central line-days. The most common rules and steps used in the algorithms were categorized as hospital-acquired rules, infection rules (infection versus contamination), deduplication, episode grouping, secondary BSI rules (secondary versus primary BSI), and catheter-associated rules. CONCLUSION: The automated surveillance systems that we identified were heterogeneous in terms of definitions, datasets and denominators used, with a combination of rules in each algorithm. Further guidelines and studies are needed to develop and implement algorithms to detect CLABSI/CRBSI, with standardized definitions, appropriate data sources and suitable denominators.

PELOD-2: an update of the PEdiatric logistic organ dysfunction score.

OBJECTIVE: Multiple organ dysfunction syndrome is the main cause of death in adult ICUs and in PICUs. The PEdiatric Logistic Organ Dysfunction score developed in 1999 was primarily designed to describe the severity of organ dysfunction. This study was undertaken to update and improve the PEdiatric Logistic Organ Dysfunction score, using a larger and more recent dataset. DESIGN: Prospective multicenter cohort study. SETTING: Nine multidisciplinary, tertiary-care PICUs of university-affiliated hospitals in France and Belgium. PATIENTS: All consecutive children admitted to these PICUs (June 2006-October 2007). INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: We collected data on variables considered for the PEdiatric Logistic Organ Dysfunction-2 score during PICU stay up to eight time points: days 1, 2, 5, 8, 12, 16, and 18, plus PICU discharge. For each variable considered for the PEdiatric Logistic Organ Dysfunction-2 score, the most abnormal value observed during time points was collected. The outcome was vital status at PICU discharge. Identification of the best variable cutoffs was performed using bivariate analyses. The PEdiatric Logistic Organ Dysfunction-2 score was developed by multivariable logistic regressions and bootstrap process. We used areas under the receiver-operating characteristic curve to evaluate discrimination and Hosmer-Lemeshow goodness-of-fit tests to evaluate calibration. We enrolled 3,671 consecutive patients (median age, 15.5 mo; interquartile range, 2.2-70.7). Mortality rate was 6.0% (222 deaths). The PEdiatric Logistic Organ Dysfunction-2 score includes ten variables corresponding to five organ dysfunctions. Discrimination (areas under the receiver-operating characteristic curve = 0.934) and calibration (chi-square test for goodness-of-fit = 9.31, p = 0.317) of the PEdiatric Logistic Organ Dysfunction-2 score were good. CONCLUSION: We developed and validated the PEdiatric Logistic Organ Dysfunction-2 score, which allows assessment of the severity of cases of multiple organ dysfunction syndrome in the PICU with a continuous scale. The PEdiatric Logistic Organ Dysfunction-2 score now includes mean arterial pressure and lactatemia in the cardiovascular dysfunction and does not include hepatic dysfunction. The score will be in the public domain, which means that it can be freely used in clinical trials.

Prognostic value of shock index in children with septic shock.

OBJECTIVES: Septic shock is frequent in children and is associated with high mortality and morbidity rates. Early recognition of severe sepsis improve outcome. Shock index (SI), ratio of heart rate (HR) and systolic blood pressure (SBP), may be a good noninvasive measure of hemodynamic instability that has been poorly studied in children. The aim of the study was to explore the usefulness of SI as an early index of prognosis for septic shock in children. METHODS: The study was retrospective and performed in 1 pediatric intensive care unit at a university hospital. The following specific data were collected at 0, 1, 2, 4, and 6 hours after admission: HR and SBP for SI calculation and lactate concentration. Patients were divided into 2 groups according to their outcome (death/survival). RESULTS: A total of 146 children admitted with septic shock between January 2000 and April 2010 were included. Shock index was significantly different between survivors and nonsurvivors at 0, 4, and 6 hours after admission (P = 0.02, P = 0.03, and P = 0.008, respectively). Age-adjusted SIs were different between survivors and nonsurvivors at 0 and 6 hours, with a relative risk of death at these time points of 1.85 (1.04-3.26) (P = 0.03) and 2.17 (1.18-3.96) (P = 0.01), respectively. Moreover, an abnormal SI both at admission and at 6 hours was predictive of death with relative risk of 1.36 (1.05-1.76). CONCLUSIONS: In our population of children with septic shock, SI was a clinically relevant and easily calculated predictor of mortality. It could be a better measure of hemodynamic status than HR and SBP alone, allowing for the early recognition of severe sepsis.

Predictive performance of automated surveillance algorithms for intravascular catheter bloodstream infections: a systematic review and meta-analysis.

BACKGROUND: Intravascular catheter infections are associated with adverse clinical outcomes. However, a significant proportion of these infections are preventable. Evaluations of the performance of automated surveillance systems for adequate monitoring of central-line associated bloodstream infection (CLABSI) or catheter-related bloodstream infection (CRBSI) are limited. OBJECTIVES: We evaluated the predictive performance of automated algorithms for CLABSI/CRBSI detection, and investigated which parameters included in automated algorithms provide the greatest accuracy for CLABSI/CRBSI detection. METHODS: We performed a meta-analysis based on a systematic search of published studies in PubMed and EMBASE from 1 January 2000 to 31 December 2021. We included studies that evaluated predictive performance of automated surveillance algorithms for CLABSI/CRBSI detection and used manually collected surveillance data as reference. We estimated the pooled sensitivity and specificity of algorithms for accuracy and performed a univariable meta-regression of the different parameters used across algorithms. RESULTS: The search identified five full text studies and 32 different algorithms or study populations were included in the meta-analysis. All studies analysed central venous catheters and identified CLABSI or CRBSI as an outcome. Pooled sensitivity and specificity of automated surveillance algorithm were 0.88 [95%CI 0.84-0.91] and 0.86 [95%CI 0.79-0.92] with significant heterogeneity (I2 = 91.9, p < 0.001 and I2 = 99.2, p < 0.001, respectively). In meta-regression, algorithms that include results of microbiological cultures from specific specimens (respiratory, urine and wound) to exclude non-CRBSI had higher specificity estimates (0.92, 95%CI 0.88-0.96) than algorithms that include results of microbiological cultures from any other body sites (0.88, 95% CI 0.81-0.95). The addition of clinical signs as a predictor did not improve performance of these algorithms with similar specificity estimates (0.92, 95%CI 0.88-0.96). CONCLUSIONS: Performance of automated algorithms for detection of intravascular catheter infections in comparison to manual surveillance seems encouraging. The development of automated algorithms should consider the inclusion of results of microbiological cultures from specific specimens to exclude non-CRBSI, while the inclusion of clinical data may not have an added-value. Trail Registration Prospectively registered with International prospective register of systematic reviews (PROSPERO ID CRD42022299641; January 21, 2022). https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022299641.

Long-Term Consequences of COVID-19: A 1-Year Analysis.

Long-lasting symptoms after SARS-CoV-2 infection have been described many times in the literature and are referred to as Long COVID. In this prospective, longitudinal, monocentric, observational study, we collected the health complaints of 474 patients (252 ambulatory and 222 hospitalized) at Lausanne University Hospital 1 year after COVID-19 diagnosis. Using a self-reported health survey, we explored cardiopulmonary, vascular, neurological, and psychological complaints. Our results show that age, Charlson comorbidity index, and smoking habits were associated with hospital admission. Regarding the vascular system, we found that having had thromboembolism before SARS-CoV-2 infection was significantly associated with a higher risk of recurrence of thromboembolism at 1 year. In the neurologic evaluation, the most frequent symptom was fatigue, which was observed in 87.5% of patients, followed by "feeling slowed down", headache, and smell disturbance in 71.5%, 68.5%, and 60.7% of cases, respectively. Finally, our cohort subjects scored higher overall in the STAI, CESD, Maastricht, and PSQI scores (which measure anxiety, depression, fatigue, and sleep, respectively) than the healthy population. Using cluster analysis, we identified two phenotypes of patients prone to developing Long COVID. At baseline, CCS score, prior chronic disease, stroke, and atrial fibrillation were associated with Long COVID. During COVID infection, mechanical ventilation and five neurological complaints were also associated with Long COVID. In conclusion, this study confirms the wide range of symptoms developed after COVID with the involvement of all the major systems. Early identification of risk factors associated with the development of Long COVID could improve patient follow-up; nevertheless, the low specificity of these factors remains a challenge to building a systematic approach.

Evaluation of a new molecular test, the BD Max Cdiff, for detection of toxigenic Clostridium difficile in fecal samples.

A new molecular assay detecting toxigenic Clostridium difficile, the BD Max Cdiff (Becton, Dickinson), was evaluated with 360 diarrheal feces samples. It exhibited high sensitivity (97.7%) and specificity (99.7%). The positive (97.7%) and negative (99.7%) predictive values of this test allow an accurate answer within 2 h.

Chemical extraction versus direct smear for MALDI-TOF mass spectrometry identification of anaerobic bacteria.

In the present study, two pre-analytic processes for mass spectrometric bacterial identification were compared: the time-consuming reference method, chemical extraction, and the direct smear technique directly using cultured colonies without any further preparation. These pre-analytic processes were compared in the identification of a total of 238 strains of anaerobic bacteria representing 34 species. The results showed that 218/238 strains were identified following chemical extraction, 185 identifications (77.7%) were secured to both genus and species [log(score) > 2.0] whereas 33 identifications (14%) were secured to genus only [log(score) between 1.7 and 2.0]. Following direct smear, 207/238 anaerobic bacteria were identified, 158 identifications (66.4%) were secured to both genus and species [log(score) > 2.0] whereas 49 identifications were secured to genus only [log(score) between 1.7 and 2.0]. Twenty strains were not identified [log(score) < 1.7] by MALDI-TOF MS following chemical extraction whereas 31 strains were not identified with the direct smear technique. Although direct smear led to a significant decrease of the log(score) values for the Clostridium genus and the Gram positive anaerobic bacteria (GPAC) group (p < 0.0001, Wilcoxon test), identification to both species and genus were not changed. However these differences were not statistically significant (p = 0.1, Chi square). Therefore, MALDI-TOF MS identification following the direct smear technique appears to both non-inferior to the reference method and relevant for anaerobic bacteria identification.

Molecular typing of Clostridioides difficile from frozen stool samples to investigate cross-transmissions: A proof of concept.

PURPOSE: Toxigenic Clostridioides difficile is responsible for up to one third of post antibiotic diarrhea and for more than 95% of pseudomembranous colitis. Nowadays, diagnosis relies on the documentation of the presence of the toxin in stools by specific antigenic or PCR tests. Stool cultures have been mostly abandoned, leading to the absence of isolates for further epidemiological analyses. METHODS: Aliquots of stool samples, frozen for up to two years, were thawed and inoculated onto commercial C. difficile media. Eighteen stools were recovered from patients hospitalized in the pediatric ward where at that time a chain of transmission was suspected. Eleven stools were recovered from patients hospitalized in a medical ward over a three months period with no suspected transmission event. Up to 16 characteristic colonies were isolates per culture. PCR of toxins genes and molecular typing by Double Locus Sequence Typing (DLST) were performed on these colonies. Whole genome multi locus sequence typing (wgMLST) was performed on selected isolates. RESULTS: Among the 29 stool specimens, no growth was observed for four stools and only one colony grew for one stool. Except the latter, all 16 colonies of the 24 stools showed identical toxin genes profiles than the original stool. However, variant DLST genotypes was observed within 20% of investigated stools. The majority of variants were single locus variant due to an IN/DEL of the repeat in one of the two DLST locus. Despite this variation, results of molecular typing overrule the putative transmission chain in the pediatric ward and revealed undetected chains of transmission in the medical ward. These results were confirmed with wgMLST. CONCLUSIONS: The developed protocol allows prospective and retrospective molecular and genomic epidemiological investigation of C. difficile infections for infection control purpose.