OBJECTIVES:Climate change and global warming are major threats for human health and impact the burden of infectious diseases. We investigated the effect of heat stress days (max. perceived temperature ≥32°C) on the incidence of Staphylococcus aureus bacteremia (SAB) and Escherichia coli bacteremia (ECB). METHODS:We performed a post-hoc analysis of a prospective multicenter cohort study with inclusion of all reported SAB and ECB episodes at six tertiary care centers in Germany from 01/2017-12/2019. The effect of the number of heat stress days on the incidence of bacteremia episodes was modelled by a negative binomial regression model with and without underlying seasonal trend. RESULTS:In the prospective multicenter cohort, we included 2870 episodes of SAB and 4421 episodes of ECB. For both entities, we found a significant seasonal variation over the year (ECB peak-to-trough ratio: 1.33, 95% CI: 1.23-1.45, p < 0.001); SAB peak-to-trough ratio: 1.19 (95% CI: 1.07-1.32, p < 0.001), especially in the subgroup of community-acquired ECB (1.47, 95%-CI: 1.32-1.64, p < 0.001). In the model with incorporation of an underlying seasonal trend, we discovered no overall significant association with the number of heat stress days for SAB and ECB. However, in the subgroup of patients with hospital-acquired SAB, we found a significant association after two days of heat (IRR 1.45, 95%-CI: 1.17-1.82, p = 0.001), that remained significant also in a sensitivity analysis focusing on summer days only (IRR 1.50, 95%-CI: 1.18-1.91, p = 0.001). However, after inclusion of an underlying seasonal trend, the incidence of bacteremia cases remained significantly associated with heat stress days only in the subgroup of patients with hospital-acquired SAB. CONCLUSION:Apart from seasonal trends, heat days did not seem to influence the incidence of SAB and ECB overall. The observed association of SAB with heat days in the subgroup of hospital-acquired SAB needs confirmation in further studies.

BACKGROUND:Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhoea with significant morbidity and mortality worldwide. In Germany, CDI incidence has declined in recent years. However, prospective multi-centre data on all-cause in-hospital mortality among CDI patients and on risk factors for death remain scarce. METHODS:We conducted a prospective multi-centre surveillance study in six German university hospitals between 2016 and 2020 to assess all-cause in-hospital mortality among CDI patients. Additionally, multi-variable logistic regression was used to identify risk factors for death. RESULTS:A total of 3592 CDI cases were recorded, of whom 46.7% were female. Overall all-cause in-hospital mortality was 11.7%, whereas CDI-attributable mortality was 0.4% (N = 16). Independent risk factors for death in CDI patients included increasing age (3% per year, adjusted odds ratio [aOR]: 1.03, 95% confidence interval [CI]: 1.02-1.04), longer hospital stay (1% per day, aOR: 1.01, 95% CI: 1.00-1.01), admission to internal medicine (aOR: 1.60, 95% CI: 1.32-1.94) or haematology-oncology (aOR: 2.38, 95% CI: 1.75-3.24) as proxies for patient complexity, and elevated creatinine levels within ± 2 days of sampling (6% per mg/dL, aOR: 1.06, 95% CI: 0.99-1.13). In contrast, diagnosis on a general ward (vs intensive care unit or intermediate care, irrespective of speciality) was associated with a lower risk of death (aOR: 0.34, 95% CI: 0.28-0.42). CONCLUSIONS:Our study provides a comprehensive assessment of all-cause in-hospital mortality among CDI patients in Germany. By identifying robust and easily accessible risk factors for death, our findings support improved risk stratification and may inform targeted management strategies for high-risk patient populations.

OBJECTIVE:Antibiotic de-escalation (ADE) is a key antimicrobial stewardship quality indicator. We aimed to evaluate the rate and patterns of ADE among clinically stable patients with bloodstream infection. METHODS:We analysed secondary data from two prospective multicentre cohort studies, BLOOMY and BLOOMY-PREDICT. ADE was assessed among patients eligible for safe ADE on day 5 after index blood culture. Narrowing of antibiotic spectrum was determined by a ranking based on WHO AWaRe-classification. Risk factors for not performing ADE (non-ADE) were studied using multivariable logistic regression. RESULTS:In total, 937 of 3824 study patients (24.50%) were eligible, of which 218 (23.27%) did not have an option for de-escalation based on antimicrobial susceptibility testing. Of 719 patients in which ADE was feasible, only 406 (56.47%) received ADE. Empiric monotherapy (OR [95% CI] = 5.68 [3.77-8.56], P < 0.001), Gram-negative pathogen (OR 2.27 [1.60-3.24], P < 0.001), healthcare-associated infection (OR 1.55 [1.01-2.39], P = 0.046), and hospital-acquisition (OR 1.63 [1.02-2.61], P = 0.042) were identified as independent factors associated with non-ADE. Conversely, ICU treatment on day 0 (OR 0.60 [0.38-0.95], P = 0.029) was independently associated with de-escalation, alongside a strong study centre effect (OR 0.26 [0.15-0.44], P < 0.001). Further, in-hospital mortality was not associated with ADE (46/406, 11.33% vs. 29/313, 9.27%, P = 0.369). Low ADE rates in patients with urogenital focus and unnecessary carbapenem use were issues of particular concern in our cohort. CONCLUSIONS:Available opportunities for ADE were frequently missed in our setting, especially in Gram-negative bloodstream infection. Antimicrobial stewardship efforts should therefore be strengthened to promote ADE.

Nosocomial infections, particularly those caused by multidrug-resistant organisms, pose a significant challenge in healthcare facilities. This study presents a novel approach that combines tracking patient contacts in the hospital with Fourier-transform infrared (FTIR) spectroscopy and whole-genome sequencing (WGS) of bacterial isolates for rapid surveillance of nosocomial pathogen transmissions. Isolates from relevant species were collected over a 2-month period, and FTIR spectroscopy and WGS were performed on strains suspected in transmission events. The integrated approach identified 94 suspected transmission events involving 103 patients, with single nucleotide polymorphism analysis confirming 32% of these transmissions. FTIR spectroscopy demonstrated good specificity and moderate sensitivity compared to WGS, with the performance highly dependent on the bacterial species analyzed. Room contact of the patients played an important role in pathogen transmission, particularly with Klebsiella pneumoniae. This described approach offers a rapid and accurate means of identifying and tracking the spread of nosocomial pathogens, thereby enhancing infection control strategies and improving patient safety.IMPORTANCEThis manuscript presents a study that employs pathogen typing and monitors hospital occupancy data for the detection of transmissions of hospital-acquired pathogens. The results demonstrate that this approach can be a powerful tool for real-time surveillance and control of nosocomial infections in healthcare settings. The findings have important implications for improving patient safety and reducing the spread of multidrug-resistant organisms in hospitals.

Mortality in Staphylococcus aureus bloodstream infections (BSI) is high. While clinical scores and host risk factors have been evaluated in large clinical cohorts, the relevance of the plethora of virulence factors produced by S. aureus for BSI mortality has remained elusive. By combining a comprehensive, standardized clinical data set with whole genome sequencing analysis of 643 S. aureus isolates from a multicentric BSI study and applying logistic regression analyses, we identified proteins associated with both increased and decreased in-hospital mortality. Adjustment with two clinical severity scores and sex revealed a diverse set of 116 staphylococcal proteins involved in immune modulation, metal homeostasis, adhesion, transcription, and translation (among other functions) as prognostic markers for in-hospital mortality. But also several uncharacterized proteins were associated with in-hospital mortality. Nine predictive proteins were confirmed with an orthogonal statistical approach. Most of the identified proteins have not previously been linked to infection outcomes and represent promising candidates for predictive biomarkers.

OBJECTIVES:For 475 ESBL-producing Escherichia coli (ESBL-Ec), and 171 ESBL-producing Klebsiella pneumoniae (ESBL-Kp) collected from human carriers, the human-polluted (hp)-environment, and food: (i) to compare the antimicrobial resistance gene (ARG) content, and (ii) to assess clonal relationships between human and non-human isolates. MATERIALS AND METHODS:Two prospective multicenter cohorts were assessed: colonized hospitalized index-subjects and household contacts, and long-term care facility (LTCF) residents. Additionally, linked hp-environment and food samples were collected. Presence of ARGs were assessed using pairwise comparisons and proportional similarity index (PSI). Clonal relationships were assessed using cgMLST distance visualizations and maximum likelihood phylogeny. RESULTS:ESBL-Ec and ESBL-Kp co-occurred in 14/65 households, 3/6 LTCFs, and in 33/202 of ESBL-positive participants. Thirty-nine percent of detected ARG types were found in both species (36/93). Frequencies of beta-lactamase, ESBL, aminoglycoside, and sulfonamide ARG types from human ESBL-Ec and ESBL-Kp overlapped considerably: PSIs 0.59-0.75, and were equal or higher compared to the overlap between ESBL-Ec from humans and food isolates: PSIs 0.33-0.72. Isolates from humans and the hp-environment were frequently clonally related, indicating human contamination of the environment. Links with food isolates were observed less frequently. For ESBL-Ec both interregional and regional clonal dissemination were observed, while for ESBL-Kp clonal dissemination was mainly regional. CONCLUSIONS:ESBL-Ec and ESBL-Kp from human carriage showed considerable overlap in ARG content. Furthermore, clonal links were observed frequently between humans and hp-environment, and with lower frequency between humans and food. These findings are consistent with human-to-human transmission as an important driver of ARG spread in humans.

BackgroundEarly life gut microbiota is known to shape the immune system and has a crucial role in immune homeostasis. Only little is known about composition and dynamics of the intestinal microbiota in infants with congenital heart disease (CHD) and potential influencing factors.MethodsWe evaluated the intestinal microbial composition of neonates with CHD (n = 13) compared to healthy controls (HC, n = 30). Fecal samples were analyzed by shotgun metagenomics. Different approaches of statistical modeling were applied to assess the impact of influencing factors on variation in species composition. Unsupervised hierarchical clustering of the microbial composition of neonates with CHD was used to detect associations of distinct clusters with intestinal tissue oxygenation and perfusion parameters, obtained by the “oxygen to see” (O2C) method.ResultsOverall, neonates with CHD showed an intestinal core microbiota dominated by the genera Enterococcus (27%) and Staphylococcus (20%). Furthermore, a lower abundance of the genera Bacteroides (8% vs. 14%), Parabacteroides (1% vs. 3%), Bifidobacterium (4% vs. 12%), and Escherichia (8% vs. 23%) was observed in CHD compared to HCs. CHD patients that were born by vaginal delivery showed a lower fraction of the genera Bacteroides (15% vs. 21%) and Bifidobacterium (7% vs. 22%) compared to HCs and in those born by cesarean section, these genera were not found at all. In infants with CHD, we found a significant impact of oxygen saturation (SpO2) on relative abundances of the intestinal core microbiota by multivariate analysis of variance (F[8,2] = 24.9, p = 0.04). Statistical modeling suggested a large proportional shift from a microbiota dominated by the genus Streptococcus (50%) in conditions with low SpO2 towards the genus Enterococcus (61%) in conditions with high SpO2. We identified three distinct compositional microbial clusters, corresponding neonates differed significantly in intestinal blood flow and global gut perfusion.ConclusionEarly life differences in gut microbiota of CHD neonates versus HCs are possibly linked to oxygen levels. Delivery method may affect microbiota stability. However, further studies are needed to assess the effect of potential interventions including probiotics or fecal transplants on early life microbiota perturbations in neonates with CHD.

We evaluated the in vitro activity of cefiderocol in combination with either taniborbactam or xeruborbactam against cefiderocol-resistant, bla NDM -positive Pseudomonas aeruginosa clinical isolates from Vietnam and Nigeria. Taniborbactam restored cefiderocol susceptibility in most isolates (20/21, 95.2%), while xeruborbactam had no effect. Resistance was reversed by dipicolinic acid, which confirmed New-Delhi Metallo-β-Lactamase (NDM-mediated) resistance. One isolate that was unresponsive to taniborbactam carried multiple copies of bla NDM-1 . These findings highlight the species-specific limitations of xeruborbactam in P. aeruginosa .

Background: Extended-spectrum b-lactamase (ESBL)-producing Enterobacterales (ESBLPE) are highly prevalent in long-term care (LTCF) settings. In order to estimate the acquisition rate of ESBL-producing Escherichia coli and Klebsiella pneumoniae in LTCF settings, and identify clinical and environmental risk factors, a multi-centre, prospective cohort study was conducted in six LTCFs in Germany, France, Spain and the Netherlands. Methods: Longitudinal screening of residents was performed over 32 weeks, collecting epidemiological and clinical data and environmental samples. The primary outcome was the rate of new acquisition of ESBL-PE among LTCF residents. Molecular epidemiology was studied using whole genome sequencing, and risk factor analysis was undertaken using logistic and Poisson regression models. Results: In total, 299 residents provided 1958 samples during follow-up. The prevalence of ESBL-PE colonization at baseline was 16.4%, and the incidence of acquisition was 0.79 per 1000 resident-days, both with high variability between LTCFs. Age >= 80 years, vascular disease and antibiotic consumption within the preceding year were risk factors for baseline colonization. Lack of hand sanitizers and a low nurse:resident ratio were associated with colonization. The presence of medical devices was associated with risk of acquisition. Vascular disease, hemiplegia, antibiotic consumption, and non-availability of private bathrooms were associated with carriage of multiple sequence types (STs). The prevalence of ESBL-PE among environmental samples was 2%, exclusively in LTCFs with high prevalence among residents. Genetic analysis showed a high prevalence of ST10 E. coli and ST405 K. pneumoniae at two study sites. Conclusion: Infection prevention interventions, including availability of hand sanitizers, the number of nurses per resident, and antimicrobial stewardship, constitute important measures to control ESBL-PE in LTCFs. Genome-based surveillance could guide targeted interventions. 2025 Published by Elsevier Ltd on behalf of The Healthcare Infection Society.

OBJECTIVES:This study investigated the impact of causative pathogens on the outcomes of central nervous system (CNS) infections and assessed clinical parameters to identify patients at risk for unfavourable outcomes. METHODS:Patients with suspected CNS infections underwent blood and cerebrospinal fluid (CSF) culture and advanced molecular testing, including real-time PCR assays for bacterial and viral pathogens. Patients were classified into clinical categories and their outcomes assessed using the Glasgow Outcome Scale. RESULTS:Pathogens were identified in 24% (80/330) of patients, with Mycobacterium tuberculosis, Klebsiella pneumoniae, and Acinetobacter baumannii being the most common. Mortality was 10%, with fungal meningitis and dual infections having the highest rates. Unfavourable outcomes were observed in 57% of patients. The most common pathogens associated with unfavourable outcomes were M. tuberculosis followed by K. pneumoniae, A. baumannii, and HSV-1. Multivariate analysis identified community-onset infection as a protective factor, while a longer duration of illness before admission (≥5 days) and altered mental status on admission were significant predictors for unfavourable outcomes. Furthermore, the timely administration of appropriate empirical therapy was significantly associated with a reduced risk of mortality. CONCLUSIONS:CNS infections in northern Vietnam have diverse causes and overlapping clinical features, complicating diagnosis and management.

Intraocular infections pose substantial diagnostic challenges due to their varied aetiologies and complex inflammatory responses. The value of combining cytological, microbiological and virological assessments remains underexplored. This extensive retrospective study conducted at a German tertiary care university hospital aims to elucidate the correlation between different inflammatory patterns and detected pathogens in vitreous fluid samples. A retrospective analysis of 374 non-neoplastic vitreous samples from 353 patients was performed, integrating cytological, microbiological and virological data with final clinical diagnoses. Cytological analysis showed 284 instances of lymphocytic uveitis and 76 of granulocytic endophthalmitis. Pathogens were identified in 46 out of 181 microbiologically tested samples; notable pathogens included Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus pneumoniae, Tropheryma whipplei, Candida albicans and Toxoplasma gondii. Virological tests on 188 samples detected viral DNA in 42 cases, predominantly varicella zoster virus and Epstein–Barr virus, correlating well with clinical suspicions of retinitis. Interestingly, no pathogens were found in 67% of the lymphocytic uveitis cases, and multiple pathogens were detected simultaneously in seven instances, suggesting potential latent infections or reactivations. A significant pattern emerged correlating increased neutrophil counts with pathogen detection, highlighting a notable association (p = 0.03) in a subset analysed for both neutrophil levels and pathogen presence. This study offers critical insights into the epidemiology of intraocular infections in Germany, underscoring the importance of comprehensive pathological assessments. It emphasizes the diagnostic value of the underlying inflammatory patterns for predicting pathogen presence and identifies notable cases of infections, including rare pathogens like Tropheryma whipplei.

Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer’s disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in the scope of research in MCI. Therefore, we investigated the ability of longitudinal taxonomic and functional gut microbiome data from 100 healthy controls (HC) to predict the progression from normal cognition to MCI over a 4-year follow-up period (4yFU). Logistic regression models were built with baseline features that best discriminated between the two groups using an ANOVA-type statistical analysis. The best model for the discrimination of MCI converters was based on functional data using Gene Ontology (GO), which included 14 features. This model achieved an area under the receiver operating characteristic curve (AUROC) of 0.84 at baseline, 0.78 at the 1-year follow-up (1yFU), and 0.75 at 4yFU. This functional model outperformed the taxonomic model, which included 38 genera features, in terms of descriptive performance and showed comparable efficacy to combined analyses integrating functional, taxonomic, and clinical characteristics. Thus, gut microbiome algorithms have the potential to predict MCI conversion in HCs over a 4-year period, offering a promising innovative supplement for early AD identification.

BACKGROUND:Small intestinal bacterial overgrowth (SIBO) is a clinical and diagnostic challenge in pediatric intestinal failure. This study aimed to assess SIBO and dysbiosis in children with intestinal failure and to analyze clinical characteristics as well as cultural and metagenomic sequencing results from different sampling methods. METHODS:Descriptive, single-center cohort study in intestinal failure patients with prospective collection of intraluminal aspirate, epithelial brush swab, mucosal biopsy, and small bowel stoma stool for SIBO diagnosis, defined as ≥103 CFU/ml of enteric, colonic-type bacteria, and microbiome analysis via whole-genome sequencing. Statistical testing included receiver operating characteristic analysis, chi-square test, and independent samples t test. RESULTS:Forty-four children with intestinal failure were analyzed (median age 58 months; female 48%; short bowel syndrome 70%). Sixty-six percent of samples were positive for SIBO. In 93%, all three endoscopic sampling methods showed congruent results. SIBO-positive cases were associated (P < 0.05) with small bowel dilatation, proton pump inhibitor use, intestinal inflammation, elevated direct bilirubin and hepatocellular enzyme levels, and a history of liver fibrosis and central venous catheter infections. Metagenomic sequencing revealed microbial dysbiosis in intestinal failure patients, with SIBO-positive cases showing higher microbial reads, lower alpha diversity, and increased abundance of Enterobacteriaceae and enteric anaerobes. CONCLUSION:SIBO and dysbiosis are common in children with intestinal failure and associated with liver injury, central line-associated bloodstream infections, and intestinal inflammation. Cultural diagnosis of SIBO using mucosal biopsies or brush swabs are alternatives to small bowel aspirates. Metagenomic sequencing is feasible, and high microbial read numbers are indicative of SIBO.

Abstract Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.

The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected between February 2020 and January 2021 at a university hospital in Munich, Germany, and analysed along with the place of work, duration of hospital stay, and ward transfers. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. An additional dataset collected at the same time at another university hospital in the same city was used to account for multiple independent introductions. Clustering analysis of 619 viral genomes generated 19 clusters ranging from 3 to 31 individuals. Sequencing-based transmission clusters showed little overlap with those based on contact tracing data. The viral genomes were significantly more closely related to each other than comparable genomes collected simultaneously at other hospitals in the same city (n = 829), suggesting nosocomial transmission. Longitudinal sampling from individual patients suggested possible cross-infection events during the hospital stay in 19.2% of individuals (14 of 73 individuals). Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals.

Objectives To analyse recent epidemiological trends of bloodstream infections (BSI) caused by Enterococcus spp. In adult patients admitted to tertiary care centres in Germany. Methods Epidemiological data from the multicentre R-NET study was analysed. Patients presenting with E. faecium or E. faecalis in blood cultures in six German tertiary care university hospitals between October 2016 and June 2020 were prospectively evaluated. In vancomycin-resistant enterococci (VRE), the presence of vanA / vanB was confirmed via molecular methods. Results In the 4-year study period, 3001 patients with BSI due to Enterococcus spp. were identified. E. faecium was detected in 1830 patients (61%) and E. faecalis in 1229 patients (41%). Most BSI occurred in (sub-) specialties of internal medicine. The pooled incidence density of enterococcal BSI increased significantly (4.0 to 4.5 cases per 10,000 patient days), which was primarily driven by VRE BSI (0.5 to 1.0 cases per 10,000 patient days). In 2020, the proportion of VRE BSI was > 12% in all study sites (range, 12.8–32.2%). Molecular detection of resistance in 363 VRE isolates showed a predominance of the vanB gene (77.1%). Conclusion This large multicentre study highlights an increase of BSI due to E. faecium , which was primarily driven by VRE. The high rates of hospital- and ICU-acquired VRE BSI point towards an important role of prior antibiotic exposure and invasive procedures as risk factors. Due to limited treatment options and high mortality rates of VRE BSI, the increasing incidence of VRE BSI is of major concern.

Background: For Clostridioides difficile infections (CDIs) in Germany no longitudinal multi-centre studies with standardized protocols for diagnosing CDI are available. Recent evaluations of general surveillance databases in Germany indicate a downward trend in CDI rates. We aimed to describe the actual burden and trends of CDI in German university hospitals from 2016 to 2020. Methods: Our study was a prospective multi-centre study covering six German university hospitals. We report the data in total, stratified by year, by medical specialty as well as by CDI severity. Multi-variable regression analyses were performed to assess risk factors for severe CDI. Results: We registered 3780 CDI cases among 1,436,352 patients. The median length of stay (LOS) of CDI cases was 20 days (interquartile range 11-37) compared with a general LOS of 4.2 days. In-hospital all-cause mortality in CDI patients was 11.7% (N = 444/3780), while mortality attributed to CDI was 0.4% (N = 16/3761). CDI recurrence rate was comparatively low at 7.2%. The incidence density of severe healthcare-associated healthcare onset (HAHO)-CDI showed a significant decrease from 2.25/10,000 patient days (pd) in 2016 to 1.49/10,000 pd in 2020 (trend calculation P=0.032). Conclusions: Compared with a European point-prevalence study in 2013/2014, where overall CDI incidence density was 11.2 cases/10,000 pd in Germany (EUCLID), we see in our study halved overall CDI rates of 5.6 cases/10,000 pd in 2020. Our study shows current data on the distribution of CDI cases in German university hospitals and thus provides international comparative data on the key indicators of CDI. under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

OXA-48-like enzymes represent the most frequently detected carbapenemases in Enterobacterales in Western Europe, North Africa and the Middle East. In contrast to other species, the presence of OXA-48-like in Proteus mirabilis leads to an unusually susceptible phenotype with low MICs for carbapenems and piperacillin-tazobactam, which is easily missed in the diagnostic laboratory. So far, there is little data available on the genetic environments of the corresponding genes, blaOXA-48-like, in P. mirabilis. In this study susceptibility phenotypes and genomic data of 13 OXA-48-like-producing P. mirabilis were investigated (OXA-48, n=9; OXA-181, n=3; OXA-162, n=1). Ten isolates were susceptible to meropenem and ertapenem and three isolates were susceptible to piperacillin-tazobactam. The gene blaOXA-48 was chromosomally located in 7/9 isolates. Thereof, in three isolates blaOXA-48 was inserted into a P. mirabilis genomic island. Of the three isolates harbouring blaOXA-181 one was located on an IncX3 plasmid and two were located on a novel MOBF plasmid, pOXA-P12, within the new transposon Tn7713. In 5/6 isolates with plasmidic location of blaOXA-48-like, the plasmids could conjugate to E. coli recipients in vitro. Vice versa, blaOXA-48-carrying plasmids could conjugate from other Enterobacterales into a P. mirabilis recipient. These data show a high diversity of blaOXA-48-like genetic environments compared to other Enterobacterales, where genetic environments are quite homogenous. Given the difficult-to-detect phenotype of OXA-48-like-producing P. mirabilis and the location of blaOXA-48-like on mobile genetic elements, it is likely that OXA-48-like-producing P. mirabilis can disseminate, escape most surveillance systems, and contribute to a hidden spread of OXA-48-like.

Introduction Syndromic panel assays, that is, using one test to simultaneously target multiple pathogens with overlapping signs and symptoms, have been integrated into routine paediatric care over the past decade, mainly for more severely ill and hospitalised patients. Their wider availability and short turnaround times open the possibility to apply them to non-hospitalised patients as well. In this context, it is important to trial how clinicians make use of pathogen detection data and if their early availability influences management decisions, particularly antibiotic use and hospitalisation.Methods and analysis Advanced Diagnostics for Enhanced QUality of Antibiotic prescription in respiratory Tract infections in Emergency rooms is an individually randomised, controlled, open-label effectiveness trial comparing the impact of a respiratory pathogen panel assay (BIOFIRE Respiratory Panel 2.1plus) used as a rapid syndromic test on nasopharyngeal swabs in addition to the standard of care versus standard of care alone. The trial will 1:1 randomise 520 participants under the age of 18 at 7 paediatric emergency departments in 5 European countries. Inclusion criteria for the trial consist of two sets, with the first describing respiratory tract infections in paediatric patients and the second describing the situation of potential management uncertainty in which test results may immediately affect management decisions. Enrolment started in July 2021 and is expected to be completed in early 2024. We will perform a two-sample t-test assuming a pooled variance estimate to compare the log-transformed mean time on antibiotic treatment (in hours) and number of days alive out of the hospital within 14 days after study enrolment between the control and intervention arms.Ethics and dissemination The trial protocol and materials were approved by research ethics committees in all participating countries. The respiratory pathogen panel assay is CE marked (assessed to meet European regulations) and FDA (United States Food and Drug Administration) cleared for diagnostic use. Participants and caregivers provide informed consent prior to study procedures commencing. The trial results will be published in peer-reviewed journals and at national and international conferences. Key messages will also be disseminated via press and social media where appropriate.Trial registration number NCT04781530.

Alterations in the gut microbiome are associated with the pathogenesis of Alzheimer’s disease (AD) and can be used as a diagnostic measure. However, longitudinal data of the gut microbiome and knowledge about its prognostic significance for the development and progression of AD are limited. The aim of the present study was to develop a reliable predictive model based on gut microbiome data for AD development. In this longitudinal study, we investigated the intestinal microbiome in 49 mild cognitive impairment (MCI) patients over a mean (SD) follow-up of 3.7 (0.6) years, using shotgun metagenomics. At the end of the 4-year follow-up (4yFU), 27 MCI patients converted to AD dementia and 22 MCI patients remained stable. The best taxonomic model for the discrimination of AD dementia converters from stable MCI patients included 24 genera, yielding an area under the receiver operating characteristic curve (AUROC) of 0.87 at BL, 0.92 at 1yFU and 0.95 at 4yFU. The best models with functional data were obtained via analyzing 25 GO (Gene Ontology) features with an AUROC of 0.87 at BL, 0.85 at 1yFU and 0.81 at 4yFU and 33 KO [Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog] features with an AUROC of 0.79 at BL, 0.88 at 1yFU and 0.82 at 4yFU. Using ensemble learning for these three models, including a clinical model with the four parameters of age, gender, body mass index (BMI) and Apolipoprotein E (ApoE) genotype, yielded an AUROC of 0.96 at BL, 0.96 at 1yFU and 0.97 at 4yFU. In conclusion, we identified novel and timely stable gut microbiome algorithms that accurately predict progression to AD dementia in individuals with MCI over a 4yFU period.