Introduction The interaction between the gut microbiota and the host immune system is implicated in the pathogenesis of inflammatory bowel disease, including ulcerative colitis (UC). Targeting the gut microbiota with faecal microbiota transplantation (FMT) from a healthy donor has shown promise in inducing remission in patients with active UC. However, mixed results and protocol heterogeneity have limited its practical application. Our previous Transfer of Faeces in Ulcerative Colitis; Restoring Homeostasis (TURN) trial found a correlation of clinical response with specific strains and butyrate production. Since most gut microbes, including many butyrate producers, are anaerobes, anoxic processing of donor stool may be essential to increase efficacy of FMT in UC. This trial aims to enhance FMT efficacy by applying strict anoxic processing, selecting donors based on microbial composition and using repetitive dual-route administration.Methods and analysis This randomised, double-blind, placebo-controlled, multicentre study evaluates the efficacy of strictly anoxic prepared donor FMT compared with anoxic prepared autologous FMT in patients with mild to moderate active UC. An open-label extension option is available for non-responders in the autologous arm. Included patients will receive 4 weekly FMTs, comprising two double-route administrations (nasoduodenal administration combined with enema) and two single enemas. Donors are selected based on their microbiota profile, informed by our previous TURN trial and literature. A total of 76 patients evaluable for the primary endpoint will be included. The primary endpoint is steroid-free clinical and endoscopic remission at week 8, assessed by the adapted Mayo score. An interim analysis will be conducted midway through the study by a Data Safety Monitoring Board to monitor efficacy and safety. Other outcomes of this study include the evaluation of clinical, endoscopic and histological response. In addition to clinical results, this study aims to provide valuable insights into specific microbial strains, metabolites and mechanisms correlated with response, aiding in the development of future microbial therapies.Ethics and dissemination Ethics approval was obtained from the medical ethics committee of the Amsterdam University Medical Centre in the Netherlands (reference number 2018_057). All participants will provide written informed consent. The results of the trial will be disseminated through publication in a peer-reviewed journal and presentations at (inter)national conferences.Trial registration number Prospectively registered in May 2018 in the Dutch Trial Register (NTR/LTR) as NL7770. Assigned NL-OMON52507 following the transition of the Dutch Trial Register to the Overview of Medical Research in the Netherlands. Also registered at ClinicalTrials.gov (NCT05998213).

OBJECTIVES: To determine (1) the rate of positive cultures in presumed aseptic nonunions, (2) the rate and microbial spectrum of positive cultures that represented occult infection, and (3) rates of nonunion healing. METHODS: Design: Retrospective cohort study. Setting: Tertiary referral center. Patients Selection Criteria: Adult patients with a presumed aseptic nonunion treated with single-stage revision between 2002 and 2022. Outcome Measures and Comparisons: The rate of positive cultures compared for 2 protocols: old: 1-2 samples cultured 7 days versus new: 5 samples cultured 14 days. The rate of positive cultures meeting occult infection criteria with the new protocol (>= 2 samples with phenotypically indistinguishable microorganisms, or >= 1 sample with a high virulent microorganism). Nonunion healing rates between protocols and between groups based on culture results with the new protocol. RESULTS: One hundred seventy-nine patients were included. The rate of positive cultures was 14% (n = 15/105) with the old protocol and 51% (n = 38/74) with the new protocol (P < 0.001). With the new protocol, the rate of positive cultures meeting occult infection criteria was 19% (n = 14/74), and coagulase-negative staphylococci (48%) and Cutibacterium acnes (38%) were the most common microorganisms. Nonunion healing rates after the primary revision did not differ between protocols (old: 82% vs. new: 86%, P = 0.41) and groups based on culture result (sterile: 86% vs. occultly infected: 93%, P = 0.66). The final overall nonunion healing rate was 97%. CONCLUSIONS: Occult infections were identified in 1 in 5 presumed aseptic nonunions using a standardized protocol with 5 intraoperative samples cultured 14 days and were predominantly caused by slow growing, gram-positive microorganisms. The local spectrum and antimicrobial sensitivity of occult infections should be considered when developing empiric antimicrobial protocols. Patients with presumed aseptic nonunions can expect high healing rates, regardless of the culture result.

Introduction In pre-operatively presumed aseptic nonunions, the definitive diagnosis of infection relies on intraoperative cultures. Our primary objective was to determine (1) the rate of surprise positive intraoperative cultures in presumed aseptic long-bone nonunion (surprise positive culture nonunion), and (2) the rate of surprise positive cultures that represent infection vs. contamination. Secondary objectives were to determine the healing and secondary surgery rates and to identify cultured micro-organisms. Materials and Methods We performed a systematic literature search of PubMed, Embase and Cochrane Libraries from 1980 until December 2021. We included studies reporting on ≥ 10 adult patients with a presumed aseptic long-bone nonunion, treated with a single-stage surgical protocol, of which intraoperative cultures were reported. We performed a meta-analysis for: (1) the rates of surprise positive culture nonunion, surprise infected nonunion, and contaminated culture nonunion, and (2) healing and (3) secondary surgery rates for each culture result. Risk of bias was assessed using the QUADAS-2 tool. Results 21 studies with 2,397 patients with a presumed aseptic nonunion were included. The rate of surprise positive culture nonunion was 16% (95%CI: 10–22%), of surprise infected nonunion 10% (95%CI: 5–16%), and of contaminated culture nonunion 3% (95%CI: 1–5%). The secondary surgery rate for surprise positive culture nonunion was 22% (95%CI: 9–38%), for surprise infected nonunion 14% (95%CI 6–22%), for contaminated culture nonunion 4% (95%CI: 0–19%), and for negative culture nonunion 6% (95CI: 1–13%). The final healing rate was 98% to 100% for all culture results. Coagulase-negative staphylococci accounted for 59% of cultured micro-organisms. Conclusion These results suggest that surprise positive cultures play a role in the clinical course of a nonunion and that culturing is important in determining the etiology of nonunion, even if the pre-operative suspicion for infection is low. High healing rates can be achieved in presumed aseptic nonunions, regardless of the definitive intraoperative culture result.

AimsPharmacokinetic/pharmacodynamic target attainment of ceftriaxone is compromised in intensive care unit (ICU) patients and non-ICU hospitalized patients in Beira, Mozambique. Whether this also accounts for non-ICU patients in a high-income setting is unknown. We therefore assessed the probability of target attainment (PTA) of the currently recommended dosing regimen of 2 g every 24 h (q24h) in this patient group. MethodsWe performed a multicentre population pharmacokinetic study in hospitalized non-ICU adult patients empirically treated with intravenous ceftriaxone. During both the acute phase of infection (i.e. first 24 h of treatment) and convalescence, a maximum of 4 random blood samples were obtained per patient for ceftriaxone total and unbound concentration measurements. PTA was calculated using NONMEM and was defined as the percentage of patients of which the unbound ceftriaxone concentration exceeded the minimum inhibitory concentration (MIC) for >50% of the first dosing interval of 24 h. Monte Carlo simulations were performed to determine PTA for different estimated glomerular filtration rates (eGFR; CKD-EPI) and MICs. PTA >90% was considered adequate. ResultsForty-one patients provided 252 ceftriaxone total and 253 unbound concentrations. The median eGFR was 65 mL/min/1.73 m(2) (5th to 95th percentile 36-122). With the recommended dose of 2 g q24h, PTA >90% was achieved for bacteria with an MIC & LE;2 mg/L. Simulations showed that PTA was insufficient for an MIC of 4 mg/L in case the eGFR was 122 mL/min/1.73 m(2) (PTA 56.9%) and for an MIC of 8 mg/L regardless of eGFR. ConclusionThe PTA of 2 g q24h ceftriaxone dosing is adequate for common pathogens during the acute phase of infection in non-ICU patients.

Abstract Objectives Evaluation of the appropriateness of the duration of antimicrobial treatment is a cornerstone of antibiotic stewardship programs, but it is time-consuming. Furthermore, it is often restricted to antibiotics prescribed during hospital admission. This study aimed to determine whether mandatory prescription-indication registration at the moment of prescribing antibiotics enables reliable automated assessment of the duration of antibiotic therapy, including post-discharge duration, limiting the need for manual chart review to data validation. Methods Antibiotic prescription and admission data, from 1-6-2020 to 31-12-2021, were electronically extracted from the Electronic Medical Record of two hospitals using mandatory indication registration. All consecutively prescribed antibiotics of adult patients who received empiric therapy in the first 24 h of admission were merged to calculate the total length of therapy (LOT) per patient, broken down per registered indication. Endpoints were the accuracy of the data, evaluated by comparing the extracted LOT and registered indication with the clinical notes in 400 randomly selected records, and guideline adherence of treatment duration. Data were analysed using a reproducible syntax, allowing semi-automated surveillance. Results A total of 3,466 antibiotic courses were analysed. LOT was accurately retrieved in 96% of the 400 evaluated antibiotic courses. The registered indication did not match chart review in 17% of antibiotic courses, of which only half affected the assessment of guideline adherence. On average, in 44% of patients treatment was continued post-discharge, accounting for 60% (± 19%) of their total LOT. Guideline adherence ranged from 26 to 75% across indications. Conclusions Mandatory prescription-indication registration data can be used to reliably assess total treatment course duration, including post-discharge antibiotic duration, allowing semi-automated surveillance.

Objectives This is a protocol for a Cochrane Review (diagnostic). The objectives are as follows: Secondary objectives To assess the influence of patient and study characteristics on the diagnostic accuracy of the index tests. To assess the influence of different reference standards for UTI on the diagnostic accuracy of the index tests.

Staphylococcus pseudintermedius can be transmitted between dogs and their owners and can cause opportunistic infections in humans. Whole genome sequencing was applied to identify the relatedness between isolates from human infections and isolates from dogs in the same households. Genome SNP diversity and distribution of plasmids and antimicrobial resistance genes identified related and unrelated isolates in both households. Our study shows that within-host bacterial diversity is present in S. pseudintermedius, demonstrating that multiple isolates from each host should preferably be sequenced to study transmission dynamics.

Background Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine. Methods In this proof-of-concept study, we prospectively included consecutive urine samples from a clinical diagnostic laboratory in Amsterdam. Urine samples were screened by DNA concentration, followed by PCR-free metagenomic sequencing of randomly selected samples with a high concentration of DNA (culture positive and negative). A diagnostic index was calculated as the product of DNA concentration and fraction of pathogen reads. We compared results with semi-quantitative culture using area under the receiver operating characteristic curve (AUROC) analyses. We used ResFinder and PointFinder for resistance gene detection and compared results to phenotypic antimicrobial susceptibility testing for six antibiotics commonly used for urinary tract infection treatment: nitrofurantoin, ciprofloxacin, fosfomycin, cotrimoxazole, ceftazidime, and ceftriaxone. Findings We screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0.85 (95% CI 0.81-0.89). At a cutoff value of 6.0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87-93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0.87 (95% CI 0.79-0.95). A diagnostic index cutoff value of 17.2 yielded a positive predictive value of 93% (95% CI 85-97) and a negative predictive value of 69% (55-80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested. Interpretation This study provides proof-of-concept of metagenomic semi-quantitative pathogen and resistome detection for the diagnosis of urinary tract infection. The findings warrant prospective clinical validation of the value of this approach in informing patient management and care. Copyright (c) 2022 The Author(s). Published by Elsevier Ltd.

Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS), which are not suitable methods for real-time transmission screening of both susceptible and resistant bacteria. The aim was to assess the typing technique Fourier transform infrared (FTIR) spectroscopy as real-time screening method to discriminate large amounts of susceptible and resistant bacteria at strain level when there is no evident outbreak in comparison with the WGS reference. Isolates of past hospital outbreak strains of Acinetobacter baumannii/calcoaceticus complex ( n = 25), Escherichia coli ( n = 31), Enterococcus faecium ( n = 22), Staphylococcus aureus ( n = 37) and Pseudomonas aeruginosa ( n = 30) were used for validation of FTIR. Subsequently, Enterococcus faecalis ( n = 106) and Enterococcus faecium ( n = 104) isolates from weekly routine screening samples when no potential outbreak was present were analysed. FTIR showed reproducibility and congruence of cluster composition with WGS for A. baumannii/calcoaceticus complex and E. faecium outbreak isolates. The FTIR results of E. faecalis and E. faecium isolates from routine samples showed reproducibility, but the congruence of cluster composition with WGS was low. For A. baumannii/calcoaceticus complex and E. faecium outbreak isolates, FTIR appears to be a discriminatory typing tool. However, our study shows the discriminatory power is too low to screen real-time for transmission of E. faecium and E. faecalis at patient wards based on isolates acquired in routine surveillance cultures when there is no clear suspicion of an ongoing outbreak.

Staphylococcus pseudintermedius is an important pathogen in dogs that occasionally causes infections in humans as an opportunistic pathogen of elderly and immunocompromised people. This study compared the genomic relatedness and antimicrobial resistance genes using genome-wide association study (GWAS) to examine host association of canine and human S. pseudintermedius isolates. Canine (n = 25) and human (n = 32) methicillin-susceptible S. pseudintermedius (MSSP) isolates showed a high level of genetic diversity with an overrepresentation of clonal complex CC241 in human isolates. This clonal complex was associated with carriage of a plasmid containing a bacteriocin with cytotoxic properties, a CRISPR-cas domain and a pRE25-like mobile element containing five antimicrobial resistance genes. Multi-drug resistance (MDR) was predicted in 13 (41%) of human isolates and 14 (56%) of canine isolates. CC241 represented 54% of predicted MDR isolates from humans and 21% of predicted MDR canine isolates. While it had previously been suggested that certain host-specific genes were present the current GWAS analysis did not identify any genes that were significantly associated with human or canine isolates. In conclusion, this is the first genomic study showing that MSSP is genetically diverse in both hosts and that multidrug resistance is important in dog and human-associated S. pseudintermedius isolates.

Objective: There is unmet need for an easy, noninvasive urine collection method to diagnose urinary tract infections (UTIs) in nursing home residents suffering from urinary incontinence or cognitive impairments. UTIs are highly prevalent in nursing home residents, and urine specimen collection can be difficult. The objective of this study was to assess if urine specimens collected from super-absorbing incontinence pads (adult diapers) are a reliable collection method for UTI diagnosis. Design: This was a paired noninferiority laboratory study, in which pairing refers to UTI diagnostics performed directly using clinical urine specimens (reference specimen) and indirectly using urine extracted from diapers (diaper specimen). Setting and participants: In this study, remnants of 250 clinical urine specimens were used to assess noninferiority in diagnosing UTIs, based on a 1-sided type I error of 2.5%, a power of 90%, and a non inferiority margin of 15%. Methods: Urine specimens were poured on super-absorbing disposable adult diapers and extracted after 3 hours, to use for dipstick urinalysis and bacterial culture. UTIs were defined as presence of leukocytes and a positive bacterial culture. Noninferiority was assessed by calculating a Wald-type test statistic. Results: Noninferiority was established for diagnosing UTIs in diaper specimens, and for each of its components (dipstick leukocyte detection and bacterial culture positivity). Positive bacterial cultures were found in 72 (29.0%) diaper specimens compared with 65 (26.2%) reference specimens (difference-2.8%, 97.5% CI-7.1% to 1.5%). Leukocytes were present in 162 (64.8%) diaper specimens, compared with 175 (70.0%) reference specimens (difference-5.7%, 97.5% CI:-10.6% to-0.7%). Conclusion and implications: Our results on diagnosing UTIs, by dipstick analysis and bacterial cultures, using super-absorbing adult diapers are promising. Before translation into clinical practice, further studies are needed to evaluate the risk of bacterial contamination by wearing adult diapers, possibly resulting in overdiagnosis of UTI. (C) 2020 The Author(s). Published by Elsevier Inc. on behalf of AMDA - The Society for Post-Acute and Long-Term Care Medicine. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Background We defined the frequency of respiratory community-acquired bacterial co-infection in patients with COVID-19, i.e. patients with a positive SARS-CoV-2 PCR or a COVID-19 Reporting and Data System (CO-RADS) score ≥ 4, based on a complete clinical assessment, including prior antibiotic use, clinical characteristics, inflammatory markers, chest computed tomography (CT) results and microbiological test results. Methods Our retrospective study was conducted within a cohort of prospectively included patients admitted for COVID-19 in our tertiary medical centres between 1-3-2020 and 1-6-2020. A multidisciplinary study team developed a diagnostic protocol to retrospectively categorize patients as unlikely, possible or probable bacterial co-infection based on clinical, radiological and microbiological parameters in the first 72 h of admission. Within the three categories, we summarized patient characteristics and antibiotic consumption. Results Among 281 included COVID-19 patients, bacterial co-infection was classified as unlikely in 233 patients (82.9%), possible in 35 patients (12.4%) and probable in 3 patients (1.1%). Ten patients (3.6%) could not be classified due to inconclusive data. Within 72 h of hospital admission, 81% of the total study population and 78% of patients classified as unlikely bacterial co-infection received antibiotics. Conclusions COVID-19 patients are unlikely to have a respiratory community-acquired bacterial co-infection. This study underpins recommendations for restrictive use of antibacterial drugs in patients with COVID-19.

Background The systemic response to an infection might influence the pharmacokinetics of antibiotics. To evaluate the desired possibility of an earlier (< 24 h) IV-to-oral switch therapy in febrile non-ICU, hospitalized patients, a systematic review was performed to assess the effect of the initial phase of a systemic infection on the bioavailability of orally administered antibiotics in such patients. Methods An electronic search was conducted in MEDLINE and Embase up to July 2020. Studies were selected when outcome data were collected during the initial stage of a febrile disease. Outcome data were (maximum) serum concentrations, time of achieving maximum serum concentration, and the area-under-the-plasma-concentration-time curve or bioavailability of orally administered antibiotics. Risk of bias was assessed. Results We identified 9 studies on 6 antibiotics. Ciprofloxacin was the most frequently studied drug. Outcomes of the studies were heterogeneous and generally had a high risk of bias. Three small studies, two on ciprofloxacin and one on clarithromycin, compared the pharmacokinetics of febrile patients with those of clinically recovered patients and suggested that bioavailability was not altered in these patients. Other studies either compared the pharmacokinetics in febrile patients with reported pharmacokinetic values from earlier studies in healthy volunteers ( n = 2), or provided no comparison at all and were non-conclusive ( n = 4). Conclusion There is a clear knowledge gap regarding the bioavailability of orally administered antibiotics in non-ICU patients during the initial phase of a systemic infection. Well-designed studies on this topic are necessary to elucidate whether patients can benefit from the advantages of an earlier IV-to-oral switch.

Objectives Antimicrobial Stewardship Programs commonly have an in-hospital focus. Little is known about the quality of antimicrobial use in hospital outpatient clinics. We investigated the extent and appropriateness of antimicrobial prescriptions in the outpatient clinics of three hospitals. Methods From June 2018 to January 2019, we performed ten point prevalence surveys in outpatient clinics of one university hospital and two large teaching hospitals. All prophylactic and therapeutic prescriptions were retrieved from the electronic medical records. Appropriateness was defined as being in accordance with guidelines. Furthermore, we investigated the extent to which the dose was adjusted to renal function and documentation of an antibiotic plan in the case notes. Results We retrieved 720 prescriptions for antimicrobial drugs, of which 173 prescriptions (24%) were prophylactic. A guideline was present for 95% of prescriptions, of which the guideline non-adherence rate was 25.6% (n = 42/164) for prophylaxis and 43.1% (n = 224/520) for therapy. Of all inappropriate prescriptions (n = 266), inappropriate prescriptions for skin and soft tissue infections (n = 60/226) and amoxicillin-clavulanic acid (n = 67/266) made up the largest proportion. In only 13 of 138 patients with impaired or unknown renal function the dosage regimen was adjusted. Amoxicillin-clavulanic acid was the drug for which most often renal function was not taken into account. In 94.6% of prescriptions the antibiotic plan was documented. Conclusions In hospital outpatient clinics, a substantial part of therapeutics were inappropriately prescribed. Amoxicillin-clavulanic acid was the most inappropriately prescribed drug, due to non-adherence to the guidelines and because dose adjustment to renal function was often not considered.

Abstract Background Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months. Methods Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors. Results Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4–5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward. Conclusion AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.

Notice of Retraction and Replacement: Oostdijk et al. Effects of Decontamination of the Oropharynx and Intestinal Tract on Antibiotic Resistance in ICUs: A Randomized Clinical Trial. JAMA. 2014;312(14):1429-1437.

Background: The prophylactic use of antimicrobial agents to prevent infections in non-surgical situations has hardly been investigated. We investigate the extent, indications and appropriateness of antimicrobial prophylaxis given outside the operating room in a tertiary care hospital.Methods: Four point-prevalence surveys were conducted in which all inpatients on that day were screened for the use of prophylactic antimicrobials: medical prophylaxis, prophylaxis around non-surgical interventions and surgical prophylaxis given on the ward. The primary endpoint was the extent of prophylaxis relative to the total number of antimicrobial prescriptions. We also investigated per prescription the presence of a (local) protocol and adherence to these protocols.Results: We registered in total 1020 antimicrobial prescriptions, of which 317 (31.1%) were given as prophylaxis. 827/ 1020 were antibiotic prescriptions. Of these antibiotic prescriptions, 17.0% was medical prophylaxis, 2.7% prophylaxis around non-surgical interventions and 6.9% surgical prophylaxis administered on a ward. For medical antibiotic prophylaxis, a protocol was present in 125 of 141 prescriptions (88.7%); the protocol was followed in 118 cases (94.4%). For prophylaxis around non-surgical interventions and surgical prophylaxis on the wards, protocol presence and adherence rates were 59.1% and 92.3%, and 73.3% and 97.6% respectively. Of the 96 antiviral and 97 antifungal prescriptions, 42.7% and 57.8%, respectively, were medical prophylaxis, of which 95.1 and 96.3% were prescribed according to protocols respectively.Conclusions: Antimicrobial prophylaxis outside the operating theatre is responsible for a considerable part of total in-hospital antimicrobial use. For most prescriptions there was a protocol and adherence to the protocols was high. The main targets for improvement were prophylaxis around non-surgical interventions and surgical prophylaxis given on the ward.

Semi-quantitative bacterial culture is the standard method to diagnose urinary tract infections (UTI), but bacterial growth rate limits diagnostic speed and it is unreliable when patients have been pre-treated with antibiotics. Metagenomics could increase diagnostic speed and accuracy by sequencing the microbiome and resistome directly from urine samples, bypassing culture. However, a semi-quantitative approach – as needed for diagnosing UTIs – has not been established.Metagenomics was deployed to identify and semi-quantify bacterial presence indicative of UTI, predict antimicrobial susceptibility (AMR), and results were compared to semi-quantitative culture. Whole genome sequencing of the corresponding uropathogens was done for comparison. Analysis time and cost were tracked.Forty-one consecutive urine samples underwent metagenomic analysis. All culture positive samples contained >200ng of DNA, suggestive of a threshold below which UTI could be ruled out solely based on DNA quantity. A semi-quantitative Diagnostic Index (DI) was created by multiplying the total DNA quantity by the relative abundance of uropathogens per urine sample. The DI allowed discrimination of UTI from non-UTI samples in all but 1 case. Metagenomic detection of AMR determinants correctly predicted the phenotype of uropathogens in 20 of 32 cases. The metagenomic work-flow was 31h and cost €116 per sample, but could be reduced to 4.5h and €5 for low-DNA-yield non-UTI samples.The genomic determinants of AMR and their distribution across uropathogens need to be better understood for prediction of AMR phenotypes by metagenomics. The introduction of the DI demonstrates the potential of semi-quantitative metagenomics to replace culture as rapid diagnostic method for UTI.

Tuberculosis is a devastating infectious disease causing many deaths worldwide. Recent investigations have implicated neutrophil extracellular traps (NETs) in the host response to tuberculosis. The aim of the current study was to obtain evidence for NETs release in the circulation during human tuberculosis. For this we measured the plasma concentrations of nucleosomes in conjunction with neutrophil elastase, in 64 patients with active pulmonary tuberculosis and 32 healthy controls. Patients with active tuberculosis had elevated plasma levels of nucleosomes and elastase when compared with local healthy blood donors. Furthermore nucleosome and elastase levels showed a positive correlation. These findings provide the first evidence for the release of NETs in the circulation of patients with active pulmonary tuberculosis.

Hard-tick-borne relapsing fever (HTBRF) is an emerging infectious disease throughout the temperate zone caused by the relapsing-fever spirochete Borrelia miyamotoi. Antibiotic treatment of HTBRF is empirically based on the treatment of Lyme borreliosis; however, the antibiotic susceptibility of B. miyamotoi has not been studied to date. Thus, we set out to determine the in vitro antimicrobial susceptibility of B. miyamotoi. A microdilution method with 96-well microtiter plates was used to determine the antibiotic susceptibilities of two B. miyamotoi strains isolated on two different continents (Asia and North America), two Borrelia burgdorferi sensu lato strains, and one Borrelia hermsii isolate for purposes of comparison. The MIC and minimal bactericidal concentration (MBC) were determined by both microscopy and colorimetric assays. We were able to show that relative to the B. burgdorferi sensu lato isolates, both B. miyamotoi strains and B. hermsii demonstrated greater susceptibility to doxycycline and azithromycin, equal susceptibility to ceftriaxone, and resistance to amoxicillin in vitro. The MIC and MBC of amoxicillin for B. miyamotoi evaluated by microscopy were 16 to 32 mg/liter and 32 to 128 mg/liter, respectively. Since B. miyamotoi is susceptible to doxycycline, azithromycin, and ceftriaxone in vitro, our data suggest that these antibiotics can be used for the treatment of HTBRF. Oral amoxicillin is currently used as an alternative for the treatment of HTBRF; however, since we found that the B. miyamotoi strains tested were resistant to amoxicillin in vitro, this issue warrants further study.