Search

Abdul Khairul Rizki Purba,1– 4 Christian F Luz,2 Riyanti R Wulandari,5 Ieneke van der Gun,2 Jan-Willem Dik,2 Alex W Friedrich,2 Maarten J Postma1,3,4,6 1Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; 2University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; 3Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; 4Unit of Pharmacotherapy, -Epidemiology and -Economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, the Netherlands; 5Department of Pharmacy, Dinas Kesehatan Kota Surabaya, Surabaya, Indonesia; 6Department of Economics, Econometrics and Finance, Faculty of Economics & Business, University of Groningen, Groningen, the NetherlandsCorrespondence: Abdul Khairul Rizki PurbaUniversitair Medisch Centrum Groningen, Hanzeplein 1, Groningen 9700RB, the Netherlands, Tel +62 81230019201Email khairul_purba@fk.unair.ac.idObjective: This study aimed to evaluate the impacts of deep surgical site infections (dSSIs) regarding hospital readmissions, prolonged length of stay (LoS), and estimated costs.Patients and Methods: We designed and applied a matched case–control observational study using the electronic health records at the University Medical Center Groningen in the Netherlands. We compared patients with dSSI and non-SSI, matched on the basis of having similar procedures. A prevailing topology of surgeries categorized as clean, clean-contaminated, contaminated, and dirty was applied.Results: Out of a total of 12,285 patients, 393 dSSI were identified as cases, and 2864 patients without SSIs were selected as controls. A total of 343 dSSI patients (87%) and 2307 (81%) controls required hospital readmissions. The median LoS was 7 days (P25-P75: 2.5– 14.5) for dSSI patients and 5 days (P25-P75: 1– 9) for controls (p-value: < 0.001). The estimated mean cost per hospital admission was € 9,016 (SE± 343) for dSSI patients and € 5,409 (SE± 120) for controls (p< 0.001). Independent variables associated with dSSI were patient’s age ≥ 65 years (OR: 1.334; 95% CI: 1.036– 1.720), the use of prophylactic antibiotics (OR: 0.424; 95% CI: 0.344– 0.537), and neoplasms (OR: 2.050; 95% CI: 1.473– 2.854).Conclusion: dSSI is associated with increased costs, prolonged LoS, and increased readmission rates. Elevated risks were seen for elderly patients and those with neoplasms. Additionally, a protective effect of prophylactic antibiotics was found.Keywords: surgical wound infection, prophylactic antibiotic, patient admission, economic evaluation, cost

Abdul KR Purba,1–5 Purwantyastuti Ascobat,4 Armen Muchtar,4 Laksmi Wulandari,6 Alfian Nur Rosyid,6 Priyo Budi Purwono,7 Tjip S van der Werf,8 Alex W Friedrich,2 Maarten J Postma1,3,5,9 1Unit of Global Health, Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; 2Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; 3Department of Pharmacology and Therapy, Faculty of Medicine, Universitas Airlangga – Dr. Soetomo Hospital, Surabaya, Indonesia; 4Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; 5Unit of PharmacoTherapy, Epidemiology and -economics (PTE2), Department of Pharmacy, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands; 6Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga – Dr. Soetomo Hospital, Surabaya, Indonesia; 7Department of Microbiology, Faculty of Medicine, Universitas Airlangga – Dr. Soetomo Hospital, Surabaya, Indonesia; 8Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; 9Department of Economics, Econometrics and Finance, Faculty of Economics & Business, University of Groningen, Groningen, The NetherlandsCorrespondence: Abdul KR PurbaUniversitair Medisch Centrum Groningen, Hanzeplein 1, Groningen 9700RB, The NetherlandsTel +31 697 52 411Email khairul_purba@fk.unair.ac.idObjectives: To evaluate the clinical and microbiological appearance among hospitalized pneumonia patients focusing on resistance and risk factors for mortality in a referral hospital.Patients and methods: The study was an observational retrospective study on patients with CAP from 2014 to 2016 at Dr Soetomo referral hospital of Surabaya, Indonesia. All positive cultures with antimicrobial susceptibility results from blood and respiratory specimens were included. Patients infected with drug-susceptible pathogens and MDR organisms were also assessed in terms of clinical characteristics, day-3 clinical improvement, and 14-day mortality.Results: Of 202 isolates, 181 possessed antimicrobial susceptibility data. S. pneumoniae was the most prevalent pathogen causing CAP (18.3%). Most patients were empirically treated with ceftriaxone (n=75; 41.4%). Among beta-lactam antibiotics, the susceptibility to the third-generation cephalosporins remained relatively high, between 67.4% and 82.3%, compared with the other beta-lactams such as amoxicillin/clavulanate and ampicillin/sulbactam (a sensitivity rate of 36.5% and 47.5, respectively). For carbapenem antibiotics, imipenem and meropenem susceptibility was 69.6% and 82.3% respectively. Approximately 22% of isolates were identified as MDR that showed significant differences in clinical outcomes of 14-day mortality rates (p

Erik Bathoorn,1 Feikje Groenhof,2 Ron Hendrix,1,3 Thys van der Molen,2,4 Bhanu Sinha,1 Huib AM Kerstjens,5 Alex W Friedrich,1 Janwillem WH Kocks2,4 1Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; 2Department of Primary Care, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; 3Department of Pulmonary Diseases and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; 4Department of Medical Microbiology, Certe – Laboratory for Infectious Diseases, Groningen, the Netherlands; 5GRIAC Research Institute, Groningen, University of Groningen, University Medical Center Groningen, the Netherlands Background: Acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are generally treated with optimization of bronchodilation therapy and a course of oral corticosteroids, mostly without antibiotics. The Dutch guidelines recommend prudent use of antibiotics, with amoxicillin or doxycycline as first choice. Here we evaluate adherence to these guidelines with regard to antibiotic prescription in AECOPD in primary care and the use of sputum cultures. Methods: We retrospectively analyzed a longitudinal cohort of patients in three primary care practices in the north-eastern region of the Netherlands from 2009 to 2013 (n=36,172 subjects) participating in the Registration Network Groningen. Antibiotics prescribed for AECOPD -10/+28 days from the start date of corticosteroid courses were evaluated. In addition, we assessed regional data on the susceptibility of respiratory pathogens from COPD patients. Results: We identified 1,297 patients with COPD. Of these, 616 experienced one or more exacerbations, resulting in a total of 1,558 exacerbations, for which 1,594 antibiotic courses were prescribed. The recommended antibiotics doxycycline and amoxicillin accounted for 56% of the prescribed antibiotics overall and for 35% in subsequent antibiotic courses. The alternative choices were not based on culture results because only in 67 AECOPD events (2.9%) sputum samples were taken. Regional data including 3,638 sputum samples showed that pathogens relevant in AECOPD were detected in 19% of cultures. Conclusion: Our study shows that guidelines regarding the prescription of antibiotics are poorly followed, particularly in recurrent exacerbations. Sputum cultures were performed in a small minority of cases. Performing sputum diagnostics in patients with early treatment failure or a repeated exacerbation when antibiotic treatment is started may further rationalize antibiotic treatment. Keywords: COPD, exacerbation, antimicrobial stewardship, bacteria, sputum cultures

An outbreak of haemolytic uraemic syndrome (HUS) among children caused by infection with sorbitol-fermenting enterohaemorrhagic Escherichia coli O157:H- (SF EHEC O157:H-) occurred in Germany in 2002. This pathogen has caused several outbreaks so far, yet its reservoir and routes of transmission remain unknown. SF EHEC O157:H- is easily missed as most laboratory protocols target the more common sorbitol non-fermenting strains. We performed active case-finding, extensive exploratory interviews and a case-control study. Clinical and environmental samples were screened for SF EHEC O157:H- and the isolates were subtyped by pulsed-field gel electrophoresis. We identified 38 case-patients in 11 federal states. Four case-patients died during the acute phase (case-fatality ratio 11%). The case-control study could not identify a single vehicle or source. Further studies are necessary to identify the pathogen's reservoir(s). Stool samples of patients with HUS should be tested with an adequate microbiological set-up to quickly identify SF EHEC O157:H-. [ABSTRACT FROM AUTHOR]

Multilocus sequence typing of 169 non-O157 enterohemorrhagic Escherichia coli (EHEC) isolated from patients with hemolytic uremic syndrome (HUS) demonstrated 29 different sequence types (STs); 78.1% of these strains clustered in 5 STs. From all STs and serotypes identified, we established a reference panel of EHEC associated with HUS (HUSEC collection). [ABSTRACT FROM AUTHOR]

We have shown previously that pls, which codes for the surface protein Pls of methicillin-resistant Staphylococcus aureus (MRSA), reduces adhesion to immobilized fibronectin, fibrinogen, laminin, and immunoglobulin G as well as invasion of host cells. Here, we tested a collection of 66 clinical MRSA isolates--48 negative for pls/Pls (pls(-)/Pls(-)), 15 positive for pls/Pls (pls(+)/Pls(+)), and 3 harboring the pls gene but not expressing Pls (pls(+)/Pls(-))--for cellular invasiveness. Invasion of 293 cells by pls(+)/Pls(+) strains was lower than that by the pls(-)/Pls(-) strains (median [range], 36% [22%-70%] vs. 93% [25%-162%]). The 3 pls(+)/Pls(-) strains (median [range], 95% [63%-103%]) were as invasive as the pls(-)/Pls(-) strains. In addition, we identified a pls(+)/Pls(+) staphylococcal chromosomal cassette mec (SCCmec) IV strain. In conclusion, 3 properties--pls/Pls, SCCmec type, and spa type--strongly predicted the cellular invasiveness of MRSA strains, as indicated by good clustering. In contrast, the spa type-deduced multilocus sequence typing clonal complex (MLST-CC) was not able to predict the invasiveness of MRSA strains equally well. The underlying mechanism remains to be elucidated. [ABSTRACT FROM AUTHOR]

Scope: The aim of these guidelines is to provide recommendations for decolonization and perioperative antibiotic prophylaxis (PAP) in multidrug-resistant Gram-positive bacteria (MDR-GPB) adult carriers before inpatient surgery., Methods: These European Society of Clinical Microbiology and Infectious Diseases/European Committee on Infection Control guidelines were developed following a systematic review of published studies targeting methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci, methicillin-resistant coagulase-negative Staphylococci, and pan-drug-resistant-GPB. Critical outcomes were the occurrence of surgical site infections (SSIs) caused by the colonizing MDR-GPB and SSIs-attributable mortality. Important outcomes included the occurrence of SSIs caused by any pathogen, hospital-acquired infections, all-cause mortality, and adverse events associated with the interventions, including resistance development to the agents used and the incidence of Clostridioides difficile infections. The last search of all databases was performed on 1 November 2023. The level of evidence and the strength of each recommendation were defined according to the Grading of Recommendations Assessment, Development, and Evaluation approach. Consensus of a multidisciplinary expert panel was reached for the final list of recommendations. Antimicrobial stewardship considerations were included., Recommendations: The guideline panel reviewed the impact of decolonization, targeted PAP, and combined interventions (e.g. decolonization and targeted PAP) on the risk of SSIs and other outcomes in MDR-GPB carriers, according to the type of bacteria and type of surgery. We recommend screening for S. aureus before high-risk operations, such as cardiothoracic and orthopaedic surgery. Decolonization with intranasal mupirocin with or without a chlorhexidine bath is recommended in patients colonized with S. aureus before cardiothoracic and orthopaedic surgery and suggested in other surgeries. The addition of vancomycin to standard prophylaxis is suggested for MRSA carriers in cardiothoracic surgery, orthopaedic surgery, and neurosurgery. Combined interventions (e.g. decolonization and targeted prophylaxis) are suggested for MRSA carriers undergoing cardiothoracic and orthopaedic surgery. No recommendation could be made regarding screening, decolonization and targeted prophylaxis for vancomycin-resistant enterococci because of the lack of data. No evidence was retrieved for methicillin-resistant coagulase-negative Staphylococci and pan-drug-resistant-GPB. Careful consideration of the laboratory workload and involvement of antimicrobial stewardship and infection control teams are warranted before implementing screening procedures or performing changes in PAP policy. Future research should focus on novel decolonizing techniques, on the monitoring of resistance to decolonizing agents and PAP regimens, and on standardized combined interventions in high-quality studies., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Introduction: Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements., Methods: This study analyzes the complete genome sequence of M. faucium , obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing., Results: Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination., Conclusion: This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics., Competing Interests: Authors TD and SB are employees of the company DNASTAR, Inc. SB is a minor shareholder in DNASTAR, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Sabat, Durfee, Baldwin, Akkerboom, Voss, Friedrich and Bathoorn.)

The threat of multidrug-resistant organisms (MDROs) and antimicrobial resistance (AMR) are real and increasing every day. They affect not only healthcare systems but also communities, causing economic and public health concerns. Governments must take action to tackle AMR and prevent the spread of MDROs and regional hubs have a critical role to play in achieving this outcome. Furthermore, bacteria have no borders, consequently, cooperation networks should be extended between countries as a crucial strategy for achieving the success of infection control. Euregions, which are a specific form of cooperation between local authorities of two or more bordering European countries, can help solve common problems and improve the lives of people living on both sides of the border. Regional collaboration strategies can enhance infection control and build resilience against antimicrobial resistance. This review identifies risk factors and the correct approaches to infection prevention and control, including education and awareness programs for healthcare professionals, appropriate prescribing practices, and infection prevention control measures. These measures can help reduce the incidence of antimicrobial resistance in the region and save lives. It is therefore essential to take concrete actions and foster the creation of more effective regional and cross-border centers to ensure the success of infection control policies and the management of healthcare-associated infections. This work sheds light on the issue of MDRO infections within healthcare settings, while also acknowledging the crucial role of the One Health concept in understanding the broader context of these infections. By recognizing the interdependence of human and animal health and the environment, we can take constructive steps toward mitigating the risks of these infections and promoting better health outcomes for all., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with the spread of OXA-48-producing Klebsiella pneumoniae clinical isolates from The Netherlands ( n  = 61) and Spain ( n  = 53). Most isolates shared a chromosomally encoded core of virulence factors, including the enterobactin gene cluster, fimbrial fim and mrk gene clusters, and urea metabolism genes ( ureAD ). We observed a high diversity of K-Locus and K/O loci combinations, KL17 and KL24 (both 16%), and the O1/O2v1 locus (51%) being the most prevalent in our study. The most prevalent accessory virulence factor was the yersiniabactin gene cluster (66.7%). We found seven yersiniabactin lineages- ybt  9, ybt  10, ybt  13, ybt  14, ybt  16, ybt  17, and ybt  27-which were chromosomally embedded in seven integrative conjugative elements (ICE Kp ): ICE Kp3 , ICE Kp4 , ICE Kp2 , ICE Kp5 , ICE Kp12 , ICE Kp10 , and ICE Kp22 , respectively. Multidrug-resistant lineages-ST11, ST101, and ST405-were associated with ybt  10/ICE Kp4 , ybt  9/ICE Kp3 , and ybt  27/ICE Kp22 , respectively. The fimbrial adhesin kpi operon ( kpiABCDEFG ) was predominant among ST14, ST15, and ST405 isolates, as well as the ferric uptake system kfuABC , which was also predominant among ST101 isolates. No convergence of hypervirulence and resistance was observed in this collection of OXA-48-producing K. pneumoniae clinical isolates. Nevertheless, two isolates, ST133 and ST792, were positive for the genotoxin colibactin gene cluster (ICE Kp10 ). In this study, the integrative conjugative element, ICE Kp , was the major vehicle for yersiniabactin and colibactin gene clusters spreading. IMPORTANCE Convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae isolates has been reported mostly related to sporadic cases or small outbreaks. Nevertheless, little is known about the real prevalence of carbapenem-resistant hypervirulent K. pneumoniae since these two phenomena are often separately studied. In this study, we gathered information on the virulent content of nonoutbreak, high-risk clones (i.e., ST11, ST15, and ST405) and other less common STs associated with the spread of OXA-48-producing K. pneumoniae clinical isolates. The study of virulence content in nonoutbreak isolates can help us to expand information on the genomic landscape of virulence factors in K. pneumoniae population by identifying virulence markers and their mechanisms of spread. Surveillance should focus not only on antimicrobial resistance but also on virulence characteristics to avoid the spread of multidrug and (hyper)virulent K. pneumoniae that may cause untreatable and more severe infections., Competing Interests: The authors declare a conflict of interest. J.W.A.R. was employed by IDbyDNA and is currently consulting for ARES-genetics. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The rising prevalence of vancomycin-resistant enterococci (VRE) is a matter of concern in hospital settings across Europe without a distinct geographical pattern. In this scoping review, we compared the epidemiology of vancomycin-resistant Enterococcus spp. in hospitals in the Netherlands and Germany, between 1991 and 2022. We searched PubMed and summarized the national antibiotic resistance surveillance data of the two countries. We included 46 studies and summarized national surveillance data from the NethMap in the Netherlands, the National Antimicrobial Resistance Surveillance database in Germany, and the EARS-Net data. In total, 12 studies were conducted in hospitals in the Netherlands, 32 were conducted in German hospitals, and an additional two studies were conducted in a cross-border setting. The most significant difference between the two countries was that studies in Germany showed an increasing trend in the prevalence of VRE in hospitals, and no such trend was observed in studies in the Netherlands. Furthermore, in both Dutch and German hospitals, it has been revealed that the molecular epidemiology of VREfm has shifted from a predominance of vanA towards vanB over the years. According to national surveillance reports, vancomycin resistance in Enterococcus faecium clinical isolates fluctuates below 1% in Dutch hospitals, whereas it follows an increasing trend in German hospitals (above 20%), as supported by individual studies. This review demonstrates that VRE is more frequently encountered in German than in Dutch hospitals and discusses the underlying factors for the difference in VRE occurrence in these two neighboring countries by comparing differences in healthcare systems, infection prevention control (IPC) guidelines, and antibiotic use in the Netherlands and Germany., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Scope: The aim of the guidelines is to provide recommendations on perioperative antibiotic prophylaxis (PAP) in adult inpatients who are carriers of multidrug-resistant Gram-negative bacteria (MDR-GNB) before surgery., Methods: These evidence-based guidelines were developed after a systematic review of published studies on PAP targeting the following MDR-GNB: extended-spectrum cephalosporin-resistant Enterobacterales, carbapenem-resistant Enterobacterales (CRE), aminoglycoside-resistant Enterobacterales, fluoroquinolone-resistant Enterobacterales, cotrimoxazole-resistant Stenotrophomonas maltophilia, carbapenem-resistant Acinetobacter baumannii (CRAB), extremely drug-resistant Pseudomonas aeruginosa, colistin-resistant Gram-negative bacteria, and pan-drug-resistant Gram-negative bacteria. The critical outcomes were the occurrence of surgical site infections (SSIs) caused by any bacteria and/or by the colonizing MDR-GNB, and SSI-attributable mortality. Important outcomes included the occurrence of any type of postsurgical infectious complication, all-cause mortality, and adverse events of PAP, including development of resistance to targeted (culture-based) PAP after surgery and incidence of Clostridioides difficile infections. The last search of all databases was performed until April 30, 2022. The level of evidence and strength of each recommendation were defined according to the Grading of Recommendations Assessment, Development and Evaluation approach. Consensus of a multidisciplinary expert panel was reached for the final list of recommendations. Antimicrobial stewardship considerations were included in the recommendation development., Recommendations: The guideline panel reviewed the evidence, per bacteria, of the risk of SSIs in patients colonized with MDR-GNB before surgery and critically appraised the existing studies. Significant knowledge gaps were identified, and most questions were addressed by observational studies. Moderate to high risk of bias was identified in the retrieved studies, and the majority of the recommendations were supported by low level of evidence. The panel conditionally recommends rectal screening and targeted PAP for fluoroquinolone-resistant Enterobacterales before transrectal ultrasound-guided prostate biopsy and for extended-spectrum cephalosporin-resistant Enterobacterales in patients undergoing colorectal surgery and solid organ transplantation. Screening for CRE and CRAB is suggested before transplant surgery after assessment of the local epidemiology. Careful consideration of the laboratory workload and involvement of antimicrobial stewardship teams before implementing the screening procedures or performing changes in PAP are warranted. High-quality prospective studies to assess the impact of PAP among CRE and CRAB carriers performing high-risk surgeries are advocated. Future well-designed clinical trials should assess the effectiveness of targeted PAP, including the monitoring of MDR-GNB colonization through postoperative cultures using European Committee on Antimicrobial Susceptibility Testing clinical breakpoints., (Copyright © 2022. Published by Elsevier Ltd.)

Purpose: To evaluate the accuracy and cost benefit of a rapid molecular point-of-care testing (POCT) device detecting COVID-19 within a traumatological emergency department., Background: Despite continuous withdrawal of COVID-19 restrictions, hospitals will remain particularly vulnerable to local outbreaks which is reflected by a higher institution-specific basic reproduction rate. Patients admitted to the emergency department with unknown COVID-19 infection status due to a- or oligosymptomatic COVID-19 infection put other patients and health care workers at risk, while fast diagnosis and treatment is necessary. Delayed testing results in additional costs to the health care system., Methods: From the 8th of April 2021 until 31st of December 2021, all patients admitted to the emergency department were tested with routine RT-PCR and rapid molecular POCT device (Abbott ID NOW™ COVID-19). COVID-19-related additional costs for patients admitted via shock room or emergency department were calculated based on internal cost allocations., Results: 1133 rapid molecular tests resulted in a sensitivity of 83.3% (95% CI 35.9-99.6%), specificity of 99.8% (95% CI 99.4-100%), a positive predictive value of 71.4% (95% CI 29-96.3%) and a negative predictive value of 99.9% (95% CI 99.5-100%) as compared to RT-PCR. Without rapid COVID-19 testing, each emergency department and shock room admission with subsequent surgery showed additional direct costs of 2631.25€, without surgery of 729.01€., Conclusion: Although rapid molecular COVID-19 testing can initially be more expensive than RT-PCR, subsequent cost savings, improved workflows and workforce protection outweigh this effect by far. The data of this study support the use of a rapid molecular POCT device in a traumatological emergency department., (© 2022. The Author(s).)

Objectives: Insights about local antimicrobial resistance (AMR) levels and epidemiology are essential to guide decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. We aimed to compare traditional data analysis and reporting versus a new approach for reliable and reproducible AMR data analysis in a clinical setting., Methods: Ten professionals who routinely work with AMR data were provided with blood culture test results including antimicrobial susceptibility results. Participants were asked to perform a detailed AMR data analysis in a two-round process: first using their software of choice and next using our newly developed software tool. Accuracy of the results and time spent were compared between both rounds. Finally, participants rated the usability using the System Usability Scale (SUS)., Results: The mean time spent on creating the AMR report reduced from 93.7 to 22.4 min ( P  < 0.001). Average task completion per round changed from 56% to 96% ( P  < 0.05). The proportion of correct answers in the available results increased from 37.9% in the first to 97.9% in the second round ( P  < 0.001). Usability of the new tools was rated with a median of 83.8 (out of 100) on the SUS., Conclusions: This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through open-source software. Integrating these tools in clinical settings can democratize the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Objective: In early 2017, the University Medical Center Groningen, the Netherlands, had an outbreak of 2 strains of vancomycin-resistant enterococci (VRE) that spread to various wards. In the summer of 2018, the hospital was again hit by a VRE outbreak, which was detected and controlled early. However, during both outbreaks, fewer patients were admitted to the hospital and various costs were incurred. We quantified the costs of the 2017 and 2018 VRE outbreaks., Design: Using data from various sources in the hospital and interviews, we identified and quantified the costs of the 2 outbreaks, resulting from tests, closed beds (opportunity costs), cleaning, additional personnel, and patient isolation., Setting: The University Medical Center Groningen, an academic hospital in the Netherlands., Results: The total costs associated with the 2017 outbreak were estimated to be €335,278 (US $356,826); the total costs associated with the 2018 outbreak were estimated at €149,025 (US $158,602)., Conclusions: The main drivers of the costs were the opportunity costs due to the reduction in admitted patients, testing costs, and cleaning costs. Although the second outbreak was considerably shorter, the costs per day were similar to those of the first outbreak. Major investments are associated with the VRE control measures, and an outbreak of VRE can lead to considerable costs for a hospital. Aggressively screening and isolating patients who may be involved in an outbreak of VRE may reduce the overall costs and improve the continuity of care within the hospital., (© The Author(s) 2023.)

Background: The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut. In particular, the mechanisms allowing S. aureus to pass the gut epithelial barrier and to invade the bloodstream were so far poorly understood. Therefore, the objective of our present study was to investigate the extent to which genetic differences between enteric S. aureus isolates and isolates that caused serious bloodstream infections contribute to the likelihood of invasive disease., Results: Here, we present genome-wide association studies (GWAS) that compare the genome sequences of 69 S. aureus isolates from enteric carriage by healthy volunteers and 95 isolates from bloodstream infections. We complement our GWAS results with a detailed characterization of the cellular and extracellular proteomes of the representative gut and bloodstream isolates, and by assaying the virulence of these isolates with infection models based on human gut epithelial cells, human blood cells, and a small animal infection model. Intriguingly, our results show that enteric and bloodstream isolates with the same sequence type (ST1 or ST5) are very similar to each other at the genomic and proteomic levels. Nonetheless, bloodstream isolates are not necessarily associated with an invasive profile. Furthermore, we show that the main decisive factor preventing infection of gut epithelial cells in vitro is the presence of a tight barrier., Conclusions: Our data show that virulence is a highly variable trait, even within a single clone. Importantly, however, there is no evidence that blood stream isolates possess a higher virulence potential than those from the enteric carriage. In fact, some gut isolates from healthy carriers were more virulent than bloodstream isolates. Based on our present observations, we propose that the integrity of the gut epithelial layer, rather than the pathogenic potential of the investigated enteric S. aureus isolates, determines whether staphylococci from the gut microbiome will become invasive pathogens. Video Abstract., (© 2022. The Author(s).)

Background: Guidelines on COVID-19 management are developed as we learn from this pandemic. However, most research has been done on hospitalised patients and the impact of the disease on non-hospitalised and their role in transmission are not yet well understood. The COVID HOME study conducts research among COVID-19 patients and their family members who were not hospitalised during acute disease, to guide patient care and inform public health guidelines for infection prevention and control in the community and household., Methods: An ongoing prospective longitudinal observational study of COVID-19 outpatients was established in March 2020 at the beginning of the COVID-19 pandemic in the Netherlands. Laboratory confirmed SARS-CoV-2 infected individuals of all ages that did not merit hospitalisation, and their household (HH) members, were enrolled after written informed consent. Enrolled participants were visited at home within 48 hours after initial diagnosis, and then weekly on days 7, 14 and 21 to obtain clinical data, a blood sample for biochemical parameters/cytokines and serological determination; and a nasopharyngeal/throat swab plus urine, stool and sperm or vaginal secretion (if consenting) to test for SARS-CoV-2 by RT-PCR (viral shedding) and for viral culturing. Weekly nasopharyngeal/throat swabs and stool samples, plus a blood sample on days 0 and 21 were also taken from HH members to determine whether and when they became infected. All participants were invited to continue follow-up at 3-, 6-, 12- and 18-months post-infection to assess long-term sequelae and immunological status., Competing Interests: The authors have declared that no competing interests exist.

The microbiological safety of medical devices is of paramount importance for patients and manufacturers alike. However, during usage medical devices will inevitably become contaminated with microorganisms, including opportunistic pathogens. This is a particular problem if these devices come in contact with body sites that carry high bacterial loads, such as the oral cavity. In the present study, we investigated whether high oxygen concentrations can be applied to disinfect surfaces contaminated with different Gram-positive and Gram-negative bacteria. We show that some opportunistic pathogens, exemplified by Pseudomonas aeruginosa, are particularly sensitive to oxygen concentrations above the atmospheric oxygen concentration of 21%. Our observations also show that high oxygen concentrations can be applied to reduce the load of P. aeruginosa on nebulizers that are used by cystic fibrosis patients, who are particularly susceptible to colonization and infection by this bacterium. We conclude that the efficacy of oxygen-mediated disinfection depends on the bacterial species, duration of oxygen exposure and the oxygen concentration. We consider these observations relevant, because gas mixtures with high oxygen content can be readily applied for microbial decontamination. However, the main challenge for oxygen-based disinfection approaches resides in a potentially incomplete elimination of microbial contaminants, which makes combined usage with other disinfectants like ethanol or hydrogen peroxide recommendable., (© 2022. The Author(s).)

The COVID-19 pandemic saw a massive investment into collaborative research projects with a focus on producing data to support public health decisions. We relay our direct experience of four projects funded under the Horizon2020 programme, namely ReCoDID, ORCHESTRA, unCoVer and SYNCHROS. The projects provide insight into the complexities of sharing patient level data from observational cohorts. We focus on compliance with the General Data Protection Regulation (GDPR) and ethics approvals when sharing data across national borders. We discuss procedures for data mapping; submission of new international codes to standards organisation; federated approach; and centralised data curation. Finally, we put forward recommendations for the development of guidelines for the application of GDPR in case of major public health threats; mandatory standards for data collection in funding frameworks; training and capacity building for data owners; cataloguing of international use of metadata standards; and dedicated funding for identified critical areas., Competing Interests: MB reports grants to UMCU from Janssen Vaccines, Novartis and CureVac, consulting fees from Astra Zeneca, Pfizer, Janssen Vaccines, Novartis,Takeda,Janssen Vaccines and payments from Sanofi for Participation on a Data Safety Monitoring Board or Advisory Board. ET, EC and RJD report H2020 funding for ORCHESTRA. JH reports H2020 funding for ORCHESTRA, funding from the German Research Council for the SEPAN Project, funding from German Ministry of Education and Research for the EMUNE and the INSIDe Project and funding from Volkswagen Stiftung for the E2 project. AS and EV report H2020 funding for SYNCHROS. TJ reports H2020 funding for ReCoDID. All other authors declare no competing interests., (© 2022 The Authors.)

Background: For years, coagulase-negative staphylococci (CoNS) were not considered a cause of bloodstream infections (BSIs) and were often regarded as contamination. However, the association of CoNS with nosocomial infections is increasingly recognized. The identification of more than 40 different CoNS species has been driven by the introduction of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Yet, treatment guidelines consider CoNS as a whole group, despite increasing antibiotic resistance (ABR) in CoNS. This retrospective study provides an in-depth data analysis of CoNS isolates found in human blood culture isolates between 2013 and 2019 in the entire region of the Northern Netherlands., Methods: In total, 10,796 patients were included that were hospitalized in one of the 15 hospitals in the region, leading to 14,992 CoNS isolates for (ABR) data analysis. CoNS accounted for 27.6% of all available 71,632 blood culture isolates. EUCAST Expert rules were applied to correct for errors in antibiotic test results., Results: A total of 27 different CoNS species were found. Major differences were observed in occurrence and ABR profiles. The top five species covered 97.1% of all included isolates: S. epidermidis , S. hominis , S. capitis , S. haemolyticus, and S. warneri . Regarding ABR, methicillin resistance was most frequently detected in S. haemolyticus (72%), S. cohnii (65%), and S. epidermidis (62%). S. epidermidis and S. haemolyticus showed 50-80% resistance to teicoplanin and macrolides while resistance to these agents remained lower than 10% in most other CoNS species., Conclusion: These differences are often neglected in national guideline development, prompting a focus on 'ABR-safe' agents such as glycopeptides. In conclusion, this multi-year, full-region approach to extensively assess the trends in both the occurrence and phenotypic resistance of CoNS species could be used for evaluating treatment policies and understanding more about these important but still too often neglected pathogens.

Objective: Climate change poses a significant threat to humanity and human activity is largely responsible for it. Clinical microbiology laboratories have their unintended shares in carbon dioxide (CO 2 ) emissions. The aim of this study is to estimate CO 2 emission of a clinical microbiology laboratory and to propose initiatives to reduce the emissions., Methods: CO 2 emission of instruments was estimated based on their electricity consumption. CO 2 emitted in producing consumables was estimated by weighing the consumables needed to perform major tests in a large academic hospital. A systematic literature review was performed to identify studies on the impact of clinical microbiology laboratories on the environment. A short survey was sent to four major manufacturers of agar plates on initiatives to reduce the environmental impact of their products. Opinion was given on activities that can reduce CO 2 emission in laboratories., Results: The study shows that the largest amount of CO 2 emission in the microbiological laboratories comes from consumables and personnel commuting. For example, the production and transportation of agar plates needed to culture samples for a year in a hospital with 1320 beds result in 16 590 kg CO 2 is emitted. All survey participants mentioned that they were committed to reduce environmental impact of their products. The initiatives to reduce CO 2 emission can be performed at the laboratory and at policy level, such as reducing the number of tests to only the necessary amount to reduce consumables., Discussion: The calculations contribute to map CO 2 -related emissions in clinical microbiology laboratory activities, and the proposed initiatives to reduce the CO 2 may serve as starting point for further discussions., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: Antimicrobial resistance (AMR) is a public health threat associated with antibiotic consumption. Community-acquired acute respiratory tract infections (CA-ARTIs) are a major driver of antibiotic consumption in primary care. We aimed to quantify the investments required for a large-scale rollout of point-of care (POC) diagnostic testing in Dutch primary care, and the impact on AMR due to reduced use of antibiotics., Methods: We developed an individual-based model that simulates consultations for CA-ARTI at GP practices in the Netherlands and compared a scenario where GPs test all CA-ARTI patients with a hypothetical diagnostic strategy to continuing the current standard-of-care for the years 2020-2030. We estimated differences in costs and future AMR rates caused by testing all patients consulting for CA-ARTI with a hypothetical diagnostic strategy, compared to the current standard-of-care in GP practices., Results: Compared to the current standard-of-care, the diagnostic algorithm increases the total costs of GP consultations for CA-ARTI by 9% and 19%, when priced at €5 and €10, respectively. The forecast increase in Streptococcus pneumoniae resistance against penicillins can be partly restrained by the hypothetical diagnostic strategy from 3.8 to 3.5% in 2030, albeit with considerable uncertainty., Conclusions: Our results show that implementing a hypothetical diagnostic strategy for all CA-ARTI patients in primary care raises the costs of consultations, while lowering antibiotic consumption and AMR. Novel health-economic methods to assess and communicate the potential benefits related to AMR may be required for interventions with limited gains for individual patients, but considerable potential related to antibiotic consumption and AMR., (© 2022. The Author(s).)

Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next-generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch-German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In-depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens., (© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Background: This study aimed to evaluate whether the implementation of extra perioperative safety measures and precautions through adopted standard operating procedures (SOPs) to ensure optimal anti-microbial conditions has led to less surgical site infections (SSI) after alloplastic breast reconstruction (BR)., Methods: This retrospective study compared two Cohorts of patients treated before and after the implementation of new SOPs (2009-2014: Cohort 1 versus 2014-2019: Cohort 2). Multivariate logistic regression analyses, adjusting for patient confounders, were implemented to compare SSI incidence between both Cohorts., Results: Overall, SSI incidence was equal in both groups (10%, p = 0.545). The incidence of deep SSI was 9% for Cohort 1 and 5% for Cohort 2 (p = 0.074). Incidence of SSI-related explantation was 8% and 5%, respectively (p = 0.136). After adjusting for patient confounders, no statistically significant difference was seen between both Cohorts in overall SSI, deep SSI incidence, and explantation due to SSI (OR adjusted : -0.31, p = 0.452, OR adjusted: 0.16, p = 0.747 and OR adjusted: 0.18, p = 0.712). Higher BMI, smoking, one-stage BR, and immediate BR were associated with the risk for SSI (p<0.001, p = 0.036, p<0.001, and p = 0.022, respectively)., Conclusion: Extra safety measures to assure optimal anti-microbial conditions did not contribute to lower SSI incidence or SSI-related explantation after alloplastic BR. Confounders such as BMI, smoking, immediate BR, and one-stage BR were correlated to an increased risk for overall SSI, deep SSI, and SSI-related explantation of TE/implants., Competing Interests: Declaration of Competing Interest None., (Copyright © 2022 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.)

Background: Ever since 2020, travelling has become complex, and increasingly so as the COVID-19 pandemic continues. To reopen Europe safely, a consensus of travel measures has been agreed between countries to enable movement between countries with as few restrictions as possible. However, communication of these travel measures and requirements for entry are not always clear and easily available. The aim of this study was to assess the availability, accessibility and harmonization of current travel information available in Europe., Methods: We performed a systematic documental analysis of online publicly available information and synthesized travel entry requirements for all countries in the European Union and Schengen Area (N = 31). For each country we assessed entry requirements, actions after entry, how risk was assessed, and how accessible the information was., Results: We found varying measures implemented across Europe for entry and a range of exemptions and restrictions, some of which were consistent between countries. Information was not always easy to find taking on average 10 clicks to locate. Twenty-one countries required pre-travel forms to be completed. Forty apps were in use, 11 serving as digital certification checkers. All countries required some form of COVID-19 certification for entry with some exemptions (e.g. children). Nineteen percent (n = 6) of countries used the ECDC risk assessment system; 80% (n = 25) defined their own. Forty-eight percent (n = 15) of countries used a traffic-light system with 2-5 risk classifications., Conclusion: A comprehensive set of measures has been developed to enable continued safe travel in Europe. However further refinements and coordination is needed to align travel measures throughout the EU to minimize confusion and maximize adherence to requested measures. We recommend that, along with developing travel measures based on a common set of rules, a standard approach is taken to communicate what these measures are., (© International Society of Travel Medicine 2022. Published by Oxford University Press.)

Aims: To estimate the prevalence of extended-spectrum-β-lactamase (ESBL)-producing enterobacterales (ESBL-E) carriage in the general population of Lower Saxony, Germany, and to identify risk factors for being colonized., Methods and Results: Participants were recruited through local press and information events. Detection of ESBL-E by culture was conducted using ESBL-selective chromagar plates containing third-generation cephalosporins. Identification of pathogens was performed using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)&#95;technology on Vitek mass spectrometry. Antibiotic susceptibility testing was conducted by microdilution (Vitek II) and an ESBL confirmation assay was carried out using a combination disk test. Of 527 randomly collected stool samples from healthy volunteers, 5.5% were tested positive for ESBL-E. Post-stratification for age and gender yielded a similar population estimate (5.9%). People traveling abroad and taking antibiotics had the greatest rectal ESBL-E carriage., Conclusions: Potential risk factors (eg, working in healthcare facilities, recent inpatient stay) did not attribute to rectal ESBL-E carriage as other factors (eg, travelling, taking antibiotics). Rectal ESBL-E carriage within the general population seems to be high., Significance and Impact of the Study: The known risk factors for carriage with MDRO might not be fully applicable to ESBL-E and require further examination in order to develop effective strategies for the prevention of ESBL-E dissemination within the general population., (© 2021 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.)

Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10 -3 substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient., (© The Author(s) 2022. Published by Oxford University Press.)

BackgroundAntimicrobial resistance poses a risk for healthcare, both in the community and hospitals. The spread of multidrug-resistant organisms (MDROs) occurs mostly on a local and regional level, following movement of patients, but also occurs across national borders.AimThe aim of this observational study was to determine the prevalence of MDROs in a European cross-border region to understand differences and improve infection prevention based on real-time routine data and workflows.MethodsBetween September 2017 and June 2018, 23 hospitals in the Dutch (NL)-German (DE) cross-border region (BR) participated in the study. During 8 consecutive weeks, patients were screened upon admission to intensive care units (ICUs) for nasal carriage of meticillin-resistant Staphylococcus aureus (MRSA) and rectal carriage of vancomycin-resistant Enterococcus faecium / E. faecalis (VRE), third-generation cephalosporin-resistant Enterobacteriaceae (3GCRE) and carbapenem-resistant Enterobacteriaceae (CRE). All samples were processed in the associated laboratories.ResultsA total of 3,365 patients were screened (median age: 68 years (IQR: 57-77); male/female ratio: 59.7/40.3; NL-BR: n = 1,202; DE-BR: n = 2,163). Median screening compliance was 60.4% (NL-BR: 56.9%; DE-BR: 62.9%). MDRO prevalence was higher in DE-BR than in NL-BR, namely 1.7% vs 0.6% for MRSA (p = 0.006), 2.7% vs 0.1% for VRE (p < 0.001) and 6.6% vs 3.6% for 3GCRE (p < 0.001), whereas CRE prevalence was comparable (0.2% in DE-BR vs 0.0% in NL-BR ICUs).ConclusionsThis first prospective multicentre screening study in a European cross-border region shows high heterogenicity in MDRO carriage prevalence in NL-BR and DE-BR ICUs. This indicates that the prevalence is probably influenced by the different healthcare structures.

Multidrug-resistant pathogens constitute a serious global issue and, therefore, novel antimicrobials with new modes of action are urgently needed. Here, we investigated the effect of a phenothiazine derivative (JBC 1847) with high antimicrobial activity on Staphylococcus aureus , using a wide range of in vitro assays, flow cytometry, and RNA transcriptomics. The flow cytometry results showed that JBC 1847 rapidly caused depolarization of the cell membrane, while the macromolecule synthesis inhibition assay showed that the synthesis rates of DNA, RNA, cell wall, and proteins, respectively, were strongly decreased. Transcriptome analysis of S. aureus exposed to sub-inhibitory concentrations of JBC 1847 identified a total of 78 downregulated genes, whereas not a single gene was found to be significantly upregulated. Most importantly, there was downregulation of genes involved in adenosintrifosfat (ATP)-dependent pathways, including histidine biosynthesis, which is likely to correlate with the observed lower level of intracellular ATP in JBC 1847-treated cells. Furthermore, we showed that JBC 1847 is bactericidal against both exponentially growing cells and cells in a stationary growth phase. In conclusion, our results showed that the antimicrobial properties of JBC 1847 were primarily caused by depolarization of the cell membrane resulting in dissipation of the proton motive force (PMF), whereby many essential bacterial processes are affected. JBC 1847 resulted in lowered intracellular levels of ATP followed by decreased macromolecule synthesis rate and downregulation of genes essential for the amino acid metabolism in S. aureus . Bacterial compensatory mechanisms for this proposed multi-target activity of JBC 1847 seem to be limited based on the observed very low frequency of resistance toward the compound., Competing Interests: AP was employed by company Unibrains. LS and KH were employed by company Bioneer A/S. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ronco, Kappel, Aragao, Biagi, Svenningsen, Christensen, Permin, Saaby, Holmstrøm, Klitgaard, Sabat, Akkerboom, Monaco, Tinelli, Friedrich, Jana and Olsen.)

Background: Along with mechanical and genetic factors, emerging evidence suggests that the presence of low-grade inflammation has a role in the pathogenesis of osteoarthritis (OA) and seems to be related to the microbiome composition of the gut., Purpose: To provide evidence whether there is clinical or preclinical evidence of gut-joint axis in the pathogenesis and symptoms of OA., Methods: An extensive review of the current literature was performed using three different databases. Human, as well as animal studies, were included. The risk of bias was identified using ROBINS and SYRCLE tools, while the quality of evidence was assessed using GRADE and CAMADARES criteria., Results: A total of nineteen articles were included. Multiple animal studies demonstrated that both obesity, and high-fat and high-sugar diets resulted in a gut dysbiosis status characterized by increased Firmicutes/Bacteroidetes (F/B) phyla ratio and increased permeability. These changes were associated with increased lipopolysaccharide serum levels, which consequently resulted in synovitis and OA severity. The administration of pre-and probiotics partially reversed this bacterial composition. In addition, in human studies, a decreased amount of gut Bacteroidetes, subsequent increased F/B ratio, have also been observed in OA patients., Conclusions: Our review confirms preliminary yet sound evidence supporting a gut-joint axis in OA in primarily preclinical models, by showing an association between diet, gut dysbiosis and OA radiological severity and self-reported symptoms. Clinical studies are needed to confirm these findings, and to investigate whether interventions targeting the composition of the microbiome will have a beneficial clinical effect., Competing Interests: The authors have declared that no competing interests exist.

Porcine respirovirus 1, also referred to as porcine parainfluenza virus 1 (PPIV-1), was first detected in deceased pigs from Hong Kong in 2013. It has since then been found in the USA, Chile and most recently in Hungary. Information on the pathogenicity and global spread is sparse. However, it has been speculated to play a role in the porcine respiratory disease complex. To investigate the porcine virome, we screened 53 pig samples from 26 farms within the Dutch-German border region using shotgun metagenomics sequencing (SMg). After detecting PPIV-1 in five farms through SMg, a real-time reverse transcriptase PCR (RT-qPCR) assay was designed, which not only confirmed the presence of the virus in 1 of the 5 farms but found an additional 6 positive farms. Phylogenetic analysis found the closest match to be the first detected PPIV-1 strain in Hong Kong. The Dutch-German region represents a significant area of pig farming within Europe and could provide important information on the characterization and circulation of porcine viruses, such as PPIV-1. With its recent detection in Hungary, these findings suggest widespread circulation of PPIV-1 in Central Europe, highlighting the need for further research on persistence, pathogenicity and transmission in Europe., (© 2021 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Coronavirus disease 2019 (COVID-19) often presents asymptomatically or milder in children compared to adults. The role of young children in the transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains largely unknown. In the Netherlands, the first action of loosening the partial lockdown that had been implemented to reduce SARS-CoV-2 transmission was the reopening of primary schools on 1 May 2020. We subsequently conducted a prospective cohort study among healthcare workers (HCWs) with primary school-attending children versus HCWs without children living at home. We tested each HCW three times for SARS-CoV-2 from May 20 to June 15 2020 at 1-week intervals. In total, 832 nasopharyngeal swabs were taken from 283 HCWs with primary school-attending children living at home and 864 nasopharyngeal swabs from 285 HCWs without children living at home. All nasopharyngeal swabs tested negative for SARS-CoV-2. In our region with a low population density and low SARS-CoV-2 prevalence, reopening of primary schools did not lead to an increase in infections. The results of this study may serve as an example for the implementation of regional strategies to reduce SARS-CoV-2 transmission in countries with large variations in both population density and SARS-CoV-2 prevalence., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Background: Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates., Results: Analysis of complete genome sequences of publicly available isolates showed variation in phage content among different lineages defined by MLST. We identified phage present in multiple STs as well as phages uniquely detected within a single lineage. Next, in silico phage typing was applied to twelve MinION sequenced isolates belonging to two different genetic backgrounds, namely ST117/CT24 and ST80/CT16. Genomic comparisons of the long-read-based assemblies allowed us to correctly identify isolates of the same complex type based on global genome architecture and specific phage signature similarity., Conclusions: For rapid identification of related VRE isolates, phage content analysis in long-read sequencing data is possible. This allows software development for real-time typing analysis of long-read sequencing data, which will generate results within several hours. Future studies are required to assess the discriminatory power of this method in the investigation of ongoing outbreaks over a longer time period., (© 2021. The Author(s).)

Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster's closest related isolates. The vanB-carrying transposon Tn 1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB -carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients., Competing Interests: JR is currently employed by IDbyDNA Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Lisotto, Couto, Rosema, Lokate, Zhou, Bathoorn, Harmsen, Friedrich, Rossen and Chlebowicz-Fliss.)

The gold standard for the diagnosis of bacterial infections in clinical samples is based on culture tests that are time-consuming and labor-intense. For these reasons, an extraordinary effort has been made to identify biomarkers as the tools for sensitive, rapid and accurate identification of pathogenic microorganisms. Moreover, biomarkers have been tested to distinguish colonization from infection, monitor disease progression, determine the clinical status of patients or predict clinical outcomes. This mini-review describes Pseudomonas aeruginosa and Staphylococcus aureus biomarkers, which contribute to pathogenesis and have been used in culture-independent bacterial identification directly from patient samples., (© 2021 Artur J. Sabat et al., published by De Gruyter, Berlin/Boston.)

Bdellovibrio bacteriovorus is a small Deltaproteobacterium which, since its discovery, has distinguished itself for the unique ability to prey on other Gram-negative bacteria. The studies on this particular "predatory bacterium", have gained momentum in response to the rising problem of antibiotic resistance, because it could be applied as a potential probiotic and antibiotic agent. Hereby, we present recent advances in the study of B. bacteriovorus , comprehending fundamental aspects of its biology, obligatory intracellular life cycle, predation resistance, and potential applications. Furthermore, we discuss studies that pave the road towards the use of B. bacteriovorus as a "living antibiotic" in human therapy, focussing on its interaction with biofilms, the host immune response, predation susceptibility and in vivo application models. The available data imply that it will be possible to upgrade this predator bacterium from a predominantly academic interest to an instrument that could confront antibiotic resistant infections.

We describe two false-negative results in the detection of meticillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 and spa type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.

Objectives: To describe a new subclass of mec class B complex identified in Staphylococcus epidermidis., Methods: Four S. epidermidis isolates obtained from bloodstream infections in patients at University Medical Center Groningen (UMCG) were analysed by phenotypic antibiotic susceptibility testing and WGS., Results: Sequence analysis revealed a new staphylococcal cassette chromosome mec (SCCmec) structure in isolate UMCG335. In this structure, plasmid pUB110 was found to be integrated into SCCmec IVc, creating a new SCCmec subtype, IVUMCG335. SCCmec IVc and a copy of plasmid pUB110 were found in other isolates, UMCG364 and UMCG341, respectively, indicating a probability that SCCmec IVUMCG335 could have evolved at the UMCG. SCCmec of UMCG337 contained a new genetic organization of the mec complex (IS431-ΔmecR1-mecA-IS431-pUB110-IS431-ψIS1272) that we have named B4. This new subclass of mec class B complex originated by IS431-mediated inversion of the DNA segment encompassing the plasmid and most of the genes of the mec complex with the exception of IS1272. As the SCCmec organization in UMCG337 differed by the inversion of an ∼10 kb sequence compared with SCCmec IVUMCG335, we have named it SCCmec subtype IVUMCG337. Isolates UMCG335 and UMCG337 carrying SCCmec IVUMCG335 and IVUMCG337, respectively, were associated with a restriction-modification system and a CRISPR-Cas system, creating a composite island of almost 70 kb., Conclusions: Our findings highlight the importance of IS431 in the evolution of the SCCmec region. The increasing genetic diversity identified in the SCCmec elements imposes a great challenge for SCCmec typing methods and highlights possible difficulties with the SCCmec nomenclature., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.)

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.

This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as "target taxa"). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway. The study entailed a monthly sampling campaign along a wastewater pathway, and taxa identification through 16S rRNA amplicon sequencing. Results indicated that clinical and non-clinical wastewaters differed in their overall bacterial composition, but that target taxa were not enriched in clinical wastewater. This suggests that treatment of clinical wastewater before release into the wastewater system would only remove a minor part of the potential total pathogen load in wastewater treatment plants. Additional findings were that the relative abundance of most target taxa was decreased after wastewater treatment, yet all investigated taxa were detected in 68% of the treated effluent samples-meaning that these bacteria are continuously released into the receiving surface water. Temporal variation was only observed for specific taxa in surface water, but not in wastewater samples.