BACKGROUND:WGS can potentially be routinely used in clinical microbiology settings, especially with the increase in sequencing accuracy and decrease in cost. Escherichia coli is the most common bacterial species analysed in those settings, thus fast and accurate diagnostics can lead to reductions in morbidity, mortality and healthcare costs. OBJECTIVES:To evaluate WGS for diagnostics and surveillance in a collection of clinical E. coli; to examine the pool of antimicrobial resistance (AMR) determinants circulating in Denmark and the most frequent STs; and to evaluate core-genome MLST (cgMLST) and SNP-based clustering approaches for detecting genetically related isolates. METHODS:We analysed the genomes of 699 E. coli isolates collected throughout all Danish Clinical Microbiology Laboratories. We used rMLST and KmerFinder for species identification, ResFinder for prediction of AMR, and PlasmidFinder for plasmid identification. We used Center for Genomic Epidemiology MLST, cgMLSTFinder and CSI Phylogeny to perform typing and clustering analysis. RESULTS:Genetic AMR determinants were detected in 56.2% of isolates. We identified 182 MLSTs, most frequently ST-69, ST-73, ST-95 and ST-131. Using a maximum 15-allele difference as the threshold for genetic relatedness, we identified 23 clusters. SNP-based phylogenetic analysis within clusters revealed from 0 to 13 SNPs, except two cases with 111 and 461 SNPs. CONCLUSIONS:WGS data are useful to characterize clinical E. coli isolates, including predicting AMR profiles and subtyping in concordance with surveillance data. We have shown that it is possible to adequately cluster isolates through a cgMLST approach, but it remains necessary to define proper interpretative criteria.

The burden of Clostridioides difficile as a nosocomial- and community-acquired pathogen has been increasing over the recent decades, including reports of severe outbreaks. Molecular and virulence genotyping are central for the epidemiological surveillance of this pathogen, but need to balance accuracy and rapid turnaround time of the results. While Illumina short-read sequencing has been adopted as the gold standard to investigate C. difficile virulence and transmission routes, little is known about the potential of Nanopore long-read sequencing in this field. The goal of our study was to compare sequencing and assembly quality of 37 C. difficile isolates using Illumina (SPAdes assembled) and Nanopore (Flye and Unicycler assembled) data alone, along with hybrid assemblies obtained with short-read polishing of long reads. Illumina sequencing produced reads with an average quality of 99.68

Inno4Vac, a public-private partnership funded by the IMI2/EU/EFPIA Joint Undertaking (IMI2 JU), brings together academic institutions, SMEs, and pharmaceutical companies to accelerate and de-risk vaccine development. The project has made significant strides in the selection and production of challenge agents for influenza, respiratory syncytial virus (RSV), and toxigenic Clostridioides difficile for controlled human infection model studies (CHIMs). A regulatory workshop held on March 20, 2024, addressed the standardisation of clinical procedures, ethical considerations, endpoints, and data integrity, highlighting the ongoing initiatives related to these CHIMs. Key discussions focused on refining trial protocols to balance statistical power with participant burden, overseen by a data safety monitoring board. The meeting emphasised the importance of harmonizing CHIM protocols to ensure robust, reproducible, and transparent research. Mandatory trial registration and adherence to the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles were recommended to enhance data reuse and scientific value. This report consolidates efforts to standardise CHIM protocols, essential for accelerating therapeutic innovations and advancing global health research.

OBJECTIVES:We aimed to identify specific anaerobic bacteria causing bacteraemia and a subsequent diagnosis of colorectal cancer. METHODS:A nationwide population-based cohort study, which included all episodes of defined specific anaerobic bacteraemia from 2010 (5,534,738 inhabitants) through 2020 (5,822,763 inhabitants) and all cases of colorectal cancer diagnosed from 2010 through 2021 in Denmark. We calculated the incidence and risk of colorectal cancer after bacteraemia with specific anaerobic bacteria using Escherichia coli bacteraemia as reference. RESULTS:Nationwide data on colorectal cancer and specific anaerobic bacteraemia (100% complete, representing 11,124 episodes). The frequencies of colorectal cancer within one year following anaerobic bacteraemia were higher for species, which almost exclusively reside in the colon, such as Phocaeicola vulgatus/dorei (5.5%), Clostridium septicum (24.2%), and Ruminococcus gnavus (4.6%) compared to 0.6% in 50,650 E. coli bacteraemia episodes. Bacteroides spp. had a subhazard ratio for colorectal cancer of 3.9 (95% confidence interval [CI], 3.0 to 5.1) and for Clostridium spp. it was 8.9 (95% CI, 6.7 to 11.8, with C. septicum 50.0 [95% CI, 36.0 to 69.5]) compared to E. coli (reference). CONCLUSION:This nationwide study identified specific colorectal cancer-associated anaerobic bacteria, which almost exclusively reside in the colon. Bacteraemia with these bacteria could be an indicator of colorectal cancer.

Burden of bacteraemia is rising due to increased average life expectancy in developed countries. This study aimed to compare the epidemiology and outcomes of bacteraemia in two similarly ageing populations with different ethnicities in Singapore and Denmark. Historical cohorts from the second largest acute-care hospital in Singapore and in the hospitals of two Danish regions included patients aged 15 and above who were admitted from 1 January 2006 to 31 December 2016 with at least 1 day of hospital stay and a pathogenic organism identified. Among 13 144 and 39 073 bacteraemia patients from Singapore and Denmark, similar 30-day mortality rates (16.5%; 20.3%), length of hospital stay (median 14 (IQR: 9-28) days; 11 (6-21)), and admission rate to ICU (15.5%; 15.6%) were observed, respectively. Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus ranked among the top four in both countries. However, Singaporeans had a higher proportion of patients with diabetes (46.8%) and renal disease (29.5%) than the Danes (28.0% and 13.7%, respectively), whilst the Danes had a higher proportion of patients with chronic pulmonary disease (18.0%) and malignancy (35.3%) than Singaporeans (9.7% and 16.2%, respectively). Our study showed that top four causative organisms and clinical outcomes were similar between the two cohorts despite pre-existing comorbidities differed.

Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of enteropathogenic microorganisms may have been reduced in Denmark during the COVID-19 pandemic. All Departments of Clinical Microbiology in Denmark provided data on the monthly incidence of Salmonella spp., Escherichia coli, Campylobacter spp., Clostridioides difficile, Norovirus GI+GII, Giardia duodenalis, and Cryptosporidium from March 2018 to February 2021. The data were divided into three periods as follows: Control Period 1 (March 2018 to February 2019); Control Period 2 (March 2019 to February 2020); and the Restriction (pandemic) Period (March 2020 to February 2021). The incidences of pathogenic Salmonella spp.-, Escherichia coli-, and Campylobacter spp.-positive samples decreased by 57.3%, 48.1%, and 32.9%, respectively, during the restriction period. No decrease in C. difficile was observed. Norovirus GI+GII-positive samples decreased by 85.6%. Giardia duodenalis-positive samples decreased by 66.2%. Cryptosporidium species decreased by 59.6%. This study demonstrates a clear decrease in the incidence of enteropathogenic bacteria (except for C. difficile), viruses, and parasites during the SARS-CoV-2 restriction period in Denmark.

Background: Little is known about the clinical characteristics and pathogens causing hospital-acquired bloodstream infections (HA-BSIs) in relation to an intensive care unit (ICU) stay. Methods: Population-based cohort study, comprising 35% of the Danish population, 2009-2016. We derived four patient groups with first-time HA-BSIs: no ICU stay during the admission (non-ICU patients) and HA-BSI acquired before, in, or after an ICU stay (before-ICU, in-ICU, and after-ICU patients). These groups were compared in relation to microbiological and clinical characteristics, including 28- and >28-day mortality. Results: Among 6888 HA-BSI patients, 4017, 792, 1388, and 691 were non-ICU, before-ICU, in-ICU, and after-ICU, respectively. The rates of several microorganisms differed between the patient groups, e.g., Enterococci (9.4% of non-ICU and 32.0% of in-ICU patients). The 28-day mortality was 26.3% in non-ICU, 45.0% in before-ICU, 35.6% in in-ICU, and 19.0% in after-ICU patients. The corresponding adjusted hazard ratios (95% confidence interval) were 2.10 (1.85-2.36), 1.67 (1.50-1.87), and 0.76 (0.63-0.91) (reference: non-ICU patients). There were few differences as regards >28-day mortality. Conclusions: We found large differences between common microorganisms and prognosis between the four patient groups. After-ICU patients had the lowest 28-day mortality despite age and comorbidity characteristics similar to the other three groups.

Objective: To investigate the rate of breakthrough SARS-CoV-2 infection and clinical outcomes in a cohort of MS patients who were treated with ocrelizumab before first, second, and third BNT162b2 mRNA vaccinations. Background: The study included participants from three MS clinics in Denmark and the University of California, San Francisco in the United States when omicron BA.1 and BA.2 were the dominating subtypes of SARS-CoV-2. Reduced humoral response is associated with ocrelizumab treatment of multiple sclerosis (MS). Design/Methods: The study was a prospective nonrandomized controlled observational multicenter trial. Participants were diagnosed with MS and received ocrelizumab treatment for >12 months prior to the three BNT162b2 mRNA vaccinations. The follow-up period was from January 2021 to May 2022. Clinical outcomes were evaluated using WHO progression scale. The humoral and cellular immunogenicity in participants were correlated with PCR confirmed breakthrough infection. Results: Out of 54 participants, 32 (59.3%) developed a positive SARS-CoV-2 PCR test in the study period. Mild infections were observed in all infected participants. After the third vaccination, the non-infected participants had higher mean antibody levels compared to the infected participants (54.3 vs. 26.5 BAU/mL, p=0.030). The difference in reactivity between spike-specific CD4+ and CD8+ T-lymphocytes in the two groups were non-significant. Additional results regarding levels of ocrelizumab, anti-ocrelizumab antibodies and SARS-CoV-2 nucleocapsid protein, together with the immunological effects of fourth vaccination will be presented at the conference. Conclusions: Our results demonstrate high rates of breakthrough infections, along with mild disease courses after 3rd SARS-CoV-2 mRNA vaccination in ocrelizumab treated MS participants. This suggests that vaccination of B-cell depleted patients provides low protection against breakthrough infection. The study findings point to the need for better prophylactic options or more specific vaccines to allow for better clinical protection. Disclosure: Dr. Novak has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Sanofi A/S. Mr. Bajwa has nothing to disclose. The institution of Prof. Coia has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Tillotts. The institution of Prof. Coia has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Tillotts. The institution of Prof. Coia has received research support from Tillotts. Dr. Nilsson has received publishing royalties from a publication relating to health care. Dr. Nielsen has nothing to disclose. Mrs. Holm has nothing to disclose. Dr. Ostergaard has nothing to disclose. Miss Hvidt has nothing to disclose. Mr. BYG has nothing to disclose. Prof. Johansen has nothing to disclose. Ms. Mittl has nothing to disclose. William Rowles has nothing to disclose. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Alexion. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Genzyme. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving as an Editor, Associate Editor, or Editorial Advisory Board Member for AAN. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving as a Advisory Board with Genzyme. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving as a Advisory Board with Genentech. Dr. Zamvil has received personal compensation in the range of $500-$4,999 for serving as a Advisory Board with Alexion. Dr. Bove has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for Biogen. Dr. Bove has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Horizon. Dr. Bove has received personal compensation in the range of $5,000-$9,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Biogen. Dr. Bove has received personal compensation in the range of $5,000-$9,999 for serving on a Scientific Advisory or Data Safety Monitoring board for EMD Serono. Dr. Bove has received personal compensation in the range of $10,000-$49,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Genzyme Sanofi. Dr. Bove has received personal compensation in the range of $10,000-$49,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Novartis. Dr. Bove has received personal compensation in the range of $10,000-$49,999 for serving on a Scientific Advisory or Data Safety Monitoring board for TG Therapeutics. Dr. Bove has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Jansen. Dr. Bove has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Alexion. The institution of Dr. Bove has received research support from Biogen. The institution of Dr. Bove has received research support from Roche Genentech. The institution of Dr. Bove has received research support from Novartis. Dr. Sabatino has received research support from Novartis. Dr. Sabatino has received research support from Roche/Genentech. Dr. Sabatino has received personal compensation in the range of $500-$4,999 for serving as a CME course instructor with eMultiple Sclerosis Review. Dr. Sabatino has received personal compensation in the range of $500-$4,999 for serving as a CME course instructor with Physician Education Resource. Tobias Sejbaek has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Biogen, Merck, Novartis, Roche. Tobias Sejbaek has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Biogen, Merck, Novartis, Teva. The institution of Tobias Sejbaek has received research support from Biogen, Merck, Novartis, Roche.

This study aimed to evaluate the impact of the severe acute respiratory syndrome coron-avirus 2 (SARS-CoV-2) restrictions such as social distancing on the occurrence of acute gastroenteritis (AGE) among children. This study is a register-based study, including every child seen in the departments of paediatrics with the initial diagnosis of AGE in three neighbouring hospitals in Denmark, from March 2018 through February 2021. The study also included every positive stool sample for AGE-causing pathogens analysed in these three hospitals from children during the same period. The Wilcoxon rank-sum test was used to determine differences between the period during the SARS-CoV-2 restrictions and before. In all, 222,157 children were seen in the three paediatric departments during this period. Of these, 3917 children were diagnosed with AGE. We found a decrease of 46.6% in AGE-related visits per month after the SARS-CoV-2 restrictions were introduced compared to before (p-value < 0.001). Positive stool samples decreased by 38.2% (p-value = 0.008) during the restrictions. This study found that cases of paediatric AGE decreased significantly the during COVID-19 restrictions, suggesting that studies should be conducted to determine whether this reduction was a result of good hand hygiene and social distancing or just a result of altered health-seeking behaviour among children.

We developed four algorithms for the automatic capture of C-reactive protein (CRP) peaks in 296 adult patients with acute myeloid leukemia who had bloodstream infection (BSI) episodes, negative blood cultures (BCs) or possible infections where no BCs were performed. The algorithms detected CRP peaks for 418-446 of the 586 documented BSI episodes (71.3-76.1%) and 2714-3118 of the 4382 negative BCs (61.9-71.2%). The four algorithms captured 382-789 CRP peaks in which there were neither BSI episodes nor negative BCs. We conclude that automatic capture of CRP peaks is a tool for the monitoring of BSI episodes and possibly other infections in patients with acute myeloid leukemia.

BACKGROUND:Our study investigated the rate of breakthrough SARS-CoV-2 infection and clinical outcomes in a cohort of multiple sclerosis (MS) patients who were treated with the anti-CD20 monoclonal antibody (Ab), ocrelizumab, before first, second and third BNT162b2 mRNA vaccinations. To correlate clinical outcomes with the humoral and cellular response.METHODS:The study was a prospective non-randomised controlled multicentre trial observational study. Participants with a diagnosis of MS who were treated for at least 12 months with ocrelizumab prior to the first BNT162b2 mRNA vaccination were prospectively followed up from January 2021 to June 2022.RESULTS:Out of 54 participants, 32 (59.3%) developed a positive SARS-CoV-2 PCR test in the study period. Mild infection was observed in all infected participants. After the third vaccination, the non-infected participants had higher mean Ab levels compared to the infected participants (54.3 binding antibody unit (BAU)/mL vs 26.5 BAU/mL, p=0.030). The difference in reactivity between spike-specific CD4+ and CD8+ T lymphocytes in the two groups was not significant.CONCLUSION AND RELEVANCE:The study results demonstrate rates of 59% in breakthrough infections after the third SARS-CoV-2 mRNA vaccination in ocrelizumab-treated patients with MS, without resulting in critical disease courses. These findings suggest the need for continuous development of prophylactic treatments when proved important in the protection of severe breakthrough infection.

Between November and December 2021, the first ever recorded outbreak of enteroinvasive Escherichia coli in Denmark occurred at national scale. We describe the investigation of this outbreak, which was initially recognised in early December 2021. A total of 88 cases (58 female; 30 male) with a median age of 52 years (range: 0-91) were detected by PCR-based diagnostic methods. Case ascertainment was complicated by current culture-free diagnostic procedures, with only 34 cases confirmed by culture, serotyping and whole genome sequencing. Isolates from cases grouped into two serotypes (O136:H7 and O96:H19), which was supported by whole-genome-sequence-phylogeny, also yielding two clusters. Interviews of 42 cases and traceback investigation pointed towards consumption of ready-to-eat salads as the outbreak cause. While the ready-to-eat salads comprised different vegetables, imported spring onions were the only common ingredient and thus the likely source. Environmental investigations failed to recover outbreak strains. This report highlights the value of fast typing (here O-typing) to confirm cases in an outbreak situation. Timely communication and data sharing are also important, and were facilitated by the national collaboration between relevant laboratories, the public health institute and the veterinary and food administration. High hygiene standards for imported fresh vegetables intended for ready-to-eat products are essential.

BackgroundOnly a subset of enteric pathogens is under surveillance in Denmark, and knowledge on the remaining pathogens detected in acute gastroenteritis is limited. Here, we present the one-year incidence of all enteric pathogens diagnosed in Denmark, a high-income country, in 2018 and an overview of diagnostic methods used for detection.MethodsAll 10 departments of clinical microbiology completed a questionnaire on test methods and provided 2018-data of persons with positive stool samples with Salmonella species, Campylobacter jejuni/coli, Yersinia enterocolitica, Aeromonas species, diarrheagenic Escherichia coli (Enteroinvasive (EIEC), Shiga toxin-producing (STEC), Enterotoxigenic (ETEC), Enteropathogenic (EPEC), and intimin-producing/attaching and effacing (AEEC)), Shigella species., Vibrio cholerae, norovirus, rotavirus, sapovirus, adenovirus, Giardia intestinalis, Cryptosporidium species, and Entamoeba histolytica.ResultsEnteric bacterial infections were diagnosed with an incidence of 229.9 cases/100,000 inhabitants, virus had an incidence of 86/100,000 and enteropathogenic parasites of 12.5/100,000. Viruses constituted more than half of diagnosed enteropathogens for children below 2 years and elderly above 80 years. Diagnostic methods and algorithms differed across the country and in general PCR testing resulted in higher incidences compared to culture (bacteria), antigen-test (viruses), or microscopy (parasites) for most pathogens.ConclusionsIn Denmark, the majority of detected infections are bacterial with viral agents primarily detected in the extremes of ages and with few intestinal protozoal infections. Incidence rates were affected by age, clinical setting and local test methods with PCR leading to increased detection rates. The latter needs to be taken into account when interpreting epidemiological data across the country.

Background Pseudomonas aeruginosa infection is seen in chronic pulmonary disease and is associated with exacerbations and poor long-term prognosis. However, evidence-based guidelines for the management and treatment of P. aeruginosa infection in chronic, non-cystic fibrosis (CF) pulmonary disease are lacking. The aim of this study is to investigate whether targeted antibiotic treatment against P. aeruginosa can reduce exacerbations and mortality in patients with chronic obstructive pulmonary disease (COPD), non-CF bronchiectasis, and asthma. Methods This study is an ongoing multicenter, randomized, controlled, open-label trial. A total of 150 patients with COPD, non-CF bronchiectasis or asthma, and P. aeruginosa -positive lower respiratory tract samples will be randomly assigned with a 1:1 ratio to either no antibiotic treatment or anti-pseudomonal antibiotic treatment with intravenous beta-lactam and oral ciprofloxacin for 14 days. The primary outcome, analyzed with two co-primary endpoints, is (i) time to prednisolone and/or antibiotic requiring exacerbation or death, in the primary or secondary health sector, within days 20–365 from study allocation and (ii) days alive and without exacerbation within days 20–365 from the study allocation. Discussion This trial will determine whether targeted antibiotics can benefit future patients with chronic, non-CF pulmonary disease and P. aeruginosa infection in terms of reduced morbidity and mortality, thus optimizing therapeutic approaches in this large group of chronic patients. Trial registration ClinicalTrials.gov NCT03262142 . Registered on August 25, 2017.

BACKGROUND:There is a well-described association between bacteremia with bovis group streptococci or Clostridium septicum and an increased probability of a colorectal cancer (CRC) diagnosis. We wanted to investigate the existence of a similar association between CRC and bacteremia with other bacteria belonging to the gut microbiota..METHODS:A population based cohort study in a population about 2 million people including 45 774 bacteremia episodes and 231 387 blood culture negative cases was performed in the Region of Southern Denmark and Region Zealand from 2007-2016. Episodes of bacteremia were combined with the Danish central register for CRC. We performed Cox's regression analysis with hazard ratios (HRs) and 95% confidence intervals (CIs).RESULTS:The study results confirmed previous findings of an increased risk of a CRC diagnosis after bacteremia with the bovis group streptococci (risk within a year: 4.3%; HR [95% CI]: 8.46 [3.51-20.4]) or C. septicum (20.8%; 76.2 [42.0-138]). Furthermore, Bacteroides ovatus (6.7%; 20.3 [5.04-81.8]), Bacteroides uniformis (5.4%; 16.2 [4.02-65.7]), Clostridium tertium (3.6 %; 13.9 [1.96-99.4]), Fusobacterium spp. (excluding F. necrophorum) (3.0 %; 8.51 [2.73-26.5]), and Gram-positive anaerobic cocci (3.6 %; 10.9 [4.50-26.3]) were also associated with an increased risk of a CRC diagnosis compared to patients with negative blood cultures (0.4%).CONCLUSIONS:Bacteremia with specific gut microbiota anaerobic bacteria is associated with a high risk of a diagnosis of CRC, indicating the need for colorectal workup. Importantly, this strategy also holds the possible additional benefit of detecting adenomas or other premalignant conditions, which were not included in the present study.

Abstract Purpose: The aim of this study was to develop highly specific primer-probes pairs for the detection of species-specific genes, and establish a multiplex ddPCR assay for the detection of low copies of genomic DNA, of common bacteria causing bloodstream infections in our institution, i.e. Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli, and Pseudomonas aerugnosa..Methods: Pubmed and GenBank databases were used to select well-characterized candidate genes for each microorganism. The newly designed primer-probe pairs were designed using AllelID 7.85 software. The designed primer-probe pairs were tested and validated using Droplet Digital PCR QX200 by using quantitative ATCC genomic DNA from S. aureus (ATCC® 29213DQ™), S. pneumoniae (ATCC® 700669DQ™), E. coli (ATCC® 25922DQ™), and P. aeruginosa (ATCC® 27853DQ™).Results: All primer-probe pairs demonstrated an optimal annealing temperature at 56°C. The ddPCR detected 162 copies for S. aureus and 152 copies S. pneumonia in singleplex reactions as compared to 152 copies and 132 copies in duplex reactions, respectively, and 324 copies for P. aeruginosa, 30 copies for E. coli in singleplex reactions as compared to 356 copies and 34 copies, respectively, in duplex reactions. The results of the limit of detection of the ddPCR assay was as low as 1 copy/reaction for S. aureus, E. coli, and P. aeruginosa and 2 copies/reaction for S. pneumonia. Conclusion: In this study, we have designed highly specific PP pairs for use in a ddPCR assay for the accurate and reliable detection and quantification of species-specific genes for four common blood culture pathogens in our institution.

Objectives Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark. Methods We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature. Results The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study. Conclusions WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

Background Since 2008, Danish national surveillance of Clostridioides difficile has focused on binary toxin-positive strains in order to monitor epidemic types such as PCR ribotype (RT) 027 and 078. Additional surveillance is needed to provide a more unbiased representation of all strains from the clinical reservoir. Aim Setting up a new sentinel surveillance scheme for an improved understanding of type distribution relative to time, geography and epidemiology, here presenting data from 2016 to 2019. Methods For 2─4 weeks in spring and autumn each year between 2016 and 2019, all 10 Danish Departments of Clinical Microbiology collected faecal samples containing toxigenic C. difficile. Isolates were typed at the national reference laboratory at Statens Serum Institut. The typing method in 2016–17 used tandem-repeat-sequence typing, while the typing method in 2018–19 was whole genome sequencing. Results During the study period, the sentinel surveillance scheme included ca 14–15% of all Danish cases of C. difficile infections. Binary toxin-negative strains accounted for 75% and 16 of the 20 most prevalent types. The most common sequence types (ST) were ST2/13 (RT014/020) (19.5%), ST1 (RT027) (10.8%), ST11 (RT078) (6.7%), ST8 (RT002) (6.6%) and ST6 (RT005/117) (5.1%). The data also highlighted geographical differences, mostly related to ST1 and temporal decline of ST1 (p = 0.0008) and the increase of ST103 (p = 0.002), ST17 (p = 0.004) and ST37 (p = 0.003), the latter three binary toxin-negative. Conclusion Sentinel surveillance allowed nationwide monitoring of geographical differences and temporal changes in C. difficile infections in Denmark, including emerging types, regardless of binary toxin status.

Background: Estimates of the severity of the emerging Omicron variant (lineage B.1.1.529) are critical to assess the public health impact associated with its rapid global dissemination. We estimated the risk of SARS-CoV-2-related hospitalizations after infection with Omicron compared to Delta overall and stratified by vaccination status in Denmark, a country with high mRNA vaccination coverage and an extensive free-of-charge PCR test capacity.Methods: Observational cohort study of all RT-PCR SARS-CoV-2 positive individuals in Denmark between 21 November and 19 December, 2021, the period Omicron emerged while Delta was still the dominant variant. Individuals including hospitalised cases, were identified in the national COVID-19 surveillance system database including results of a variant specific RT-PCR detecting Omicron cases (vPCR), the National Patient Registry, the National Vaccination Registry, as well as other nationwide registers. The risk ratio (RR) of admission for Omicron compared to Delta infection, overall and stratified by vaccination status, was calculated in a Poisson regression model with robust standard errors, adjusted à priori for reinfection status, sex, age, region, comorbidities, and calendar week of sampling.Findings: Among the 188,980 SARS-CoV-2 infected individuals, 38,669 (20.1%) were Omicron vPCR positive. SARS-CoV-2 related hospitalisations and Omicron cases increased during the study period. Overall, 65.8 % were vaccinated and vaccination was associated with a lower risk of hospitalisation (adjusted RR 0.25, 95%CI 0.22-0.27), compared to cases with no or one vaccination. Compared to Delta infection, Omicron was associated with an adjusted RR of hospitalisation of 0.64 (95%CI 0.56-0.75). The RR of hospitalisation was 0.57 (95%CI 0.44-0.75) among cases with no or one vaccination, 0.71 (95%CI 0.60-0.86) among two-dose vaccinated, and 0.50 (95%CI 0.32-0.76) among three-dose vaccinated.Interpretation: We found a significantly lower risk of hospitalisation with Omicron infection compared to Delta among both vaccinated and unvaccinated individuals suggesting an inherent reduced severity of Omicron. Our results can guide modelling of the impact of the rapid spread of Omicron globally and thus health care system preparedness.Funding Information: The authors received no specific funding for this work. Declaration of Interests: We declare no competing interest.Ethics Approval Statement: All analyses were based on information from the national COVID-19 surveillance system database updated and extracted on 4 January, 2022. This study was done with use of administrative register data. According to Danish law, ethics approval is not needed for such research.