Escherichia coli clonal complex 38 (CC38) is a genetically diverse lineage increasingly linked to antimicrobial resistance and extraintestinal infections in humans. Despite its clinical and epidemiological relevance, its population structure, zoonotic potential, and ecological associations remain poorly understood. We analyzed 242 human E. coli CC38 bloodstream isolates collected through Danish national surveillance, 83 isolates from food and production animals, and 2313 international genomes to investigate host associations and transmission dynamics. Phylogenetic reconstruction, Bayesian host prediction based on mobile genetic elements, and statistical testing of plasmid–host associations were used to delineate population structure and identify potential host-associated markers. Here we show that Danish CC38 isolates belong to multiple sub-lineages, with no evidence of foodborne outbreaks and limited hospital transmission. Bayesian host prediction supports a poultry origin for several distinct human sub-lineages. Global analyses of 2638 genomes reveal two major clusters: a poultry-associated Cluster I and a predominantly human-associated Cluster II, which subdivides into eight sub-lineages with distinct host, resistance, and virulence profiles. Two small plasmids, ColRNAI and Col(MG828), are strongly enriched in poultry and livestock isolates but largely absent from human-associated sub-clusters, indicating their value as host-associated genetic markers. Our findings refine the phylogenetic structure of E. coli CC38 and identify plasmid markers that may enhance genomic surveillance of zoonotic transmission. These results highlight the importance of a One Health approach to monitor antimicrobial resistance across human, food, and animal reservoirs. Together, these insights support data-driven One Health surveillance and intervention strategies. Antibiotic-resistant bacteria are a growing concern for both human and animal health. This study examined a specific group of E. coli bacteria, which can cause serious infections. By comparing the genomes of bacteria, isolated from people, food, and animals in Denmark and around the world, the researchers mapped how different lineages are related and where they are most likely to come from. The results show that some strains found in humans may have originated in poultry. The study also identified two small DNA elements strongly linked to bacteria from poultry and livestock. These elements could help trace how resistant bacteria move between animals and humans, supporting more effective disease surveillance and antibiotic resistance prevention. Roer et al. analyze genomes of Escherichia coli clonal complex 38 from humans, animals, and food to investigate its spread and host associations. They find distinct human and poultry lineages and identify plasmid markers linked to animal adaptation and zoonotic transmission.

BACKGROUND:In February, 2023, an outbreak of Enterobacter hormaechei ST79 carrying blaNDM-5 and blaOXA-48 was linked to contaminated dicloxacillin capsules administered to approximately 79 000 individuals in Denmark. Initial clonal outbreak investigations identified 11 patients with the E hormaechei ST79 outbreak strain, which carried blaNDM-5 on a distinct IncX3 plasmid, and in nine cases, blaOXA-48 was on a distinct IncL plasmid. Interspecies plasmid transfer was observed in one patient, suggesting a potential plasmid-mediated outbreak involving other Enterobacterales. However, no studies have characterised the progression of a clonal outbreak originating from a contaminated medicine into plasmid-mediated dissemination of carbapenemase genes. Hence, we aimed to characterise the clonal and plasmid-mediated spread of carbapenemase genes in this outbreak. METHODS:We conducted a retrospective genomic and epidemiological investigation using existing short-read whole-genome sequencing data from all carbapenemase-producing Enterobacterales (CPE) from the Danish national surveillance, collected between Jan 1, 2014, and Oct 1, 2023. All confirmed CPE isolates were eligible for inclusion. Using in-silico screening for unique fragments of the two outbreak plasmids, we selected 160 isolates for long-read sequencing to obtain complete plasmid sequences for outbreak investigation. Analyses were descriptive and included comparison of sequence identity and coverage to define outbreak-associated plasmids and summary statistics of patient characteristics. FINDINGS:Data from 1829 isolates were obtained. We detected 16 of 53 isolates involved in the outbreak using conventional outbreak detection methods. The remaining 37 isolates were detected using plasmid-specific screening and long-read sequencing. 15 patients carried the outbreak E hormaechei strain, including the 11 patients previously reported. Three of the 15 patients presented with at least one additional bacterial species carrying one or both outbreak plasmids (pDcap_OXA-48 and pDcap_NDM-5). A further 24 patients, sampled between July 1, 2020, and Oct 1, 2023, presented with other Enterobacterales carrying one or both outbreak-associated plasmids but not the original E hormaechei ST79 strain. In four cases, outbreak-associated plasmids differed structurally from the original outbreak plasmid. INTERPRETATION:This study describes how a clonal CPE outbreak caused by a contaminated medicine evolved into a complex plasmid-mediated outbreak involving multiple Enterobacterales species. Most patients related to the outbreak did not present with the original E hormaechei ST79 outbreak strain and were therefore not identified using standard outbreak detection methods. These findings highlight the importance of using plasmid-focused approaches in outbreak investigations. FUNDING:The Danish Ministry of Health, SSI-Seq (cofunded by EU4Health).

BACKGROUND Increasing incidence rates of invasive Streptococcus dysgalactiae subspecies equisimilis (iSDSE) have been detected worldwide. AIM We aimed to investigate iSDSE infection incidence rates in Denmark during 2014–2024, and characterise the genomic population structure of a subset of iSDSE isolates and their antimicrobial resistance (AMR). METHODS Using national register data, we estimated overall and sex-/age-stratified iSDSE incidences during 2014–2024, by retrospectively identifying cases of invasive infections with group C and G streptococci or S. dysgalactiae (including specified as subspecies equisimilis). From the voluntary national beta-haemolytic streptococci laboratory surveillance system, whole-genome-sequenced isolates from August 2020−September 2022 were used to investigate the iSDSE genomic population structure. Susceptibility to penicillin, erythromycin and clindamycin was determined and AMR genes identified. RESULTS During 2014–2024, iSDSE incidence rates increased significantly (linear trend analysis p < 0.001) with mean annual incidence ranging between 10.3 and 16.4 per 100,000, peaking in 2023. Incidence was higher in males, increasing with older age. Nearly 75% of the 1,223 iSDSE isolates belonged to four of 14 genetic clusters. Sequence types (STs) ST20 and ST17 were most prevalent, while emm-type stG62647, a variant associated internationally with higher virulence, dominated. All isolates were phenotypically susceptible to penicillin but approximately 10% were respectively erythromycin and clindamycin resistant. High erythromycin resistance prevalence (57%; 39/68), coinciding with gene ermA, occurred in one genetic cluster. CONCLUSION The findings illustrate the need for national registry-based surveillance to detect epidemiological changes and potential outbreaks. Further, continuous genomic surveillance can monitor the occurrence and expansion of genetic clades and AMR genes.

In seven EU/EEA countries, the emergence of NDM-5-producing Enterobacter hormaechei ST1344 among patients has been detected. In minimum spanning tree analysis of core genome-multilocus sequence-typing (cgMLST) profiles, isolates cluster with ≤ 4 allelic differences. The outbreak includes 57 cases (29 female/28 male; median age: 73 years), which occurred between March 2025 and April 2026. Many were hospitalised (n = 45), some with extensive prior medical treatment, and only three reported travel abroad. A cross-border investigation, including coordinated exposure questionnaires, has not yet identified a source.

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.

Background Vancomycin-resistant enterococci (VRE) are increasing in Denmark and Europe. Linezolid and vancomycin-resistant enterococci (LVRE) are of concern, as treatment options are limited. Vancomycin-variable enterococci (VVE) harbour the vanA gene complex but are phenotypically vancomycin-susceptible. Aim The aim was to describe clonal shifts for VRE and VVE in Denmark between 2015 and 2022 and to investigate genotypic linezolid resistance among the VRE and VVE. Methods From 2015 to 2022, 4,090 Danish clinical VRE and VVE isolates were whole genome sequenced. We extracted vancomycin resistance genes and sequence types (STs) from the sequencing data and performed core genome multilocus sequence typing (cgMLST) analysis for Enterococcus faecium. All isolates were tested for the presence of mutations or genes encoding linezolid resistance. Results In total 99% of the VRE and VVE isolates were E. faecium. From 2015 through 2019, 91.1% of the VRE and VVE were vanA E. faecium. During 2020, to the number of vanB E. faecium increased to 254 of 509 VRE and VVE isolates. Between 2015 and 2022, seven E. faecium clusters dominated: ST80-CT14 vanA, ST117-CT24 vanA, ST203-CT859 vanA, ST1421-CT1134 vanA (VVE cluster), ST80-CT1064 vanA/vanB, ST117-CT36 vanB and ST80-CT2406 vanB. We detected 35 linezolid vancomycin-resistant E. faecium and eight linezolid-resistant VVEfm. Conclusion From 2015 to 2022, the numbers of VRE and VVE increased. The spread of the VVE cluster ST1421-CT1134 vanA E. faecium in Denmark is a concern, especially since VVE diagnostics are challenging. The finding of LVRE, although in small numbers, ia also a concern, as treatment options are limited.

BACKGROUND:Bacteroides fragilis group species are the most frequently encountered bacteria involved in anaerobic bacteraemia and associated with high mortality rates. In 2012, we performed the first national study of antimicrobial susceptibility in the B. fragilis group from blood cultures in Denmark. OBJECTIVES:The purpose of the present study was to compare the antimicrobial susceptibility rates of piperacillin-tazobactam, meropenem, clindamycin and metronidazole in the B. fragilis group from blood cultures in Denmark in 2022 with susceptibility rates from 2012. In addition, we wanted to investigate whether changes to susceptibility was related to the overall use of the specified antimicrobial agents from 2012 to 2022. METHODS:Antimicrobial susceptibility testing was performed in accordance with EUCAST guidelines using the agar dilution method and the disc diffusion method. RESULTS:The study showed a seemingly considerable increase in resistance in the B. fragilis group (n = 234) to piperacillin-tazobactam from a reported 8.5% in 2012 to 42.7% in 2022. Resistance towards meropenem also increased from a reported 3.4% to 10.7%. Most of the increase in resistance for piperacillin-tazobactam and meropenem is caused by a recent EUCAST breakpoint change. Metronidazole still has the lowest resistance rate for the B. fragilis group (one isolate, 0.4%) in this study. The sales of piperacillin-tazobactam in the same period revealed a corresponding increase (+130%), whereas meropenem sales were stable. CONCLUSION:The results underscore the need for timely routine antimicrobial susceptibility testing of B. fragilis group species and questions piperacillin-tazobactam monotherapy as empiric treatment for septic patients with a suspected abdominal source.

A surge in gonorrhoea in Denmark has occurred since 2022, a 46% increase from 2021. National surveillance, leveraging mandatory reporting and epidemiological data, highlights three distinct clades linked to heterosexual transmission. Despite the rise, these exhibit high susceptibility, contrasting MSM-associated strains. Geographical hotspots and age-specific patterns further illuminate transmission dynamics. The combination of genomic and epidemiological data provides novel insights into the evolving landscape of gonorrhoea, indicating potential shifts in infection dynamics and transmissibility.

Urinary tract infections (UTIs) are a leading infectious cause of emergency department admission. Early UTI diagnosis is challenging, and a faster, preferably point-of-care urine analysis is necessary. We aimed to evaluate the diagnostic accuracy of urine flow cytometry (UFC) and urine dipstick analysis (UDA) in identifying bacteriuria and UTIs. This study included adults suspected of an infection admitted to three Danish emergency departments. UFC and UDA were the index tests, and urine culture and an expert panel diagnosis were the reference tests. We used logistic regression and receiver operator characteristics curves to find each test’s optimal model and cut-off. We enrolled 966 patients and performed urine cultures on 786. Urine culture was positive in 337, and 200 patients were diagnosed with a UTI. The UFC model ruled out bacteriuria in 10.9% with a negative predictive value (NPV) of 94.6% and ruled out UTI in 38.6% with an NPV of 97.0%. UDA ruled out bacteriuria in 52.1% with an NPV of 79.2% and UTI in 52.8% with an NPV of 93.9%. Neither UFC nor UDA performed well in ruling out bacteriuria in our population. In contrast, both tests ruled out UTI safely and in clinically relevant numbers.

BACKGROUND:Rapid and accurate detection of pathogens is needed in community-acquired pneumonia (CAP) to enable appropriate antibiotics and to slow the development of antibiotic resistance. We aimed to compare the effect of point-of-care (POC) polymerase chain reaction (PCR) detection of respiratory pathogens added to standard care with standard care only (SCO) on antibiotic prescriptions after acute hospital admission. METHODS AND FINDINGS:We performed a superiority, parallel-group, open-label, multicentre, randomised controlled trial (RCT) in 3 Danish medical emergency departments (EDs) from March 2021 to February 2022. Adults acutely admitted with suspected CAP during the daytime on weekdays were included and randomly assigned (1:1) to POC-PCR (The Biofire FilmArray Pneumonia Panel plus added to standard care) or SCO (routine culture and, if requested by the attending physician, target-specific PCR) analysis of respiratory samples. We randomly assigned 294 patients with successfully collected samples (tracheal secretion 78.4% or expectorated sputum 21.6%) to POC-PCR (n = 148, 50.4%) or SCO (146, 49.6%). Patients and investigators owning the data were blinded to the allocation and test results. Outcome adjudicators and clinical staff at the ED were not blinded to allocation and test results but were together with the statistician, blinded to data management and analysis. Laboratory staff performing standard care analyses was blinded to allocation. The study coordinator was not blinded. Intention-to-treat and per protocol analysis were performed using logistic regression with Huber-White clustered standard errors for the prescription of antibiotic treatment. Loss to follow-up comprises 3 patients in the POC-PCR (2%) and none in the SCO group. Intention-to-treat analysis showed no difference in the primary outcome of prescriptions of no or narrow-spectrum antibiotics at 4 h after admission for the POC-PCR (n = 91, 62.8%) odds ratio (OR) 1.13; (95% confidence interval (CI) [0.96, 1.34] p = 0.134) and SCO (n = 87, 59.6%). Secondary outcomes showed that prescriptions were significantly more targeted at 4-h OR 5.68; (95% CI [2.49, 12.94] p < 0.001) and 48-h OR 4.20; (95% CI [1.87, 9.40] p < 0.001) and more adequate at 48-h OR 2.11; (95% CI [1.23, 3.61] p = 0.006) and on day 5 in the POC-PCR group OR 1.40; (95% CI [1.18, 1.66] p < 0.001). There was no difference between the groups in relation to intensive care unit (ICU) admissions OR 0.54; (95% CI [0.10, 2.91] p = 0.475), readmission within 30 days OR 0.90; (95% CI [0.43, 1.86] p = 0.787), length of stay (LOS) IRR 0.82; (95% CI [0.63, 1.07] p = 0.164), 30 days mortality OR 1.24; (95% CI [0.32, 4.82] p = 0.749), and in-hospital mortality OR 0.98; (95% CI [0.19, 5.06] p = 0.986). CONCLUSIONS:In a setting with an already restrictive use of antibiotics, adding POC-PCR to the diagnostic setup did not increase the number of patients treated with narrow-spectrum or without antibiotics. POC-PCR may result in a more targeted and adequate use of antibiotics. A significant study limitation was the concurrent Coronavirus Disease 2019 (COVID-19) pandemic resulting in an unusually low transmission of respiratory virus. TRIAL REGISTRATION:ClinicalTrials.gov (NCT04651712).

A highly virulent sub-lineage of the Streptococcus pyogenes M1 clone has been rapidly expanding throughout Denmark since late 2022 and now accounts for 30% of the new invasive group A streptococcal infections. We aimed to investigate whether a shift in variant composition can account for the high incidence rates observed over winter 2022/23, or if these are better explained by the impact of COVID-19-related restrictions on population immunity and carriage of group A Streptococcus.

Objectives: This study aimed to characterise carbapenemase-producing Acinetobacter baumannii ( A. baumannii ) isolates from Danish patients using whole genome sequencing (WGS). It also compared typing and epidemiological data for further investigation of the spread and origin of the carbapenemaseproducing A. baumannii isolates.Methods: From 1 January 2014 to 30 September 2021, 141 carbapenemase-producing A. baumannii isolates, received at the national reference laboratory at Statens Serum Institut, were investigated using WGS. Multilocus sequence typing (ML ST) and cgML ST data, obtained by SeqSphere + software, were linked to data related to source of isolation, patient age and sex, hospital admission and travel history.Results: Most of the carbapenemase-producing A. baumannii isolates were from males ( n = 100, 71%). Most patients ( n = 88, 63%) had travelled outside Scandinavia before admission to a Danish hospital. The most prevalent carbapenemase gene was bla OXA-23 ( n = 124). Isolates belonging to the dominating international clone IC2 accounted for 78% of all isolates. A new international ST164/OXA-91 clone, proposed to be named IC11, was recognised and described. The cgMLST analysis revealed 17 clusters, reflecting both sporadic travel to similar geographical areas and confirmed outbreaks in Danish hospitals.Conclusions: The occurrence of carbapenemase-producing A. baumannii in Denmark was still low; how-ever, isolates belonging to major international clones with a high potential to spread within hospitals, mainly IC2, dominated. OXA-23 was by far the most prevalent carbapenemase detected. Sporadic and travel-related introductions to Danish hospitals, also intra-hospital transmission, could be confirmed, em-phasising the need for continuing vigilance.(C) 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/ )

Objectives: The aim of this study was to evaluate the logistics and diagnostic performances of dipstick analyses compared to their counterpart central laboratory analyses for detection of bacteriuria, proteinuria, hypergly-cemia, ketosis and hematuria.Design and methods: Urine dipstick results, urine culture results, flow cytometric cell counts, U-albumin-to-creatinine ratio, P-glucose and P-beta-hydroxybutyrate were retrospectively reviewed in a cohort of consecutive patients admitted to the medical emergency departments of two Danish hospitals. Sensitivity, specificity and predictive values of traditional dipstick analysis were estimated and dipstick was compared to flow cytometry for detection of significant bacteriuria using logistic regression. Turn-around-time for central laboratory analyses were assessed.Results: For each comparison, 1,997 patients or more were included. Traditional dipstick analyses for proteinuria, bacteriuria and ketosis reached sensitivities of up to 90%, while sensitivity for hyperglycemia was 59%. Flow cytometry outperformed traditional dipstick analysis for detection of bacteriuria with a difference in the area under the ROC-curve of 0.07. Turn-around-times for 95% delivery of central laboratory analysis results ranged from approximately 11/2 to 2 h. Conclusions: For the detection of bacteriuria and albuminuria, central laboratory analyses reach better perfor-mance than dipstick analysis while achieving acceptable turn-around-times and are thus viable alternatives to dipstick analysis. For detection of ketosis and hyperglycemia, dipstick analysis does not perform adequately, but as very short turn-around-time is often required, these conditions may be best diagnosed by point-of-care blood test rather than dipstick or central laboratory analyses. Dipstick hemoglobin analysis, flow cytometry and microscopic evaluation may serve each their distinct purposes, and thus are relevant in the emergency department.

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.

Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles.

BACKGROUND:The major obstacle in prescribing an appropriate and targeted antibiotic treatment is insufficient knowledge concerning whether the patient has a bacterial infection, where the focus of infection is and which bacteria are the agents of the infection. A prerequisite for the appropriate use of antibiotics is timely access to accurate diagnostics such as point-of-care (POC) testing.The study aims to evaluate diagnostic tools and working methods that support a prompt and accurate diagnosis of hospitalised patients suspected of an acute infection. We will focus on the most common acute infections: community-acquired pneumonia (CAP) and acute pyelonephritis (APN). The objectives are to investigate (1) patient characteristics and treatment trajectory of the different acute infections, (2) diagnostic and prognostic accuracy of infection markers, (3) diagnostic accuracy of POC urine flow cytometry on diagnosing and excluding bacteriuria, (4) how effective the addition of POC analysis of sputum to the diagnostic set-up for CAP is on antibiotic prescriptions, (5) diagnostic accuracy of POC ultrasound and ultralow dose (ULD) computerized tomography (CT) on diagnosing CAP, (6) diagnostic accuracy of specialist ultrasound on diagnosing APN, (7) diagnostic accuracy of POC ultrasound in diagnosing hydronephrosis in patients suspected of APN.METHODS AND ANALYSIS:It is a multifaceted multicentre diagnostic study, including 1000 adults admitted with suspicion of an acute infection. Participants will, within the first 24 hours of admission, undergo additional diagnostic tests including infection markers, POC urine flow cytometry, POC analysis of sputum, POC and specialist ultrasound, and ULDCT. The primary reference standard is an assigned diagnosis determined by a panel of experts.ETHICS, DISSEMINATION AND REGISTRATION:Approved by Regional Committees on Health Research Ethics for Southern Denmark, Danish Data Protection Agency and clinicaltrials.gov. Results will be presented in peer-reviewed journals, and positive, negative and inconclusive results will be published.TRIAL REGISTRATION NUMBERS:NCT04661085, NCT04681963, NCT04667195, NCT04652167, NCT04686318, NCT04686292, NCT04651712, NCT04645030, NCT04651244.

Candida albicans and Candida glabrata are opportunistic fungal pathogens with increasing incidence worldwide and higher-than-expected prevalence in Denmark. We whole-genome sequenced yeast isolates collected from Danish Clinical Microbiology Laboratories to obtain an overview of the Candida population in the country. The majority of the 30 C. albicans isolates were found to belong to three globally prevalent clades, and, with one exception, the remaining isolates were also predicted to cluster with samples from other geographical locations. Similarly, most of the eight C. glabrata isolates were predicted to be prevalent subtypes. Antifungal susceptibility testing proved all C. albicans isolates to be susceptible to both azoles and echinocandins. Two C. glabrata isolates presented azole-resistant phenotypes, yet all were susceptible to echinocandins. There is no indication of causality between population structure and resistance phenotypes for either species.

OBJECTIVES:The aim of this study was to identify clonally-related carbapenemase-producing Klebsiella pneumoniae complex members that could be involved in outbreaks among hospitalized patients in Denmark, and to identify possible epidemiological links.METHODS:From January 2014 to June 2018, 103 isolates belonging to the K. pneumoniae complex were collected from 102 patients. From the whole-genome sequencing (WGS) data, presence of genes encoding carbapenemase and multilocal sequence typing (MLST) data were extracted. Core genome MLST (cgMLST) cluster analysis was performed. Using data from the Danish National Patient Registry (DNPR) and reported travel history, presumptive outbreaks were investigated for possible epidemiological links.RESULTS:The most common detected carbapenemase gene was blaOXA-48, followed by blaNDM-1. The 103 K. pneumoniae complex isolates belonged to 47 sequence types (STs) and cgMLST subdivided the isolates into 80 different complex types. cgMLST identified 13 clusters with 2-4 isolates per cluster. For five of the 13 clusters, a direct link (the patients stayed at the same ward on the same day) could be detected between at least some of the patients. In two clusters, the patients resided simultaneously at the same hospital, but not the same ward. A possible link (same ward within 1-13 days) was detected for the patients in one cluster. For five clusters detected by cgMLST, no epidemiological link could be detected using data from DNPR.CONCLUSION:In this study, cgMLST combined with patient hospital admission data and travel information was found to be a reliable and detailed approach to detect possible clonal transmission of carbapenemase-producing K. pneumoniae complex members.

Work in wastewater treatment plants (WWTPs) can be associated with respiratory symptoms and diarrhea. The aim of this study was to obtain knowledge about WWTP workers' exposure to airborne bacteria and endotoxin, and the inflammatory potential (TIP) of their exposure, and to evaluate the risk posed by the exposure by 1) calculating a hazard index and relating the exposure to suggested occupational exposure limits (OELs), 2) estimating the potential deposition of bacteria in the airways, 3) relating it to the risk group classification of bacteria by the European Union, and 4) estimating the TIP of the personal exposure. A cohort of 14 workers were followed over one year. Bioaerosols were collected using personal and stationary samplers in a grid chamber house and an aeration tank area. Airborne bacteria were identified using (MALDI-TOF MS), and TIP of exposure was measured using HL-60 cells. A significant effect of season, work task, and person was found on the personal exposure. A hazard index based on exposure levels indicates that the risk caused by inhalation is low. In relation to suggested OELs, 14% and 34% of the personal exposure were exceeded for endotoxin (≥50 EU/m3) and bacteria (≥500 CFU/m3). At least 70% of the airborne bacteria in the grid chamber house and the aeration tank area could potentially deposit in the lower respiratory tract. From the personal samples, three of 131 bacterial species, Enterobacter cloacae, Staphylococcus aureus, and Yersinia enterocolitica are classified within Risk Group 2. Seven additional bacteria from the stationary samples belong to Risk Group 2. The bacterial species composition was affected significantly by season (p = 0.014) and by sampling type/area (p = 0.001). The TIP of WWTP workers' exposure was higher than of a reference sample, and the highest TIP was measured in autumn. TIP of personal exposure correlated with bacterial exposure. Based on the geometric average exposures to endotoxin (9.2 EU/m3) and bacteria (299 CFU/m3) and based on the calculated hazard index, the risk associated with exposure is low. However, since 43 of 106 exposure levels exceed suggested OELs, the TIP of exposure was elevated and associated with bacterial exposure, and WWTP workers were exposed to pathogenic bacteria, a continued focus on preventive measures is important. The identification of bacteria to species level in personal samples was necessary in the risk assessment, and measurement of the microbial composition made the source tracking possible.

Background Carbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark. Aim Molecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019. Methods For the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST). Results In total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark. Conclusion Import of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.