First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023.

We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant with many spike gene mutations was classified as a variant under monitoring by the World Health Organization on 17 August 2023. Further global monitoring of COVID-19, BA.2.86 and other SARS-CoV-2 variants is highly warranted.

Rectally shed SARS-CoV-2 in COVID-19 inpatients is consistently lower than respiratory shedding and lacks infectivity.

OBJECTIVES: Assessment of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been propagated during intestinal passage and infectivity is conserved when shed rectally by hospitalized individuals. METHODS: An exploratory cohort study including 28 inpatients with coronavirus disease 2019 with estimation of RNA levels by RT-PCR and of viral infectivity by culturing of viral material sampled concomitantly and identically from pharynx and rectum. RESULTS: SARS-CoV-2 RNA was detected more frequently (91%, 30/33 versus 42%, 14/33, p <0.0001) and at higher concentrations (median levels 2 190 186 IU/mL versus 13 014 IU/mL, p <0.0001) in the pharyngeal swabs than in the rectal swabs. For all sample pairs (n = 33) the rectal swabs contained undetectable or lower SARS-CoV-2 RNA concentrations than their paired pharyngeal swabs. Replicative virus was found in 37% (11/30) of the PCR-positive pharyngeal swabs, whereas none of the PCR-positive rectal swabs could be cultured (0%, 0/14) despite containing SARS-CoV-2 RNA concentrations up to 1 544 691 IU/mL. CONCLUSIONS: Our data draw into question whether SARS-CoV-2 is transmitted readily from faeces.

Prolonged viral shedding of SARS-CoV-2 in two immunocompromised patients, a case report.

BACKGROUND: The duration of viable Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) shedding in immunocompromised patients is still unknown. This case report describes the duration of viable SARS-CoV-2 in two immunocompromised patients with completely different clinical courses and further addresses the immunological aspects. CASE PRESENTATIONS: Oropharyngeal swaps were collected continuously during hospitalization for two immunocompromised patients infected with SARS-CoV-2 and sent for analysis to real time reverse transcription polymerase chain reaction (RT-PCR), viral culture assessed by plaque assay and full genome sequencing. Blood samples for flow cytometry and further immunological analysis were taken once during admission. One patient was without symptoms of Coronavirus disease 2019 (COVID-19) whereas the other had severe respiratory symptoms requiring a stay at an intensive care unit (ICU) and treatment with remdesivir and dexamethasone. Despite their difference in clinical courses, they both continuously shed SARS-CoV-2 with high viral loads in culture. Both patients had undetectable anti SARS-CoV-2 IgG levels about 2 weeks after the first positive real time RT-PCR test of SARS-CoV-2, marked expansions of virus reactive CD8+ T cells but cellular markers indicative of attenuated humoral immunity. CONCLUSIONS: Our case illustrates the importance of distinguishing isolation guidelines for patients infected with SARS-CoV-2 according to their immunological status. Furthermore, it demonstrates the need for immune markers relating to viral shedding in immunocompromised patients.

Using core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak.

OBJECTIVES: Until July 2016, vancomycin-resistantEnterococcus faecium (VREfm) was sporadically detected in Odense University Hospital, Denmark. After July 2016, the number of VREfm cases increased. This study aimed to apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to type and analyse VREfm isolates collected at a single Danish hospital and to compare the results with cgMLST data from other regions of Denmark to trace transmission. METHODS: A total of 38 VREfm clinical isolates from inpatients at the hospital in the period January 2014 through June 2017 were included in the study and analysed using whole-genome sequencing. Use of SeqSphere + software was initiated from the beginning of June 2017 to obtain MLST, cgMLST and epi curves. Admission histories were incorporated and national surveillance data on cgMLST were used to identify transmission routes. RESULTS: Six different sequence types (STs) were identified, the most frequent being ST80, ST117 and ST203. cgMLST subdivided the 38 isolates into 18 different complex types (CTs) with 13 isolates (34%) belonging to ST80-CT993. Epi curves indicated transmission of ST80-CT993 in several departments. Transmission from patients transferred from other hospitals was not identifiable. Infection control interventions launched in one department ended the outbreak. CONCLUSION: The high resolution of cgMLST allowed for detailed interpretation with evidence of nosocomial transmission of specific CTs. cgMLST made it easy to compare our local isolates with national findings, thereby clarifying transmission routes. Supplemented with admission histories, cgMLST targeted the epidemiological investigation and delineated the expensive and time-consuming infection control interventions.

Potential anti-EBV effects associated with elevated interleukin-21 levels: a case report.

BACKGROUND: Germinal center derived memory B cells and plasma cells constitute, in health and during EBV reactivation, the largest functional EBV reservoir. Hence, by reducing germinal center derived formation of memory B cells and plasma cells, EBV loads may be reduced. Animal and in-vitro models have shown that IL-21 can support memory B and plasma cell formation and thereby potentially contribute to EBV persistence. However, IL-21 also displays anti-viral effects, as mice models have shown that CD4+ T cell produced IL-21 is critical for the differentiation, function and survival of anti-viral CD8+ T cells able to contain chronic virus infections. CASE PRESENTATION: We present immunological work-up (flow-cytometry, ELISA and genetics) related to a patient suffering from a condition resembling B cell chronic active EBV infection, albeit with moderately elevated EBV copy numbers. No mutations in genes associated with EBV disease, common variable immunodeficiency or pertaining to the IL-21 signaling pathway (including hypermorphic IL-21 mutations) were found. Increased (> 5-fold increase 7 days post-vaccination) CD4+ T cell produced (p < 0.01) and extracellular IL-21 levels characterized our patient and coexisted with: CD8+ lymphopenia, B lymphopenia, hypogammaglobulinemia, compromised memory B cell differentiation, absent induction of B-cell lymphoma 6 protein (Bcl-6) dependent peripheral follicular helper T cells (pTFH, p = 0.01), reduced frequencies of peripheral CD4+ Bcl-6+ T cells (p = 0.05), compromised plasmablast differentiation (reduced protein vaccine responses (p < 0.001) as well as reduced Treg frequencies. Supporting IL-21 mediated suppression of pTFH formation, pTFH and CD4+ IL-21+ frequencies were strongly inversely correlated, prior to and after vaccination, in the patient and in controls, Spearman's rho: - 0.86, p < 0.001. CONCLUSIONS: To the best of our knowledge, this is the first report of elevated CD4+ IL-21+ T cell frequencies in human EBV disease. IL-21 overproduction may, apart from driving T cell mediated anti-EBV responses, disrupt germinal center derived memory B cell and plasma cell formation, and thereby contribute to EBV disease control.

Changes in genetically drifted H3N2 influenza A viruses and vaccine effectiveness in adults 65 years and older during the 2016/17 season in Denmark.

BACKGROUND: In Denmark, influenza A virus of the subtype H3N2 has been dominating the 2016/17 season, as in most countries of the Northern Hemisphere. OBJECTIVES: This study was conducted as part of the Danish seasonal influenza surveillance programme to genetically characterize circulating H3N2 viruses and determine the seasonal vaccine effectiveness (VE) overall in the Danish population and further on the virus cluster level. STUDY DESIGN: Influenza virus positive samples submitted for the national surveillance programme were genetically characterized by sequencing. VE estimates against influenza A and the circulating virus clusters were determined in patients above 65 years using the test-negative case-control design. RESULTS: The genetic characterization revealed several genetically drifted viruses, which could be divided into four main clusters by the defining amino acid substitutions: 3C.2a/N121K/S144K, 3C.2a/T131K/R142K, 3C.2a1, and 3C.2a1/N121K. Some of the drifted viruses appeared to be more prominent in vaccinated or non-vaccinated individuals, respectively. Overall the adjusted VE was 7.4% (95% confidence interval (CI): -6.0-19.2) among inpatients and 19.3% (95% CI: -5.7-38.4) among outpatients, respectively. VE for the four main virus clusters was; cluster 3C.2a1: 38.8% (95% CI: -29.8-71.1), cluster 3C.2a/N121K/S144K: 9.2% (95% CI: -63.0-49.4), cluster 3C.2a/T131K/R142K: 19.0% (95% CI: -85.3-64.6), and cluster 3C.2a1/N121K: -12.2% (95%CI: -129.7-45.2). CONCLUSIONS: Several genetically drifted H3N2 viruses have been circulating in Denmark in the 2016-17 influenza season. An overall low VE was estimated and VE for the four main virus cluster indicate different VEs between the circulating drifted H3N2 viruses.

Influenza vaccine effectiveness in adults 65 years and older, Denmark, 2015/16 - a rapid epidemiological and virological assessment.

In Denmark, both influenza A(H1N1)pdm09 and influenza B co-circulated in the 2015/16 season. We estimated the vaccine effectiveness (VE) of the trivalent influenza vaccine in patients 65 years and older using the test-negative case-control design. The adjusted VE against influenza A(H1N1)pdm09 was 35.0% (95% confidence interval (CI): 11.1-52.4) and against influenza B 4.1% (95% CI: -22.0 to 24.7). The majority of influenza A(H1N1)pdm09 circulating in 2015/16 belonged to the new genetic subgroup subclade 6B.1.

Fatal Septicemia Linked to Transmission of MRSA Clonal Complex 398 in Hospital and Nursing Home, Denmark.

We describe 2 fatal cases of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 septicemia in persons who had no contact with livestock. Whole-genome sequencing of the isolated MRSA strains strongly suggest that both were of animal origin and that the patients had been infected through 2 independent person-to-person transmission chains.

Campylobacter jejuni and Campylobacter coli in wild birds on Danish livestock farms.

BACKGROUND: Reducing the occurrence of campylobacteriosis is a food safety issue of high priority, as in recent years it has been the most commonly reported zoonosis in the EU. Livestock farms are of particular interest, since cattle, swine and poultry are common reservoirs of Campylobacter spp. The farm environment provides attractive foraging and breeding habitats for some bird species reported to carry thermophilic Campylobacter spp. We investigated the Campylobacter spp. carriage rates in 52 wild bird species present on 12 Danish farms, sampled during a winter and a summer season, in order to study the factors influencing the prevalence in wild birds according to their ecological guild. In total, 1607 individual wild bird cloacal swab samples and 386 livestock manure samples were cultured for Campylobacter spp. according to the Nordic Committee on Food Analysis method NMKL 119. RESULTS: The highest Campylobacter spp. prevalence was seen in 110 out of 178 thrushes (61.8 %), of which the majority were Common Blackbird (Turdus merula), and in 131 out of 616 sparrows (21.3 %), a guild made up of House Sparrow (Passer domesticus) and Eurasian Tree Sparrow (Passer montanus). In general, birds feeding on a diet of animal or mixed animal and vegetable origin, foraging on the ground and vegetation in close proximity to livestock stables were more likely to carry Campylobacter spp. in both summer (P < 0.001) and winter (P < 0.001) than birds foraging further away from the farm or in the air. Age, fat score, gender, and migration range were not found to be associated with Campylobacter spp. carriage. A correlation was found between the prevalence (%) of C. jejuni in wild birds and the proportions (%) of C. jejuni in both manure on cattle farms (R(2) = 0.92) and poultry farms (R(2) = 0.54), and between the prevalence (%) of C. coli in wild birds and the proportions (%) of C. coli in manure on pig farms (R(2) = 0.62). CONCLUSIONS: The ecological guild of wild birds influences the prevalence of Campylobacter spp. through the behavioural patterns of the birds. More specifically, wild birds eating food of animal or mixed animal and vegetable origin and foraging on the ground close to livestock were more likely to carry Campylobacter spp. than those foraging further away or hunting in the air. These findings suggest that wild birds may play a role in sustaining the epidemiology of Campylobacter spp. on farms.

Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems.

We compared two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Shimadzu/SARAMIS and Bruker) on a collection of consecutive clinically important anaerobic bacteria (n = 290). The Bruker system had more correct identifications to the species level (67.2% versus 49.0%), but also more incorrect identifications (7.9% versus 1.4%). The system databases need to be optimized to increase identification levels. However, MALDI-TOF MS in its present version seems to be a fast and inexpensive method for identification of most clinically important anaerobic bacteria.

16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures.

A comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n = 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times for identification were 1.5 days and 2.8 days, respectively.