Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022.

Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.

Three cases of Sutterella wadsworthensis bacteremia secondary to abdominal infections.

The anaerobic bacterium Sutterella wadsworthensis has previously been isolated from the human intestine, both in healthy individuals and patients with gastrointestinal disorders, and the clinical significance of this bacterium is unknown. In this case report, we describe three cases of bacteremia with Sutterella wadsworthensis, from patients with recent intraabdominal surgery.

Helicobacter cinaedi bacteraemia secondary to enterocolitis in an immunocompetent patient.

BACKGROUND: Helicobacter cinaedi are motile, gram-negative spiral rods with a natural reservoir in the intestinal tract of hamsters and rhesus monkeys. In humans, H. cinaedi has been reported in different human infections like fever, abdominal pain, gastroenteritis, proctitis, diarrhoea, erysipelas, cellulitis, arthritis, and neonatal meningitis typically diagnosed by positive blood cultures. Even though H. cinaedi has been detected from human blood and stool the entry of H. cinaedi into the blood stream was undocumented until quite recently. The use of pulse-field gel electrophoresis (PFGE) demonstrated that stool- and blood-derived H. cinaedi strains were consistent. CASE PRESENTATION: Here, we describe a rare Danish case of H. cinaedi bacteraemia in an immunocompetent 44-year-old male with diarrhoea. We isolated H. cinaedi from a blood culture taken at admission, and from a FecalSwab taken at day six despite ongoing antibiotic therapy. Next, we made a genetic comparison of both isolates by use of Multi-locus sequence typing (MLST)- and Single nucleotide polymorphism (SNP)-analysis. The two isolates were identical with zero SNPs and by use of MLST the isolate was identified as a novel ST20, confirming previous data of the intestinal tract as a route of H. cinaedi bacteraemia. The results of our AST showed a resistance pattern with higher MICs for ciprofloxacin and clarithromycin than for ampicillin, amoxicillin, gentamicin, and imipenem. The patient was cured with targeted therapy with pivampicillin; however, the primary source of transmission was unknown. CONCLUSIONS: In conclusion, this case of H. cinaedi bacteraemia secondary to enterocolitis in an immunocompetent patient provide clear evidence that one route of infection occurs through translocation from the intestinal tract to the bloodstream. Helicobacter cinaedi from blood and faeces were identical with a novel ST20, resistant to ciprofloxacin and clarithromycin however, the patient was cured with oral pivampicillin.

Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Immunocompromised Host Displaying Treatment Induced Viral Evolution.

We report a coronavirus disease 2019 case with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persisting beyond 333 days in an immunocompromised patient with chronic lymphocytic leukemia, asymptomatically carrying infectious SARS-CoV-2 at day 197 postdiagnosis. In addition, viral sequencing indicates major changes in the spike protein over time, temporally associated with convalescent plasma treatment.

First Danish case of infective endocarditis caused by Enterococcus hirae.

Enterococcus hirae, a member of the Enterococcus genus, is known to cause infections, including infective endocarditis (IE), in animal species. In humans, E. hirae is an uncommon pathogen, but has been associated with severe and recurrent disease. Here, we report the first Danish case of E. hirae native aortic valve IE in a 62-year-old woman with no history of heart disease. She presented to the hospital with symptoms of gastroenteritis but no signs of heart disease. Nevertheless, blood culture revealed growth of E. hirae, and a transoesophageal echocardiography demonstrated a mobile mass adherent to the aortic valve, compatible with a vegetation. The patient was successfully treated for E. hirae native aortic valve IE with 4 weeks of intravenous benzylpenicillin in combination with gentamicin for the initial 2 weeks. To the best of our knowledge, this is the first documented case of E. hirae IE in Denmark and the sixth documented case worldwide.

Rare Elizabethkingia anophelis meningitis case in a Danish male.

INTRODUCTION: Elizabethkingia anophelis is a Gram-negative, aerobic, non-motile rod belonging to the family Flavobacteriaceae. Over the last 5 years, it has emerged as an opportunistic human pathogen involved in neonatal meningitis and sepsis, as well as nosocomial outbreaks. It has been isolated from the midgut of the Anopheles gambiae mosquito, but there is no evidence for a role of the mosquito in human infections, and very little is known regarding the routes of transmission to humans. Recent studies, primarily from South-East Asia, suggest that E. anophelis, and not Elizabethkingia meningoseptica, is the predominant human pathogen of this genus. However, identification to the species level has been difficult due to the limitations of the current MALDI-TOF MS (matrix-associated laser desorption ionization-time of flight MS) systems for correct species identification. CASE PRESENTATION: Here, we present a rare case of E. anophelis meningitis in a Danish male, who had a travel exposure to Malaysia 7 weeks before hospitalization. A multidrug-resistant Elizabethkingia species was isolated from blood and cerebrospinal fluid, and genomic sequencing was used to characterize the phylogenetic position of the isolate, which was determined as associated with previously described sublineage 11. The patient was successfully treated with intravenous moxifloxacin and rifampicin for 2 weeks with no major sequelae, but we did not find the source of transmission. CONCLUSION: All clinical microbiologists should be aware of the present limitations of the MALDI-TOF MS systems for correct species identification, and therefore we recommend the use of genome sequencing for the correct identification at the species and sublineage level.

The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction.

Studies of the kinetics of dissimilatory sulfate reduction in marine sediment have shown that a mixture of marine sulfate-reducing bacteria (SRB) can reduce sulfate with both a high and low apparent sulfate half-saturation constant (Km). However, all marine pure cultures investigated have shown only low-sulfate affinity sulfate reduction kinetics. It remains unknown whether marine high sulfate-affinity sulfate reduction is catalyzed by unknown SRB or whether known SRB possess unrecognized high-affinity sulfate reduction systems. We used 35S-sulfate incubation experiments to show that cultures of Desulfobacterium autotrophicum HMR2 will switch from low-affinity to high-affinity sulfate reduction when sulfate concentrations fall below 500 µM. The mean Km was 150 µM at high sulfate concentrations and 8 µM at low sulfate concentrations. The high-affinity Km value is comparable to values found in SRB inhabiting freshwater sediments and D. autotrophicum cultures could deplete sulfate to below our detection limit of 25 nM. The switch in Km value was accompanied by a change in the expression of genes encoding membrane-bound transport proteins putatively involved in sulfate uptake in D. autotrophicum. Our results demonstrate that a marine sulfate reducer can efficiently reduce sulfate at both high and low sulfate concentrations, possibly by activation of different sulfate transporters in the membrane.