Reassortant Influenza A(H1N1)pdm09 Virus in Elderly Woman, Denmark, January 2021.

A case of human infection with influenza A(H1N1)pdm09 virus containing a nonstructural gene highly similar to Eurasian avian-like H1Nx swine influenza virus was detected in Denmark in January 2021. We describe the clinical case and report testing results of the genetic and antigenic characterizations of the virus.

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen.

The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria. Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy. Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.

Aerococcus urinae and Aerococcus sanguinicola: Susceptibility Testing of 120 Isolates to Six Antimicrobial Agents Using Disk Diffusion (EUCAST), Etest, and Broth Microdilution Techniques.

BACKGROUND: Aerococcus urinae and Aerococcus sanguinicola are relatively newcomers and emerging organisms in clinical and microbiological practice. Both species have worldwide been associated with urinary tract infections. More rarely cases of bacteremia/septicemia and infective endocarditis have been reported. Treatment options are therefore important. Just recently, European recommendations on susceptibility testing and interpretive criteria have been released. OBJECTIVE: In this investigation 120 A. urinae and A. sanguinicola isolates were tested for susceptibility to six antimicrobial agents: Penicillin, cefotaxime, meropenem, vancomycin, linezolid, and rifampicin. METHODS: Three susceptibility testing methods were used; disk diffusion according to The European Committee on Antimicrobial Susceptibility Testing (EUCAST) standardized disk diffusion methodology and MIC determination with Etest and broth microdilution (BMD). All testing was performed with EUCAST media for fastidious organisms. RESULTS: Data obtained in this study were part of the background data for establishing EUCAST breakpoints. MIC values obtained by Etest and BMD were well correlated with disk diffusion results. CONCLUSION: All isolates were found susceptible to all six antimicrobial agents: penicillin, cefotaxime, meropenem, vancomycin, linezolid, and rifampicin.

In silico assessment of virulence factors in strains of Streptococcus oralis and Streptococcus mitis isolated from patients with Infective Endocarditis.

Purpose. Streptococcus oralis and Streptococcus mitis belong to the Mitis group, which are mostly commensals in the human oral cavity. Even though S. oralis and S. mitis are oral commensals, they can be opportunistic pathogens causing infective endocarditis. A recent taxonomic re-evaluation of the Mitis group has embedded the species Streptococcus tigurinus and Streptococcus dentisani into the species S. oralis as subspecies. In this study, the distribution of virulence factors that contribute to bacterial immune evasion, colonization and adhesion was assessed in clinical strains of S. oralis (subsp. oralis, subsp. tigurinus and subsp. dentisani) and S. mitis. Methodology. Forty clinical S. oralis (subsp. oralis, subsp. dentisani and subsp. tigurinus) and S. mitis genomes were annotated with the pipeline PanFunPro and aligned against the VFDB database for assessment of virulence factors.Results/Key findings. Three homologues of pavA, psaA and lmb, encoding adhesion proteins, were present in all strains. Seven homologues of nanA, nanB, ply, lytA, lytB, lytC and iga, of importance regarding survival in blood and modulation of the human immune system, were variously present in the genomes. Few S. oralis subspecies specific differences were observed. iga homologues were identified in S. oralis subsp. oralis, whereas lytA homologues were identified in S. oralis subsp. oralis and subsp. tigurinus. Conclusion. Differences in the presence of virulence factors among the three S. oralis subspecies were observed. The virulence gene profiles of the 40 S. mitis and S. oralis (subsp. oralis, subsp. dentisani and subsp. tigurinus) contribute with important new knowledge regarding these species and new subspecies.

Species identification of Streptococcus bovis group isolates causing bacteremia: a comparison of two MALDI-TOF MS systems.

This study compared two MALDI-TOF MS systems (Biotyper and VITEK MS) on clinical Streptococcus bovis group isolates (n=66). The VITEK MS gave fewer misidentifications and a higher rate of correct identifications than the Biotyper. Only the identification of S. lutetiensis by the VITEK MS was reliable. Additional optimization of the available system databases is needed.

Bacteremia with the bovis group streptococci: species identification and association with infective endocarditis and with gastrointestinal disease.

DNA sequencing of the intergenic spacer (ITS) region was used to identify 53 blood culture isolates that had previously been designated to the bovis group streptococci and clinical data was collected retrospectively from patients' records using a standardized protocol. ITS sequencing identified 19 (35.8%) isolates as Streptococcus gallolyticus subsp. gallolyticus, 12 (22.6%) as S. gallolyticus subsp. pasteurianus, two (3.8%) as S. gallolyticus subsp. macedonicus, seven (13.2%) as S. infantarius subsp. infantarius, 12 (22.6%) as S. lutetiensis and one (1.9%) as S. equinus. The association of S. gallolyticus subsp. gallolyticus with colorectal neoplasia and with infective endocarditis and the association between S. gallolyticus subsp. pasteurianus and pancreatic cancer were found to be clinically important. Also, a very high 1-year mortality rate with S. lutetiensis (66.7%) and S. gallolyticus subsp. pasteurianus (58.7%) bacteremia calls for intensive investigation for underlying disease focusing on the pancreas and the hepatobiliary system.

Draft Genome Sequence of Type Strain Streptococcus gordonii ATCC 10558.

Streptococcus gordonii ATCC 10558(T) was isolated from a patient with infective endocarditis in 1946 and announced as a type strain in 1989. Here, we report the 2,154,510-bp draft genome sequence of S. gordonii ATCC 10558(T). This sequence will contribute to knowledge about the pathogenesis of infective endocarditis.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Gram-positive, catalase-negative cocci not belonging to the Streptococcus or Enterococcus genus and benefits of database extension.

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry with a Bruker Daltonics microflex LT system was applied to 90 well-characterized catalase-negative, Gram-positive cocci not belonging to the streptococci or enterococci. Biotyper version 2.0.43.1 software was used singly or in combination with a database extension generated in this study with 51 collection strains from 16 genera. Most strains were identified by using both databases individually, and some were identified only by applying the combined database. Thus, the methodology is very useful and the generated database extension was helpful.

Unusual distribution of Burkholderia cepacia complex species in Danish cystic fibrosis clinics may stem from restricted transmission between patients.

Forty-four of 48 Burkholderia cepacia complex strains cultured from Danish cystic fibrosis patients were Burkholderia multivorans, a distribution of species that has not been reported before. Although cases of cross infections were demonstrated, no major epidemic clone was found. The species distribution may represent the sporadic acquisition of bacteria from the environment.

Report of the first human case of Caulobacter sp. infection.

A Caulobacter sp. isolate was recovered from the dialysis fluid of a patient undergoing peritoneal dialysis. Bacterial identification included electron microscopy and 16S rDNA sequencing. To our knowledge, this is the first report of human Caulobacter infection. Special growth requirements suggest that Caulobacter spp. may be overlooked in the clinical microbiology laboratory.

[Bacterial meningitis in Denmark 2002-2003. A nation-wide laboratory-based registration]. / Bakteriel meningitis i Danmark 2002 og 2003. Landsdaekkende registrering baseret på laboratoriedata.

UNLABELLED: Notification of bacterial meningitis (BM) is likely to be incomplete, and a recent Danish study indicated that unbalanced notification may bias expected aetiology of BM. Therefore the Danish Bacterial Meningitis Group initiated a national registration of culture-positive BM. METHODS: Laboratory data on all bacterial isolates from cerebrospinal fluid deemed to be clinically relevant were identified on a national basis during 2002 and 2003. Bacterial findings were compared to cases notified during the same period. RESULTS: A total of 404 BM cases were identified. The distribution of bacterial species differed from the national notification data during the same period especially with respect to Staphylococcus aureus (6.7% vs. 0.6%), Escherichia coli (3.5% vs. 0%) and non-Streptococcus pneumoniae streptococci (10% vs. 1.9%). The overall notification-rate was 66%, and was below 20% for S. aureus, E. coli, Enterococcus faecalis, non-S. pneumoniae streptococci and for 13 cases of "other bacteria". Sensitivity to antibiotics in the BM cases was as expected for Northern Europe. Reduced sensitivity to penicillin was found in 2/202 S. pneumoniae, in 2/10 Listeria monocytogenes, and 21/27 S. aureus were penicillin resistant. E. coli was resistant to ampicillin in 5 of 13 cases and to gentamicin in 1 of 11 cases. DISCUSSION: A suboptimal notification rate with an unbalanced species distribution was found. Laboratory based data thus constitute an improved basis for future recommendations for empirical treatment of BM. A continued national collaboration may promote the development of quality indicators for diagnosis and initial treatment of BM.