Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants.

The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.

Raoultibacter phocaeensis sp. nov., A New Bacterium Isolated from a Patient with Recurrent Clostridioides difficile Infection.

Strain Marseille-P8396T is a new species isolated from a patient with recurrent Clostridioides difficile infection. Its optimal growth condition was observed at pH of 7.5, at a temperature of 37 °C after 72 h of incubation on Columbia agar (BioMérieux, France) with 5% sheep blood, under an anaerobic atmosphere. Strain Marseille-P8396T cells are Gram-positive rods, nonspore-forming, and nonmotile. 9-Octadecenoic acid (41.9%), hexadecanoic acid (22.5%), and 11-Octadecenoic acid (11.0%) represent the major fatty acid of strain Marseille-P8396T. The optimal growth condition of strain Marseille-P8396T was observed at 37 °C after 72 h of incubation under an anaerobic atmosphere, pH ranging from 6.5 to 8.5, and salinity of 0.5 to 7.5%. Its genome (Genbank Accession Number NZ_CABDUX000000000) size was 3.86 Mb with 59.4 mol% of G+C content, and 3,124 protein-coding genes. The 16S rRNA gene sequence (Genbank accession number NR_148574.1) of strain Marseille-P8396T shared a similarity of 98.71% with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number NR_148574.1), currently the most closely related species. However, the OrthoANI and digital DNA-DNA hybridization values with Raoultibacter timonensis strain Marseille-P3277T (Genbank accession number OEPT01000000) were 80.15% and 24.6 ± 4.8%, respectively. Taken together, these results clearly demonstrate that strain Marseille-P8396T represents a new species within the genus Raoultibacter described here as Raoultibacter phocaeensis sp. nov. (type strain: Marseille-P8396T=CSUR8396T=CECT 30202T).

Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients.

While populations at risk for severe SARS-CoV-2 infections have been clearly identified, susceptibility to the infection and its clinical course remain unpredictable. As the nasopharyngeal microbiota may promote the acquisition of several respiratory infections and have an impact on the evolution of their outcome, we studied the nasopharyngeal microbiota of COVID-19 patients in association with baseline disease-related clinical features compared to that of patients tested negative. We retrospectively analyzed 120 nasopharyngeal pseudonymized samples, obtained for diagnosis, divided into groups (infected patients with a favorable outcome, asymptomatic, and deceased patients) and patients tested negative for SARS-CoV-2, by using Illumina-16S ribosomal ribonucleic acid (rRNA) sequencing and specific polymerase chain reaction (PCR) targeting pathogens. We first found a depletion of anaerobes among COVID-19 patients, irrespective of the clinical presentation of the infection (p < 0.029). We detected 9 taxa discriminating patients tested positive for SARS-CoV-2 from those that were negative including Corynebacterium propinquum/pseudodiphtericum (p ≤ 0.05), Moraxella catarrhalis (p ≤ 0.05), Bacillus massiliamazoniensis (p ≤ 0.01), Anaerobacillus alkalidiazotrophicus (p ≤ 0.05), Staphylococcus capitis subsp. capitis (p ≤ 0.001), and Afipia birgiae (p ≤ 0.001) with 16S rRNA sequencing, and Streptococcus pneumoniae (p ≤ 0.01), Klebsiella pneumoniae (p ≤ 0.01), and Enterococcus faecalis (p ≤ 0.05) using real-time PCR. By designing a specific real-time PCR, we also demonstrated that C. propinquum is decreased in asymptomatic individuals compared to other SARS-CoV 2 positive patients. These findings indicate that the nasopharyngeal microbiota as in any respiratory infection plays a role in the clinical course of the disease. Further studies are needed to elucidate the potential role in the clinical course of the disease of M. catarrhalis, Corynebacterium accolens, and more specifically Corynebacterium propinquum/diphteriticum in order to include them as predictors of the severity of COVID-19.

Description of Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., three new bacteria isolated from human blood.

Blood is precious tissue that is normally sterile. With the aim of diagnosing the cause of bacteremia, three bacterial strains were isolated from three different individuals. Strains Marseille-P7157T and Marseille-Q2854T are Gram-stain positive, non-spore-forming rod-shaped bacteria, while strain Marseille-P8049T is a Gram-stain negative, motile, non-spore-forming and rod-shaped bacterium. The major fatty acids found (>30%) were hexadecanoic acid for strain Marseille-P8049T and 12-methyl tetradecanoic acid for both strains Marseille-P7157T and Marseille-P2854T. The 16S rRNA gene sequence analysis shows that strains Marseille-P8049 and Marseille-Q2854T have sequence similarity of 96.8%, 99.04%, and 98.3% with Acinetobacter ursingii strain LUH3792 (NR_025392.1), Gulosibacter faecalis strain B187 (NR_041812.1), and Schaalia canis strain CCUG 41706 (NR_025366.1), respectively. In addition, strains Marseille-Q2854T, Marseille-P8049T and Marseille-P7157T shared with their closely related species cited above the following DDH values: 19.5%, 24.4%, and 20.2%, respectively. Based on these phenotypic and genomic findings, we consider that strains Marseille-P8049T (= CSUR P8049 = CECT 30350), Marseille-P2854T ( = CSUR Q2854 = CECT 30120) and Marseille-P7157T ( = CSUR P7157 = CECT 30048) are new bacterial species, for which the names Acinetobacter ihumii sp. nov., Microbacterium ihumii sp. nov., and Gulosibacter massiliensis sp. nov., are proposed.