Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

Introduction: We studied the trend of antimicrobial resistance and consumption at Saint George Hospital University Medical Center (SGHUMC), a tertiary care center in Beirut, Lebanon, with a focus on the SARS-CoV-2 pandemic. Materials and Methods: We calculated the isolation density/1000 patient-days (PD) of the most isolated organisms from 1 January 2015–31 December 2020 that included: E. coli (Eco), K. pneumoniae (Kp), P. aeruginosa (Pae), A. baumannii (Ab), S. aureus (Sau), and E. faecium (Efm). We considered March–December 2020 a surrogate of COVID-19. We considered one culture/patient for each antimicrobial susceptibility and excluded Staphylococcus epidermidis, Staphylococcus coagulase-negative, and Corynebacterium species. We analyzed the trends of the overall isolates, the antimicrobial susceptibilities of blood isolates (BSI), difficult-to-treat (DTR) BSI, carbapenem-resistant Enterobacteriaceae (CRE) BSI, and restricted antimicrobial consumption as daily-defined-dose/1000 PD. DTR implies resistance to carbapenems, beta-lactams, fluoroquinolones, and additional antimicrobials where applicable. Results and Discussion: After applying exclusion criteria, we analyzed 1614 blood cultures out of 8314 cultures. We isolated 85 species, most commonly Eco, at 52%. The isolation density of total BSI in 2020 decreased by 16%: 82 patients were spared from bacteremia, with 13 being DTR. The isolation density of CRE BSI/1000 PD decreased by 64% from 2019 to 2020, while VREfm BSI decreased by 34%. There was a significant decrease of 80% in Ab isolates (p-value < 0.0001). During COVID-19, restricted antimicrobial consumption decreased to 175 DDD/1000 PD (p-value < 0.0001). Total carbapenem consumption persistently decreased by 71.2% from 108DDD/1000 PD in 2015–2019 to 31 DDD/1000 PD in 2020. At SGHUMC, existing epidemics were not worsened by the pandemic. We attribute this to our unique and dynamic collaboration of antimicrobial stewardship, infection prevention and control, and infectious disease consultation.

The Microbial Culturomics Project aiming to discover several bacterial species made it possible to isolate the strain Marseille-P4308^T from a stool sample of a healthy indigenous Congolese volunteer. Strain Marseille-P4308^T is a Gram-positive coccus shaped bacterium that optimally grows at 37 °C. The 16S rRNA gene sequence of the strain has a 96.2% sequence similarity to Peptostreptococcus anaerobius strain NCTC 11460^T (GenBank accession number: NR_042847.1). In addition, the average nucleotide identity of strain Marseille-P4308^T with its closest related species was 71.1%, which was far below the recommended threshold (>95–96%). The genome of the strain Marseille-P4308^T has a length of 2.14 Mbp with G + C content of 30.4 mol%. Based on phenotypic, biochemical, genomic and phylogenetic analysis, strain Marseille-P4308^T (= CSUR P4308 = CECT 9960) clearly appears to be a new species for which the name Peptostreptococcus faecalis sp. nov., is proposed.

In 2018, Corynebacterium sanguinis strain Marseille-P8776 was isolated from the blood of a 64-year-old woman suffering from breast cancer who had undergone chemotherapy and radiotherapy. Following whole-genome sequencing, the chromosome of strain Marseille-P8776 was 2,613,836 bp long with a G+C content of 64.92%, 2,568 protein-coding genes, and 64 RNA genes.

The capacity of the 49 sub-Saharan African countries, which account for 85% of tuberculosis cases in Africa (WHO, 2025), to monitor the genomic dynamics of Mycobacterium tuberculosis complex strains responsible for the disease was examined for the period 2000-2025. A total of 8141 GenBank entries, supplemented by 163 as yet unreported whole genome sequences prepared at the Institut Hospitalier-Universitaire, Marseille, France and the Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation, Dakar, Sénégal were analysed using TB-Profiler. M. tuberculosis sub-lineage L2.2.1 dominated the sub-continent, while other lineages and sub-lineages featured a discrete pattern of geographical distribution, here illustrated by interactive maps. Although three-quarters of the genomes showed a predicted antibiotic-susceptibility, the predicted resistant recovered in 80% countries largely comprised multidrug-resistant (MDR) genomes (12.19% of genomes), followed by Rifampicin-susceptible, isoniazid-resistant (HR-TB) genomes (4.47%), Rifampicin-resistant TB (RR-TB) genomes (3.31%), extensively drug-resistant (XDR) genomes (1.78%), and pre-XDR genomes (0.64%). Resistance to second-line antibiotics was observed with prevalence lower than that of first-line drugs. This review gives an updated, accurate, and interactive overview of tuberculosis in sub-Saharan Africa and provides a strong basis for following the current evolution of tuberculosis in African regions.