Colibacillosis, the most common bacterial disease affecting poultry, is mainly treated by antibiotics. Due to the increased prevalence of multidrug-resistant avian-pathogenic Escherichia coli , there is an urgent need to assess the efficacy of alternatives to antibiotherapy, such as phage therapy.

Despite the importance of the B. cereus group as major foodborne pathogens that may cause diarrheal and/or emetic syndrome(s), no study in Tunisia has been conducted in order to characterize the pathogenic potential of the B. cereus group. The aim of this study was to assess the sanitary potential risks of 174 B. cereus group strains isolated from different foodstuffs by detecting and profiling virulence genes (hblA, hblB, hblC, hblD, nheA, nheB, nheC, cytK, bceT and ces), testing the isolates cytotoxic activity on Caco-2 cells and antimicrobial susceptibility towards 11 antibiotics. The entertoxin genes detected among B. cereus isolates were, in decreasing order, nheA (98.9%), nheC (97.7%) and nheB (86.8%) versus hblC (54.6%), hblD (54.6%), hblA (29.9%) and hblB (14.9%), respectively encoding for Non-hemolytic enterotoxin (NHE) and Hemolysin BL (HBL). The isolates are multi-toxigenic, harbouring at least one gene of each NHE and HBL complexes associated or not to bceT, cytK-2 and ces genes. Based on the incidence of virulence genes, the strains were separated into 12 toxigenic groups. Isolates positive for cytK (37,9%) harbored the cytK-2 variant. The detection rates of bceT and ces genes were 50.6 and 4%, respectively. When bacteria were incubated in BHI-YE at 30 °C for 18 h and for 5 d, 70.7 and 35% of the strains were shown to be cytotoxic to Caco-2 cells, respectively. The cytotoxicity of B. cereus strains depended on the food source of isolation. The presence of virulence factors is not always consistent with cytotoxicity. However, different combinations of enterotoxin genetic determinants are significantly associated to the cytotoxic potential of the bacteria. All strains were fully sensitive to rifampicin, chloramphenicol, ciprofloxacin, and gentamycin. The majority of the isolates were susceptible to streptomycin, kanamycin, erythromycin, vancomycin and tetracycline but showed resistance to ampicillin and novobiocin. Our results contribute data that are primary to facilitate risk assessments in order to prevent food poisoning due to B. cereus group.

Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict—but potentially huge—consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20–30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics’ tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE’s 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics’ rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.

Increasing evidence suggests that the human blood hosts microbes including bacteria and eukaryotic viruses, which could have important implications for health. Bacteriophages of the blood are challenging to study and have been overlooked, but could translocate to this environment from different body-sites. We thus developed specific virome protocols and analysis methods to study the viral communities of blood samples obtained from healthy individuals and Crohn’s disease (CD) patients. We uncovered a diverse viral community in the human blood, dominated by phages infecting Pseudomonadota bacteria. We found that an important fraction of those phages overlaps with the gut virome, consolidating the idea that gut phages can translocate to the blood. Strikingly, viral communities of the blood were different between CD patients and healthy individuals, revealing a new signature of disease. This was not the case for fecal viral communities. Collectively, these results advance our knowledge of the microorganisms present in the human blood and pave the way for further studies of this environment in the context of disease.

Bacillus cereus is a major foodborne pathogen responsible for food spoilage and foodborne illness, including strains producing emetic toxins. In this study, two bacteriophages, PBC_MG88 and PBC_MG99, were isolated from wastewater using emetic B. cereus strains as hosts and were comprehensively characterized. Both phages formed clear plaques with halos and exhibited siphovirus morphology. Host range analysis against 172 B. cereus strains showed that PBC_MG88 and PBC_MG99 infected 50 and 60 strains, respectively. One-step growth experiments revealed efficient lytic activity, with latent periods of 20–25 min and burst sizes of 59–63 PFU per infected cell. More than 90% of phage particles adsorbed to host cells within 15 min. Both phages were stable across a wide temperature range (4–55 °C) and pH values (4–11). Genome sequencing revealed ~37 kb double-stranded DNA genomes lacking antibiotic resistance or virulence genes; however, the presence of lysogeny-related genes suggests a temperate lifestyle. Comparative genomic analyses indicated that both phages represent novel species within the genus Lwoffvirus. Biofilm assays demonstrated significant inhibition of B. cereus biofilm formation and reduction of pre-established biofilms. Overall, this study expands knowledge of B. cereus phage diversity and highlights the importance of genomic characterization in phage-based biocontrol research.