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All the 36 known species to date of the genus Aeromonas are mesophilic except the species Aeromonas salmonicida, which includes both psychrophilic and mesophilic subspecies. For 20 years, more and more mesophilic A. salmonicida strains have been discovered. Only A. salmonicida subsp. pectinolytica has officially been classified as a mesophilic subspecies. Most mesophiles have been isolated in hot countries. We present, for the first time, the characterization of two new mesophilic isolates from Quebec (Canada). Phenotypic and genomic characterizations were carried out on these strains, isolated from dead fish from a fish farm. Isolates 19-K304 and 19-K308 are clearly mesophiles, virulent to the amoeba Dictyostelium discoideum, a surrogate host, and close to strain Y577, isolated in India. To our knowledge, this is the first time that mesophilic strains isolated from different countries are so similar. The major difference between the isolates is the presence of plasmid pY47-3, a cryptic plasmid that sometimes presents in mesophilic strains. More importantly, our extensive phylogenetic analysis reveals two well-defined clades of mesophilic strains with psychrophiles associated with one of these clades. This helps to have a better understanding of the evolution of this species and the apparition of psychrophilic subspecies. Key words: Aeromonas salmonicida, mesophile, phylogeny, Dictyostelium discoideum, pathogenesis, plasmid, Introduction The genus Aeromonas is currently known to comprise exclusively mesophilic species except for the species salmonicida. Indeed, Aeromonas salmonicida has the particularity of being composed of mesophilic and psychrophilic [...]

Flavobacterium is a genus of microorganisms living in a variety of hosts and habitats across the globe. Some species are found in fish organs, and only a few, such as Flavobacterium psychrophilum and Flavobacterium columnare, cause severe disease and losses in fish farms. The evolution of flavobacteria that are pathogenic to fish is unknown, and the protein changes accountable for the selection of their colonization to fish have yet to be determined. A phylogenetic tree was constructed with the complete genomic sequences of 208 species of the Flavobacterium genus using 861 softcore genes. This phylogenetic analysis revealed clade CII comprising nine species, including five pathogenic species, and containing the most species that colonize fish. Thirteen specific amino acid changes were found to be conserved across 11 proteins within the CII clade compared with other clades, and these proteins were enriched in functions related to replication, recombination, and repair. Several of these proteins are known to be involved in pathogenicity and fitness adaptation in other bacteria. Some of the observed amino acid changes can be explained by preferential selection for certain codons and tRNA frequency. These results could help explain how species belonging to the CII clade adapt to fish environments. [ABSTRACT FROM AUTHOR]

Objectives: This project studied the impact of a chlortetracycline treatment in weaning piglets on the taxonomy and antibiotic resistance gene (ARG) content of the microbiomes on carcasses and loins. Methods: Two groups of piglets from two farrowing barns with either an average or a lower sanitary health status were used. Each group was divided in half: a control group and a treatment group receiving feed supplemented with 660 g of chlortetracycline per tonne for 21 days. The piglets then went through fattening and were sent to the abattoir when they reached the targeted slaughter weight. Results: The microbiomes of the pig carcasses and loins were sampled, and DNA was extracted and sequenced with a whole-genome approach. The microbiomes of the carcasses differed depending on the farrowing barn source in both taxonomical composition and ARG content; however, the microbiomes on the loins were similar, regardless of the farrowing barn source and the treatment group. Conclusions: While there were differences in the carcass microbiomes between treatments after processing by the abattoir, the loin microbiomes were consistent and unaffected by treatment with chlortetracycline or the sanitary status of the farrowing barn. [ABSTRACT FROM AUTHOR]

Candida auris has emerged as a significant healthcare-associated pathogen due to its multidrug-resistant nature. Ongoing constraints in the discovery and provision of new antifungals create an urgent imperative to design effective remedies to this pressing global blight. Herein, we screened a chemical library and identified aryl-carbohydrazide analogs with potent activity against both C. auris and the most prevalent human fungal pathogen, C. albicans. SPB00525 [N'-(2,6-dichlorophenyl)-5-nitro-furan-2-carbohydrazide] exhibited potent activity against different strains that were resistant to standard antifungals. Using drug-induced haploinsufficient profiling, transcriptomics and metabolomic analysis, we uncovered that Ole1, a D(9) fatty acid desaturase, is the likely target of SPB00525. An analog of the latter, HTS06170 [N'-(2,6-dichlorophenyl)-4-methyl-1,2,3-thiadiazole-5-carbohydrazide], had a superior antifungal activity against both C. auris and C. albicans. Both SPB00525 and HTS06170 act as antivirulence agents and inhibited the invasive hyphal growth and biofilm formation of C. albicans. SPB00525 and HTS06170 attenuated fungal damage to human enterocytes and ameliorate the survival of Galleria mellonella larvae used as systemic candidiasis model. These data suggest that inhibiting fungal D(9) fatty acid desaturase activity represents a potential therapeutic approach for treating fungal infection caused by the superbug C. auris and the most prevalent human fungal pathogen, C. albicans. [ABSTRACT FROM AUTHOR]

A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils" ("Introduction to bioinformatics and bioinformatics tools"), given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada). This course requires neither a bioinformatics background nor specific skills in informatics. The underlying main goal was to produce a completely online up-to-date bioinformatics course, including practical exercises, with an intuitive pedagogical framework. The course, BIF-1901, was conceived to cover the three fundamental aspects of bioinformatics: (1) informatics, (2) biological sequence analysis, and (3) structural bioinformatics. This article discusses the content of the modules, the evaluations, the pedagogical framework, and the challenges inherent to a multidisciplinary, fully online course.

The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium. Here, we used PacBio long-read technology to sequence the genome of PPF-1, a strain of P. aeruginosa isolated from a dental unit waterline. Generating this closed genome was an opportunity to investigate genomic features that are difficult to accurately study in a draft genome (contigs state). It was possible to shed light onputative genomic islands, some shared with other reference genomes, new prophages, and the complete content of insertion sequences. In addition, four different group II introns were also found, including two characterized here and not listed in the specialized group II intron database. Key words: dental unit waterlines, Pseudomonas aeruginosa, PacBio, mobilome, insertion sequences, introns, genomic islands, prophages. Résumé: La bactérie à Gram négatif Pseudomonas aeruginosa est présente dans plusieurs habitats, tant naturels que façonnés par l'homme, et elle est particulièrement connue pour sa présence récurrente à titre d'agent pathogène dans les poumons de patients atteints de la fibrose kystique, une maladie génétique. En raison de son importance clinique, plusieurs études d'envergure ont étudié l'adaptation génomique de P. aeruginosa aux poumons et sa transition lorsque des infections aigues deviennent chroniques. Cependant, les connaissances sur la diversité et l'adaptation du génome du P. aeruginosa dans des environnements non-cliniques restent limitées, en partie enraisondumanque de génomes de référence pour des souches issues de nombreux environnements colonisés par cette bactérie. Dans ce travail, les auteurs ont utilisé la technologie de séquençage PacBio (à lectures longues) pour séquencer le génome de la souche PPF-1, une souche de P. aeruginosa isolée à partir l'alimentation en eau d'un appareil de rinçage en cabinet dentaire. La production de ce génome achevé a fourni la possibilité d'investiguer les caractéristiques génomiques qui sont difficiles à étudier avec justesse à l'aide de génomes inachevés (sous forme de contigs). Il a été possible de révéler de possibles îlots génomiques, dont certains étaient en commun avec d'autres génomes de référence, sur de nouveaux prophages ainsi que sur le contenu complet en séquences d'insertion. De plus, quatre introns du groupe II ont également été trouvés, dont deux qui sont caractérisés ici et qui ne figuraient pas dans la base de données spécialisées sur les introns du groupe II. [Traduit par la Rédaction] Mots-clés : arrivée d'eau d'un appareil de rinçage dentaire, Pseudomonas aeruginosa, PacBio, mobilome, séquences d'insertion, introns, îlots génomiques, prophages., Introduction The Gram-negative bacterium Pseudomonas aeruginosa is known to efficiently colonize several environments, including both clinical settings and natural habitats (Moradali et al. 2017). This pathogen, which is the causative [...]

This study aimed to characterise the physiological response of rabbits to feed withdrawal without stress caused by crating and transport to the slaughterhouse. A total of 72 recently weaned Grimaud rabbits were allocated into 12 cages, each with 6 rabbits (3 females and 3 males, to reflect commercial practices). A preslaughter feed withdrawal time (FWT) was randomly assigned to each of the 12 cages (t=0, 3, 6, 8, 10, 12, 14, 16, 18, 20, 22 or 24 h). Blood lactate and cortisol concentrations were measured at exsanguination. These observations did not indicate an elevated level of stress in the rabbits (P>0.05). The maximum Longissimus lumborum glycolytic potential was observed for rabbits that fasted for 3 and 6 h and was relatively stable from 127.78 to 139.04 µmol/g for rabbits with FWT longer than 12 h. As expected, gastrointestinal tract and stomach content weights were lower for rabbits with longer FWT (P<0.0001), while caecum weights did not (P=0.051). Rabbits with longer FWT had lower stomach pH and higher caecum pH (both P<0.0001). Metataxonomic 16S analysis revealed that FWT had a significant effect (all P<0.01) on microbiome beta diversity in faeces and caecum. The polymerase chain reaction analysis using specific primers revealed Enterobacteriaceae presence in the faeces of male rabbits only at 18 and 22 h. Our results suggest that the caecotrophic behaviour of rabbits allows them to be particularly resistant to hunger despite their small size. However, to limit Enterobacteriaceae shedding, the FWT should not exceed 18 h. [ABSTRACT FROM AUTHOR]