A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022.

Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.

The First Bacterial Endocarditis Due to Achromobacter xylosoxidans in a Dog.

Infectious endocarditis (IE) in dogs is often associated with a high mortality rate as diagnostic work-up as well as antibiotic treatment might be challenging. The present case describes bacteremia in a dog caused by Achromobacter xylosoxidans, leading to an infectious endocarditis. Achromobacter xylosoxidans (A. xylosoxidans) is an aerobic Gram-negative rod-shaped bacterium, which has been associated with multiple nosocomial opportunistic diseases in human medicine. One such manifestation of A. xylosoxidans infection is endocarditis. A. xylosoxidans infections are challenging to treat due to the reduced effectiveness of a wide range of antimicrobial agents. To date, only a few case reports of infections with A. xylosoxidans in animals have been described. This is the first case report of A. xylosoxidans endocarditis in a dog. Whole-genome sequencing was performed to determine the sequencing type and to gain more information about this bacterium regarding its intrinsic resistance genes. With this case report, we seek to increase awareness of A. xylosoxidans as an opportunistic nosocomial pathogen in dogs and to provide a short summary regarding the current state of general knowledge and known resistance patterns.

[Emerging bacteria in cystic fibrosis and non-cystic fibrosis bronchiectasis from a microbiologist's perspective]. / Bactéries émergentes dans la mucoviscidose et les dilatations des bronches hors mucoviscidose. Le point de vue du microbiologiste.

INTRODUCTION: Common major pathogens like Pseudomonas aeruginosa are identified in the airways of patients with cystic fibrosis (CF) and non-CF bronchiectasis. However, other opportunistic bacterial pathogens like Achromobacter xylosoxidans complex, Stenotrophomonas maltophilia and non-tuberculous mycobacteria are currently emerging in CF and are also reported in non-CF bronchiectasis. BACKGROUND: The emergence of opportunistic bacterial pathogens has been recognized in CF through annual national reports of sputum microbiology data. Despite common factors driving the emergence of bacteria identified in CF and non-CF bronchiectasis patients, bronchiectasis registries have been created more recently and no longitudinal analysis of recorded microbiological data is currently available in the literature, thereby preventing the recognition of emerging bacteria in patients with non-CF bronchiectasis. OUTLOOK: A longitudinal follow-up of microbiological data is still needed in non-CF bronchiectasis to identify emerging opportunistic bacterial pathogens. Homogeneity in practice of sputum microbiological examination is also required to allow comparative analysis of data in CF and non-CF bronchiectasis. CONCLUSION: Bacterial pathogens recognized as emerging in CF have to be more carefully monitored in non-CF bronchiectasis in view of their association with deterioration of the lung disease.

'Brevibacterium ihuae' sp. nov., isolated from a stool sample of a healthy 25-year-old woman.

We report the main characteristics of 'Brevibacterium ihuae' strain cv3T isolated from a stool sample of a healthy 25-year-old woman.

Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics.

Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.

'Lactobacillus raoultii' sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis.

We report the isolation of a new bacterium species, 'Lactobacillus raoultii' strain Marseille P4006 (CSUR P4006), isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis.

Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.

Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: 'Clostridium amazonitimonense' strain LF2T, 'Clostridium massilidielmoense' strain MT26T, 'Clostridium nigeriense' strain Marseille-P2414T and 'Clostridium merdae' strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

'Phoenicibacter massiliensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman.

This study supports the main characteristics of the new genus and new species 'Phoenicibacter massiliensis' strain Marseille-P3241T (CSUR P3241), a new bacterium isolated from a stool sample of a healthy 47-year-old pygmy woman.

'Raoultibacter timonensis' gen. nov., sp. nov. , a new bacterium isolated from the human gut of a Pygmy woman.

We report the main characteristics of a new species 'Raoultibacter timonensis' strain Marseille-P3277 (CSUR P3277), a new member of the genus Raoultibacter, that was isolated from a stool sample of a healthy 11-year-old Pygmy woman.

'Pygmaiobacter massiliensis' sp. nov., a new bacterium isolated from the human gut of a Pygmy woman.

This study supports the main characteristics of a new genus 'Pygmaiobacter' and a new species 'Pygmaiobacter massiliensis' strain Marseille-P3336 (CSUR P3336); that was isolated from a stool sample of a healthy 47-year-old Pygmy woman. The Institut Fédératif de Recherche ethics committee, gave approval for this study under the number 09-022. Samples were collected for microbial content description as part of the human microbiome description by culturomics.

'Gabonibacter timonensis' sp. nov., a new bacterium isolated from the human gut of a Pygmy woman.

This study supports the main characteristics of a new genus 'Gabonibacter timonensis' strain Marseille-P3388 (CSUR P3388); a new member of the Gabonibacter genus and Porphyromonadaceae family, that was isolated from a stool sample of a healthy 47-year-old Pygmy woman.

"Libanicoccus massiliensis" gen. nov., sp. nov., a new bacterium isolated from a stool sample from a pygmy woman.

This study supports the main characteristics of a new genus "Libanicoccus massiliensis" strain Marseille-P3237 (CSURP3237); a new member of the order Coribacteriaceae that was isolated from a stool sample from a healthy 35-year-old pygmy woman.

'Mobilibacterium massiliense' gen. nov. and 'Mobilibacterium timonense' sp. nov., identified in a human stool specimen.

This study presents the main characteristics of 'Mobilibacterium massiliense' strain P2510 (CSUR P2510) and 'Mobilibacterium timonense' strain P3194 (CSUR P3194), isolated from a stool sample of a patient at the Timone hospital and from a stool sample of a healthy 50-year-old pygmy (Baka) woman, respectively.

'Congobacterium massiliense' gen. nov. sp. nov., a new bacterium isolated from the gut of a pygmy (Baka) woman.

We report the main characteristics of a new genus, 'Congobacterium,' and a new species, 'Congobacterium massiliense,' strain Marseille-P3295 (CSUR P3295), a new member in the order Coribacteriacea, which was isolated from a stool sample of a healthy 50-year-old pygmy (Baka) woman.

"Collinsella bouchesdurhonensis" sp. nov., identified in human stool sample.

We report the main characteristics of "Collinsella bouchesdurhonensis" strain Marseille-P3296, which was isolated from a stool sample of a healthy 50-year-old pygmy (Baka) woman.

"Eggerthella timonensis" gen. nov. isolated from a human stool sample.

We report the main characteristics of "Eggerthella timonensis" strain Marseille-P3135 which was isolated from a stool sample of a healthy 8-year-old pygmy (Baka) girl.

'Olsenella congonensis' sp.nov., identified in human stool sample.

We report the main characteristics of 'Olsenella congonensis' strain Marseille-P3359T (CSUR P3359), which was isolated from the stool sample of a healthy 47-year-old pygmy female.

Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics.

Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600T, Bacillus mediterraneensis strain Marseille-P2384T, Bacillus massilinigeriensis strain Marseille-P2366T, Bacillus tuaregi strain Marseille-P2489T and Bacillus phocaeensis strain SIT16T are each the type strain of the corresponding bacterial species. These strains, the genomes of which are described here, are facultative anaerobic Gram-positive bacilli. Here, we describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

"Raoultibacter massiliensis" gen. nov., sp. nov., a new bacterium isolated from the human gut of a Saudi Bedouin.

We propose the description of a new bacterial genus and new bacterial species, "Raoultibacter massiliensis," isolated from a faecal specimen of a 19-year-old healthy Saudi Bedouin.

'Neglecta timonensis' gen. nov., sp. nov., a new human-associated species.

We herein describe the main characteristics of 'Neglecta timonensis' strain SN17 (CSUR P2265) that was isolated from the stool of an 88-year-old woman with type 2 diabetes.