Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood

Leyer, Caroline; Sassi, Mohamed; Gourmelen, Frédéric; Burel, Agnès; Beyrouthy, Racha; Kayal, Samer; Bonnet, Richard; Cattoir, Vincent

doi:10.1016/j.syapm.2020.126124

Cited by 3 publications

(1 citation statement)

References 35 publications

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“…Most of the homologs were from the Flavobacteriales order of environmental organisms. Some of them are opportunistic pathogens that have been shown to cause diseases including C. indologenes, E. anopheles (Wang et al, 2022) and, Avrilella dinanensis is a novel bacterium that was isolated from blood of a septic patient for the rst time in 2016 (Leyer et al, 2020). C. indologenes, as an environmental bacterium, can potentially survive in harsh environments as a unique heat-stable metalloprotease with a non-typical substrate recognition pro le was puri ed from C. indologenes previously (Venter et al, 1999) Among the homologs of CIM-1, more than half of the top 100 homologs were predicted to be lipoproteins (Lipoprotein Likelihood > 50%).…”

Section: Discussionmentioning

confidence: 99%

Adding to the family of resistance factors against last resort antibiotics: Identification and characterization of a novel carbapenemase, CIM-1

Wang,

Sapula,

Whittall

et al. 2023

Preprint

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The increasing rate of carbapenem-resistant bacteria within healthcare environments is an issue of great concern that needs urgent attention. This resistance is driven by metallo-β-lactamases (MBLs), which can catalyse the hydrolysis of almost all clinically available β-lactams and are resistant to all the available β-lactamase inhibitors. In this study, a novel MBL was identified in a multidrug resistant isolate of the opportunistic pathogen, Chryseobacterium indologenes. Sequence analysis predicted this MBL (CIM-1) to be a lipoprotein with an atypical lipobox. Characterization of CIM-1 revealed it to be a membrane-associated, high-affinity carbapenemase with a broad spectrum of activity that includes all cephalosporins and carbapenems. This is the first report of the identification and characterisation of an MBL with an atypical lipobox and only the second lipidated MBL to be characterised after critically important NDM-1. We also identified more lipidated MBLs with non-canonical lipoboxes highlighting the necessity in further investigation of lipidated MBLs.

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Section: Discussionmentioning

confidence: 99%

Adding to the family of resistance factors against last resort antibiotics: Identification and characterization of a novel carbapenemase, CIM-1

Wang,

Sapula,

Whittall

et al. 2023

Preprint

View full text Add to dashboard Cite

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Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics

Wang,

Sapula,

Whittall

et al. 2024

Commun Biol

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The increasing rate of carbapenem-resistant bacteria within healthcare environments is an issue of great concern that needs urgent attention. This resistance is driven by metallo-β-lactamases (MBLs), which can catalyse the hydrolysis of almost all clinically available β-lactams and are resistant to all the clinically utilized β-lactamase inhibitors. In this study, an uncharacterized MBL is identified in a multidrug resistant isolate of the opportunistic pathogen, Chryseobacterium indologenes. Sequence analysis predicts this MBL (CIM-1) to be a lipoprotein with an atypical lipobox. Characterization of CIM-1 reveals it to be a high-affinity carbapenemase with a broad spectrum of activity that includes all cephalosporins and carbapenems. Results also shown that CIM-1 is potentially a membrane-associated MBL with an uncharacterized lipobox. Using prediction tools, we also identify more potentially lipidated MBLs with non-canonical lipoboxes highlighting the necessity of further investigation of lipidated MBLs.

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Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium

Kim,

Cha,

Lee

et al. 2023

Microbiol Spectr

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Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium . Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.

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Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood

Cited by 3 publications

References 35 publications

Adding to the family of resistance factors against last resort antibiotics: Identification and characterization of a novel carbapenemase, CIM-1

Adding to the family of resistance factors against last resort antibiotics: Identification and characterization of a novel carbapenemase, CIM-1

Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics

Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium

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