Abstract
The genus Herbaspirillum is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the Herbaspirillum genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of H. frisingense AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16–41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that H. frisingense has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts.
Highlights
The genus Herbaspirillum belongs to the beta class of the phylum Proteobacteria
We describe the genome of H. frisingense AU14559 isolated from sputum obtained from patients with cystic fibrosis and its comparison with the genomes of other strains of this species for which genome sequence data are available in public databases
Through the search performed by GIPSy, in which the genome of the strain H. frisingense IAC152 was used as a reference, we found a total of 14 genomic islands
Summary
The genus Herbaspirillum belongs to the beta class of the phylum Proteobacteria. Thirteen species are currently assigned to this genus; they have been isolated from various environments, including water [1], the rhizosphere [2], and plant tissues [3]. Three species of this genus, Herbaspirillum frisingense, Herbaspirillum seropedicae, and Herbaspirillum rubrisubalbicans, are described as nitrogen-fixing bacteria These bacteria can convert atmospheric nitrogen (N2) into ammonium ions (NH4+), a form that can be assimilated by plants, through the nitrogenase enzyme complex encoded by nifHDK genes [4]. Phylogenetic analysis showed that these strains represented various species of this genus; one, an isolate of H. frisingense, was designated as strain AU14559 It is not entirely clear whether Herbaspirillum bacteria are opportunistic, and only occasionally found in clinical samples, or whether they are pathogens that can cause secondary infections and worsen the condition of patients
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