Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts

BMC Genomics

Leonardo M. Cruz¹  Vinicius A. Weiss¹  Helisson Faoro¹  Doumit Camilios-Neto¹  Rodrigo L. Cardoso¹  Fabio O. Pedrosa¹  Eduardo Balsanelli¹  Michelle Z. Tadra-Sfeir¹  Emanuel M. Souza¹  Liziane C. C. Brusamarello-Santos¹  Cyntia M. T. Fadel-Picheth²  Ana C. Q. Marques²  John LiPuma³  Roberto T. Raittz⁴  Willian K. Oliveira⁴ 

[1] Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná;Department of Clinical Analyses, Universidade Federal do Paraná, Av. Lothário Meissner 632;Department of Pediatrics, University of Michigan;Graduate Program on Bioinformatics, Universidade Federal do Paraná;

关键词: Herbaspirillum seropedicae;    Clinical isolates;    Genome comparison;    Genomic adaptation;    LPS substitution;   

DOI  :  10.1186/s12864-019-5982-9

来源: DOAJ

【 摘 要 】

Abstract Background Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. Results Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system. Conclusions Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.

【 授权许可】

Unknown