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

BACKGROUND: Herbaspirillum seropedicae is an environmental ß-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.

Natural antimicrobials for control of Salmonella Enteritidis in feed and in vitro model of the chicken digestive process.

This study evaluated the antimicrobial effect of essential oils (EO) and organic acids (OA) against Salmonella Enteritidis in chicken feed and during an in vitro model that mimics the chicken digestive process. The minimal inhibitory concentration (MIC) of allyl isothiocyanate (AITC), carvacrol (CV), propionic acid (PROP) and caproic acid (CAP) were individually determined. Then, based on the MICs of each compound, combinations of EOs and/or OAs were tested to evaluate their synergic antimicrobial effect. The synergic effect of AITC and CAP was the most efficient against the bacterial strain tested. Commercial feed was inoculated with a 5-strain cocktail of S. Enteritidis and treated with different doses of AITC + CAP to evaluate their effect on the growth/survival of the pathogen. In addition, the simulated digestion model was used to access the antimicrobial effect of AITC + CAP added to the feed towards S. Enteritidis and Lactobacillus plantarum. Synergistic effect was found between AITC (0.065 mM) and CAP (17.5 mM) against S. Enteritidis in chicken feed, where S. Enteritidis was reduced to undetectable levels (<1.00 log CFU/g). AITC (1.95 mM) + CAP (45 mM) also decreased (p < 0.05) the population of S. Enteritidis in the simulated digestion, while the growth of L. plantarum was not affected. Therefore, the addition of AITC + CAP in feed might be a potential natural antimicrobial able to prevent economic losses caused for Salmonella in chicken.

Resistome analysis of bloodstream infection bacterial genomes reveals a specific set of proteins involved in antibiotic resistance and drug efflux.

Bacterial resistance to antibiotics is a global public health problem. Its association with bloodstream infections is even more severe and may easily evolve to sepsis. To improve our response to these bacteria, it is essential to gather thorough knowledge on the main pathogens along with the main mechanisms of resistance they carry. In this paper, we performed a large meta-analysis of 3872 bacterial genomes isolated from blood samples, from which we identified 71 745 antibiotic resistance genes (ARGs). Taxonomic analysis showed that Proteobacteria and Firmicutes phyla, and the species Klebsiella pneumoniae and Staphylococcus aureus were the most represented. Comparison of ARGs with the Resfams database showed that the main mechanism of antibiotic resistance is mediated by efflux pumps. Clustering analysis between resistome of blood and soil-isolated bacteria showed that there is low identity between transport and efflux proteins between bacteria from these environments. Furthermore, a correlation analysis among all features showed that K. pneumoniae and S. aureus formed two well-defined clusters related to the resistance mechanisms, proteins and antibiotics. A retrospective analysis has shown that the average number of ARGs per genome has gradually increased. The results demonstrate the importance of comprehensive studies to understand the antibiotic resistance phenomenon.