Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis

Abstract

The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph. The genome also encodes an extensive secretory machinery including types I, II, III, IV, and Vb secretion systems, and several genes for pili production including the new usher/chaperone system (pfam 05,229). The implications of these systems for opportunistic pathogenesis are discussed.

Description of the First Case of Catheter-Related Bloodstream Infection Due To Pantoea eucrina in a Cancer Patient

“…In our report, a blood-borne contamination of the PICC line by gut microbial translocation is likely. Indeed, species of the genus Pantoea are mainly environmental strains and plant pathogens and are rarely responsible for human infection [1][2][3][4], but they could reflect human gut microbiota imbalance, defined as dysbiosis [5][6][7], which has been associated with a higher risk of microbial translocation. Indeed, the imbalance between anti-inflammatory and pro-inflammatory gut bacteria could be responsible for intestinal macrophage activation and gut barrier damage, thus increasing the risk of bacterial entry into the bloodstream, especially in immunocompromised subjects such as this patient [6].…”

“…Indeed, the imbalance between anti-inflammatory and pro-inflammatory gut bacteria could be responsible for intestinal macrophage activation and gut barrier damage, thus increasing the risk of bacterial entry into the bloodstream, especially in immunocompromised subjects such as this patient [6]. The presence of genes encoding for a complete flagellum assembly and a type I pilus system in the genome of P. eucrina may explain its ability to form biofilms and to colonize catheters [7], with a potential for causing a catheter-related bloodstream infection. Increasingly frequent identification of such previously unknown species can be accounted for by the spread of tools such as routine MALDI-TOF MS technology or 16s rDNA sequencing in bacteriology laboratories: the MALDI Biotyper-IVD 7171 database contains 408 genera and 2428 species of bacteria and is periodically incremented.…”

“…Moghadam et al published a draft genome analysis of a strain of P. eucrina and showed that its genome clustered with Pantoea sp. PSNIH1 which was previously isolated from hospitalized patients and shown to carry plasmids with antibiotic resistance cassettes [7].…”

“…are Gram-negative motile rods of the Enterobacteriaceae family. The species belonging to this genus are usually isolated from soil, fruits, and vegetables [1][2][3][4], but can be ubiquitously found in host-associated microbiome such as the human gut [5,6] and plant microbiome [7]. Pantoea species can occasionally be involved in human infections and have been recently described as causing nosocomial outbreaks [3,[8][9][10].…”

“…The species Pantoea eucrina has rarely been isolated from humans. A strain isolated from a trashcan on a US university campus was sequenced and annotated for the first time by Moghadam et al in 2016 [7]. To our knowledge, there is no description of Pantoea eucrina bacteremia to date.…”