SYMBIOSIS IN THE COLD: IDENTIFICATION AND CHARACTERIZATION OF A NEW FRANCISELLA ENDOSYMBIONT FROM THE POLAR CILIATE, EUPLOTES PETZI

Ciliates of the genus Euplotes are commonly found in polar environments, and different species isolated from Arctic and Antarctic coastal seawaters are currently studied for their genome evolution and adaptation. In analyzing whole genome sequences of a wild-type E. petzi strain collected from Terra Nova Bay (Antarctica), it appeared that more than 3% of the assembled contigs had a bacterial origin and overlapped (one contig containing rDNA operon included) with DNA sequences of the gammaproteobacterium Francisella (represented by extremely infectious species to a wide array of different organisms man included). Given that an Euplotes species of temperate seawaters, E. raikovi, has already been found to host a Francisella species (namely F. endociliophora), we searched for and succeeded in isolating Francisella-like endosymbionts from E. petzi cells. Colonies of these endosymbionts (grown optimally at a temperature range from 4 to maximum 30 °C) have been analyzed for their genome and found to represent a new clade with a basal position in the Francisella phylogenetic tree. This clade is unequivocally distinct from F. endociliophora (living in E. raikovi) as well as from all the other well recognised Francisella clades. The finding that Francisella is adapted to live in the extreme environmental conditions of the polar regions implies that this bacterium is much more common and geographically widespread than previously known, and that free-living Euplotes species may represent a natural reservoir of Francisella in every aquatic environments

Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215

Abstract Background A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings. Results We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination’s role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30–50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2. Conclusions This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings

The ciliate Euplotes petzi is the natural reservoir of the bacterium Francisella in the Antarctic region.

Euplotes petzi is a strict psychrophilic ciliate isolated from coastal waters of Terra Nova Bay (Antarctica). In analyzing the results from a draft genome sequencing of total E. petzi DNA preparations, we found that more than 3% of the assembled contigs had a bacterial origin. All the bacterial DNA sequences, including one containing rRNA genes, overlapped with DNA sequences of the genus Francisella, which comprises a large number of species classified as facultative intracellular γ-proteobacteria potential noxious to their hosts. Based on these findings, we undertook the isolation, characterization and genome determination of the Francisella-like bacteria – tentatively named F. adeliensis sp. nov. – hosted in the cytoplasm of E. petzi. Genome sequence comparisons provide evidence that F. adeliensis forms a new clade in the Francisella phylogenomic tree. In addition to being well separated from all the recognised pathogenic Francisella species, this clade is distinct also from F. endociliophora, symbiont in the congeneric species E. raikovi, as well as from the Allofrancisella species that are collectively known as ‘environmental francisellas’. The inclusion of F. adeliensis in the Francisella phylogenomic tree does not support the separation of this genus between ‘intracellular’ and ‘environmental’ forms

Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish

Background: Prior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F. noatunensis, a serious pathogen of farmed fish, and other less well described endosymbiotic species. Results: We determined the phylogenetic relationships of all known Francisella species, including some for which the phylogenetic positions were previously uncertain. The genus Francisella could be divided into two main genetic clades: one included F. tularensis, F. novicida, F. hispaniensis and Wolbachia persica, and another included F. philomiragia and F. noatunensis. Some Francisella species were found to have significant recombination frequencies. However, the fish pathogen F. noatunensis subsp. noatunensis was an exception due to it exhibiting a highly clonal population structure similar to the human pathogen F. tularensis. Conclusions: The genus Francisella can be divided into two main genetic clades occupying both terrestrial and marine habitats. However, our analyses suggest that the ancestral Francisella species originated in a marine habitat. The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in F. tularensis (infecting mammals) and F. noatunensis subsp. noatunensis (infecting fish)

The ciliate Euplotes petzi is the natural reservoir of the bacterium Francisella in the Antarctic region.

Euplotes petzi is a strict psychrophilic ciliate isolated from coastal waters of Terra Nova Bay (Antarctica). In analyzing the results from a draft genome sequencing of total E. petzi DNA preparations, we found that more than 3% of the assembled contigs had a bacterial origin. All the bacterial DNA sequences, including one containing rRNA genes, overlapped with DNA sequences of the genus Francisella, which comprises a large number of species classified as facultative intracellular -proteobacteria potential noxious to their hosts. Based on these findings, we undertook the isolation, characterization and genome determination of the Francisella-like bacteria--tentatively named F. adeliensis sp. nov.--hosted in the cytoplasm of E. petzi. Genome sequence comparisons provide evidence that F. adeliensis forms a new clade in the Francisella phylogenomic tree. In addition to being well separated from all the recognised pathogenic Francisella species, this clade is distinct also from F. endociliophora, symbiont in the congeneric species E. raikovi, as well as from the Allofrancisella species that are collectively known as ‘environmental francisellas’. The inclusion of F. adeliensis in the Francisella phylogenomic tree does not support the separation of this genus between ‘intracellular’ and ‘environmental’ forms

A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species

The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms