Whole genome relationships among Francisella bacteria of diverse origin define new species and provide specific regions for detection.

Challacombe JF1, Petersen JM2, Gallegos-Graves V1, Hodge D3, Pillai S4, Kuske CR5.

Author information

Abstract

Francisella tularensis (Ft) is a highly virulent zoonotic pathogen that causes tularemia, and because of weaponization efforts in past world wars, is considered a Tier 1 biothreat agent. Detection and surveillance of Ft may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 17 new Francisella genomes and a comparison of their characteristics to each other and to 14 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features - for example, when some are virulent pathogens in humans and animals, while others are non-pathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, LPS biosynthesis, pathogenicity island) and whole genome comparisons (nucleotide and protein) gave congruent results, but with different discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisellas IMPORTANCE: DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near-relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics and environmental surveillance, where response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisellas identified in clinical samples or environmental surveys.