What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

Abstract

Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade’s refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts.

Pathogenic <i>Leptospira</i>: Advances in understanding the molecular pathogenesis and virulence

“…A recent detailed analysis of 20 genome sequences of isolates representing 20 of the 22 known Leptospira species was used to estimate the phylogenetic distances between species (Fouts et al, 2016). The results revealed clustering of the species into three groups, namely pathogenic, intermediately pathogenic and non-pathogenic (saprophytes) (Fouts et al, 2016). These results confirmed the genetic relatedness among Leptospira species as previously established by DNA hybridization (DDH) techniques (Ramadass et al, 1992;Brem et al, 1999;Bourhy et al, 2014).…”

“…These results suggest tremendous progress in understanding the various mechanisms involved in the biological process of Leptospira species infections. Previous investigations (Nascimento et al, 2004;Picardeau et al, 2008;Ko et al, 2009), and more recent analysis (Alt et al, 2015;Fouts et al, 2016;Vinod Kumar et al, 2016) have focused on genome and genetic technologies in an attempt to define the mechanisms that underlie the pathogenesis of Leptospira species. As such, mutant organisms that mimic leptospirosis have been generated, that have significantly enhanced the identification of metabolic systems such as amino acid synthesis utilized by Leptospira species.…”

“…Overall, these studies show that the morphological orientation of the flagella coiling protein modulates Leptospira infectivity. Numerous studies have investigated the phylogeny of pathogenic and non-pathogenic Leptospira (Ravishankar et al, 2014;Fouts et al, 2016;Gomard et al, 2016). A recent detailed analysis of 20 genome sequences of isolates representing 20 of the 22 known Leptospira species was used to estimate the phylogenetic distances between species (Fouts et al, 2016).…”

“…Numerous studies have investigated the phylogeny of pathogenic and non-pathogenic Leptospira (Ravishankar et al, 2014;Fouts et al, 2016;Gomard et al, 2016). A recent detailed analysis of 20 genome sequences of isolates representing 20 of the 22 known Leptospira species was used to estimate the phylogenetic distances between species (Fouts et al, 2016). The results revealed clustering of the species into three groups, namely pathogenic, intermediately pathogenic and non-pathogenic (saprophytes) (Fouts et al, 2016).…”

Emerging Infectious Disease Implications of Invasive Mammalian Species: The Greater White-Toothed Shrew (Crocidura russula) Is Associated With a Novel Serovar of Pathogenic Leptospira in Ireland

“…santarosai and L . weilii [55–57]. However, the serologic and genomic based typing mechanisms are not mutually exclusive, as exemplified by serovar Hardjo, a significant pathogen in bovine populations throughout the world[58], which may belong to either L .…”