Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

Abstract

Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen.IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

Keywords: Plesiomonas shigelloides; comparative genomics; horizontal gene transfer; pan-genome; pathogenesis.

FIG 1

Phylogenetic analysis and whole-genome nucleotide and amino acid identities. (A) ML phylogeny was constructed based on SNPs across 307 single-copy core gene families shared by the 20 P. shigelloides genomes and 59 reference genomes of other Enterobacterales. (B) The heat map presents average nucleotide identities (red upper section of matrix) and amino acid identities (blue lower section of matrix). (C) Distribution of COG categories for each set of species-specific gene repertoires.

FIG 2

Genetic diversity of genome in P. shigelloides. (A) Strain-specific gene families of 20 P. shigelloides genomes. The number of core gene families shared by all strains is shown in the center. (B) Core and pan-genome curves showing the downward trend of the core gene families and the upward trend of the pan-gene families with the increase in the number of genomes. The error bars indicate standard deviations of the number of core and pan-gene families. The deduced mathematical functions of the core and pan-genome curves are also reported. (C) ML phylogeny constructed based on SNPs across 1,522 single-copy core gene families shared by the 20 P. shigelloides genomes. The interior node values shown in the tree represent bootstrap values (100 replicates). (D) Comparison between the core genome tree and pan-genome tree. Normalized Robinson-Foulds (nRF) and normalized matching cluster (nMC) scores were used to measure the congruence of the two trees.

FIG 3

Functional categories and evolutionary dynamics of gene families. (A) Distribution of COG categories for each gene family set. (B) Expansion and contraction of gene families in each branch of the core genome tree. The number of expanded genes (+; blue) and the number of contracted genes (−; red) are shown in each branch. (C) Distribution of horizontal genes in P. shigelloides genomes. (D) The potential donor bacterial taxa providing donor genes for HGT.

FIG 4

Mobile genetic elements (MGEs) and macromolecular secretion systems in P. shigelloides. (A) The distribution of MGEs and macromolecular secretion systems. (B) The genetic organization of macromolecular secretion systems. Identical genes are shown in the same color and linked by dotted lines. The percentages of protein identities of all homologous genes are shown. Due to the fragmentation of the draft genome, the T3SSs of A. cavernicola MDC 2508 were located in two contigs (PGGC01000011.1 and PGGC01000031.1).

FIG 5

The genotypic and phenotypic profiles of virulence factors and resistance genes across all 20 P. shigelloides genomes. Blue coloring represents the presence of a gene, and gray represents absence. (A) Heat map of the distribution of virulence factors. For the current presentation, we removed the virulence factors of the previous macromolecular section systems and O-antigen/LPS/capsule. (B) Heat map of resistance gene distribution. (C) Antimicrobial susceptibility profiles of P. shigelloides.