Genealogy of the Genome Components in the Highly Homogeneous Pandemic Vibrio parahaemolyticus Population

Abstract

Bacterial genomes evolve through two different mechanisms: 1) changes in or occasional loss of ancestral genes, which preserve the founder clonal genealogy or frame, and 2) sporadic gains of new genes via horizontal gene transfer, which introduces DNA with a different genealogy or clonal frame. Evolution has led to the emergence of a pathogenic strain pandemic of Vibrio parahaemolyticus, which has propagated globally, causing large outbreaks of seafood-associated diarrhea. The low sequence diversity of the pathogenic strain of Vibrio parahaemolyticus genome provides a model that can reveal evolutionary mechanisms that are hidden in bacteria with a greater diversity. Here, we assess the clonal genealogy of the genome components of Vibrio parahaemolyticus and identify recombinant segments in 31 isolates obtained worldwide. By comparing whole genomes using a procedure that accounts for at least 98% of the reads obtained from any isolate after high throughput sequencing, we determined that the fraction of the whole genome retaining the founder clonal frame varied from 96.7%-100% of the accountable reads. The fraction in chromosomes with other genealogies varied from 0%-3.3% and in extra-chromosomal elements from 0%-4.2%, with the relative impact of mutation and recombination varying greatly between isolates. The likely causes for this variation are proposed.

Insight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain

“…Early analysis of a few genes ( tdh , trh , orf8 , and toxRS ) and molecular techniques applied to isolates with serotype O3:K6 obtained after 1996 showed that they were undifferentiated, and the population was considered clonal (genes deriving from a same common ancestor) even though only a few genes were tested. Later analysis using a large number of isolates and techniques with higher resolution such as RFLP-PFGE ( Chowdhury et al, 2000 ), direct genome restriction enzyme analysis (DGREA) by conventional gel electrophoresis ( Fuenzalida et al, 2006 ), multilocus sequence typing (MLST) ( Chowdhury et al, 2004 ; González-Escalona et al, 2008 ; Chao et al, 2011 ), multilocus variable-number tandem-repeat analysis (MLVA) ( Kimura et al, 2008 ; García et al, 2012 ), microarray analysis ( Izutsu et al, 2008 ) and finally whole-genome sequencing ( Chen et al, 2011 ; Loyola et al, 2015 , 2016 ), confirmed the clonal nature of the group. However, these techniques also showed the existence of variants that were considered evolutionary products of the initial clone, and showed numerous cases of genomic regions with numerous SNVs indicating origin from a different ancestor.…”

“…Whole-genome sequence analysis of three pandemic isolates, including one with a different serotype (O4:K68) ( Chen et al, 2011 ), showed high similarity along the whole genome in this clonal complex except in the O- and K-antigen-encoding gene clusters, which contained 94% of the SNVs. Later, in ClonalframeML analysis of whole genomes, the O and K coding regions were identified as recombinant regions in three pandemic isolates with a serotype other than O3:K6 ( Loyola et al, 2016 ). These and other less direct observations indicated that serotype conversion was due to a recombination or gene conversion event.…”

“…Whole-genome comparisons of pandemic isolates have been published for three strains from three geographically distinct regions ( Chen et al, 2011 ), eight from Chile ( Loyola et al, 2015 ), and 31 worldwide isolates ( Loyola et al, 2016 ). These studies have expanded our knowledge on the diversity and evolution of the pandemic strain.…”

“…This observation indicates the need for comparing the whole genome when studying evolution, incorporating exclusive DNA of each isolate and not only that shared by all isolates (core genome) which is used for building phylogenetic trees. Accordingly, a procedure called “reads accounting” was proposed when comparing genome sequences obtained by high-throughput sequencing ( Loyola et al, 2016 ). This procedure aims to include in the comparison all the reads obtained after high-throughput sequencing of the bacterial DNA.…”

“…This procedure aims to include in the comparison all the reads obtained after high-throughput sequencing of the bacterial DNA. It was used for genome comparison of 31 pandemic isolates obtained worldwide ( Loyola et al, 2016 ). Further analysis of the clonal frames in the core genome of each isolate using ClonalFrameML ( Didelot and Wilson, 2015 ) allowed inference of recombinant regions.…”