Core and Accessory Genome Analysis of Vibrio mimicus

Abstract

Vibrio mimicus is an emerging pathogen, mainly associated with contaminated seafood consumption. However, little is known about its evolution, biodiversity, and pathogenic potential. This study analyzes the pan-, core, and accessory genomes of nine V. mimicus strains. The core genome yielded 2424 genes in chromosome I (ChI) and 822 genes in chromosome II (ChII), with an accessory genome comprising an average of 10.9% of the whole genome for ChI and 29% for ChII. Core genome phylogenetic trees were obtained, and V. mimicus ATCC-33654 strain was the closest to the outgroup in both chromosomes. Additionally, a phylogenetic study of eight conserved genes (ftsZ, gapA, gyrB, topA, rpoA, recA, mreB, and pyrH), including Vibrio cholerae, Vibrio parilis, Vibrio metoecus, and Vibrio caribbenthicus, clearly showed clade differentiation. The main virulence genes found in ChI corresponded with type I secretion proteins, extracellular components, flagellar proteins, and potential regulators, while, in ChII, the main categories were type-I secretion proteins, chemotaxis proteins, and antibiotic resistance proteins. The accessory genome was characterized by the presence of mobile elements and toxin encoding genes in both chromosomes. Based on the genome atlas, it was possible to characterize differential regions between strains. The pan-genome of V. mimicus encompassed 3539 genes for ChI and 2355 genes for ChII. These results give us an insight into the virulence and gene content of V. mimicus, as well as constitute the first approach to its diversity.

Transcriptome reveals the role of the htpG gene in mediating antibiotic resistance through cell envelope modulation in Vibrio mimicus SCCF01

“…V. mimicus is an emerging zoonotic gram-negative bacterial pathogen that can infect a wide range of fish species (Guardiola-Avila et al, 2021 ), including Siluriformes, Cypriniformes, and Perciformes (Elgendy et al, 2022 ), as well as crustaceans (Jiang et al, 2022 ), resulting in severe vibriosis. The disease has rapid onset, rapid progression, and high mortality that can reach 80–100% (Geng et al, 2014 ).…”

Cross-Platform Transcriptomic Data Integration, Profiling, and Mining in Vibrio cholerae

“…The internal reference genes are very important for transcriptional-level studies, and a good internal reference gene needs to meet a certain amount of expression and stable expression. The common internal reference genes selected for V. cholerae transcription were ompT ( vc0862 ) ( 15 ), rpoA ( vc2571 ) ( 16 , 17 ), gyrB ( vc0015 ) ( 18 , 19 ), thyA ( vc0675 ) ( 20 ), and recA ( vc0543 ) ( 21 ). Under all conditions, we found that the expression levels of these internal reference genes were not stable under specific conditions ( Fig.…”

Seafood-Associated Outbreak of ctx-Negative Vibrio mimicus Causing Cholera-Like Illness, Florida, USA

“…In a phylogenetic analysis based on the core genome ( 9 ) ( Appendix ), the 2 Florida strains clustered within a single, well-supported clade consistent with their high similarity, indicating a very recent common origin ( Figure ). Although the maximum-likelihood tree of available V. mimicus sequences shows several independent lineages of strains sampled worldwide with no apparent geographic structure, the closest lineages to the Florida strains were clinical isolates from the United Kingdom, as well as clinical and environmental strains from the United States, albeit with no strong bootstrap support.…”