Análisis de genómica comparativa entre cepas aisladas de Piscirickettsia salmonis

76 p.Piscirickettsia salmonis es el agente etimológico causante de la Septicemia Rickettsial de Salmónidos (SRS) o Piscirickettsiosis, enfermedad que afecta gravemente la producción de salmón en diversas partes del mundo, con un impacto en el sur de Chile, en donde ha sido responsable de grandes pérdidas económicas. A pesar de la importancia que ha tenido este patógeno en la industria, existe escasa información acerca de su genoma y otros aspectos de su ciclo de vida y patogénesis, así como también en el diagnóstico, tratamiento, prevención y control. En las últimas décadas, las bases de datos con información y datos biológicos se han convertido en un recurso esencial para investigadores de todo el mundo, ya que son una herramienta que permite mantener grandes volúmenes de información, de forma ordenada, rápida y segura, a disposición para futuras investigaciones. Las bases de datos públicas y herramientas bioinformáticas, incluyendo protocolos automatizados, son estrategias útiles frente a análisis genómicos comparativos entre cepas microbianas. Aquí el avance tecnológico ha jugado un papel importante en cuanto a técnicas de secuenciación, posibilitando hoy la obtención de una gran cantidad de datos genómicos a bajo costo y con mayor rapidez. El presente trabajo entrega un análisis comparativo entre cepas aisladas de Piscirickettsia salmonis para la construcción de un "core" y pangenoma. Además este trabajo proporcionara el proceso automatizado, en cuanto a predicción de genes y ubicación de genes ortólogos, así como también una plataforma de información que permitirá poner a disposición de la comunidad científica la información analizada y clasificada de cada una de las cepas de Piscirickettsia salmonis./ABSTRACT: Piscirickettsia salmonis is etiologic agent responsible for the Salmonid Rickettsial Septicemia (SRS) or Piscirickettsiosis, disease that seriously a ects the production of salmon in various parts of the world, with an impact in southern Chile, where has been responsible for large economic losses. Despite the signi cant role played by this pathogen in the industry, there is limited information about their genome and other aspects of their life cycle and pathogenesis, as well as in the diagnosis, treatment, prevention and control. In recent decades, biological databases have become an essential resource for researchers around the world, because using them as tool for maintaining large volumes of information, neatly, quickly and safely, available for future research. The public databases and bioinformatics tools, including automated protocols are useful strategies against comparative genomic analysis between microbial strains. This technological progress has played an important role in terms of sequencing techniques, which allows to obtain genomic data at low cost and more quickly available to research. This work provide a comparative analysis of isolates strains of Piscirickettsia salmonis for the construction of a "core" and pangenome. Furthermore, this work will provide the automated process, in terms of gene prediction and location of orthologous genes, as well as an information platform which will make available to the scienti c community the information analyzed and classi ed in each strains of Piscirickettsia salmonis

Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts

The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming

Patagonian sheepdog: Genomic analyses trace the footprints of extinct UK herding dogs to South America.

Most modern dog breeds were developed within the last two hundred years, following strong and recent human selection based predominantly on aesthetics, with few modern breeds constructed solely to maximize their work potential. In many cases, these working breeds represent the last remnants of now lost populations. The Patagonian sheepdog (PGOD), a rare herding breed, is a remarkable example of such a population. Maintained as an isolated population for over 130 years, the PGOD offers a unique opportunity to understand the genetic relationship amongst modern herding breeds, determine key genomic structure of the founder PGOD populations, and investigate how canine genomic data can mirror human migration patterns. We thus analyzed the population structure of 159 PGOD, comparing them with 1514 dogs representing 175 established breeds. Using 150,069 SNPs from a high-density SNP genotyping array, we establish the genomic composition, ancestry, and genetic diversity of the population, complementing genomic data with the PGOD's migratory history to South America. Our phylogenetic analysis reveals that PGODs are most closely related to modern herding breeds hailing from the United Kingdom. Admixture models illustrate a greater degree of diversity and genetic heterogeneity within the very small PGOD population than in Western European herding breeds, suggesting the PGOD predates the 200-year-old construction of most pure breeds known today. We thus propose that PGODs originated from the foundational herding dogs of the UK, prior to the Victorian explosion of breeds, and that they are the closest link to a now-extinct population of herding dogs from which modern herding breeds descended

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection

Inorganic Polyphosphate Affects Biofilm Assembly, Capsule Formation, and Virulence of Hypervirulent ST23 Klebsiella pneumoniae

The emergence of hypervirulent Klebsiella pneumoniae (hvKP) strains poses a significant threat to public health due to high mortality rates and propensity to cause severe community-acquired infections in healthy individuals. The ability to form biofilms and produce a protective capsule contributes to its enhanced virulence and is a significant challenge to effective antibiotic treatment. Polyphosphate kinase 1 (PPK1) is an enzyme responsible for inorganic polyphosphate synthesis and plays a vital role in regulating various physiological processes in bacteria. In this study, we investigated the impact of polyP metabolism on the biofilm and capsule formation and virulence traits in hvKP using Dictyostelium discoideum amoeba as a model host. We found that the PPK1 null mutant was impaired in biofilm and capsule formation and showed attenuated virulence in D. discoideum compared to the wild-type strain. We performed a proteomic analysis to gain further insights into the underlying molecular mechanism. The results revealed that the PPK1 mutant had a differential expression of proteins involved in capsule synthesis (Wzi-Ugd), biofilm formation (MrkC-D-H), synthesis of the colibactin genotoxin precursor (ClbB), as well as proteins associated with the synthesis and modification of lipid A (ArnB-LpxC-PagP). These proteomic findings corroborate the phenotypic observations and indicate that the PPK1 mutation is associated with impaired biofilm and capsule formation and attenuated virulence in hvKP. Overall, our study highlights the importance of polyP synthesis in regulating extracellular biomolecules and virulence in K. pneumoniae and provides insights into potential therapeutic targets for treating K. pneumoniae infections