학술논문
Epidemiology and taxogenomics of the genus arcobacter
Document Type
Dissertation/Thesis
Author
Source
TDX (Tesis Doctorals en Xarxa)
Subject
Language
English
Abstract
El género Arcobacter pertenece a la familia Campylobacteraceae e incluye especies consideradas patógenos emergentes ya que producen infecciones en humanos y animales. Las bacterias de este género presentan una amplia distribución a nivel mundial y se cree que se transmiten por el consumo de aguas o alimentos contaminados. Existen diversas herramientas para el estudio epidemiológico que nos ayudarían a esclarecer estas rutas de contagio. Sin embargo, los mecanismos de acción de estas bacterias son todavía poco conocidos y no existe tratamiento estandarizado. El número de especies del género ha aumentado considerablemente en los últimos años y el uso de nuevas técnicas de aislamiento ha provocado el hallazgo de otras especies nuevas. En esta tesis, se ha demostrado que el uso de la técnica de Multilocus Sequence Typing (MLST) para el estudio epidemiológico es poco precisa. Además, se evidenció la elevada resistencia a determinados antibióticos que sugieren la necesidad de introducir un cambio en el uso de las terapias utilizadas hasta ahora en las infecciones ptoducidas por Arcobacter. También se describieron un total de 4 nuevas especies utilizando técnicas como el análisis fenotípico, el Multilocus Phylogenetic Analysis (MLPA) mediante la concatenación de 5 genes (atpA, gyrA, gyrB, hsp60 y rpoB) y la información extraída de los genomas secuenciados de dichas especies y de las especies filogenéticamente cercanas. El uso de los genomas, su comparación y el análisis filogenético evidenció además que la especie A. cryaerophilus está formada por 4 genomovares, que representan especies genómicas pero que no se pudieron diferenciar fenotípicamente. Finalmente, el análisis filogenético de los genomas de todas las especies del género, junto con el cálculo de diferentes índices genómicos (ANI, isDDH, AAI, POCP y RSCU) permitió descubrir que el género Arcobacter está en realidad formado por al menos 7 géneros, diferenciables genéticamente y mediante combinación de pruebas fenotípicas.
The genus Arcobacter belongs to the family Campylobacteraceae and includes species considered emergent pathogens because they can produce infections in humans and animals. The species of the genus are widely distributed worldwide and the consumption of contaminated food or water is considered the source of the infection. There are several tools for the epidemiological characterization of the strains that could help to clarify the routes of infection. However, the mechanisms of action of these bacteria are still poorly understood and there is no standardized treatment. The number of species of the genus has increased considerably in recent years and the use of new isolation techniques has led to the discovery of other new species. In this thesis, it was demonstrated that the epidemiological analysis using the Multilocus Sequence Typing (MLST) technique is not precise. In addition, the high resistance to certain antibiotics suggested the need for introducing changes in the treatments used in Arcobacter infections. A total of 4 new species were described using phenotypic characterization, Multilocus Phylogenetic Analysis (MLPA) of 5 genes (atpA, gyrA, gyrB, hsp60 and rpoB) and information extracted from the sequenced genomes of these species and the phylogenetically close ones. The use of genomes and their comparison and phylogenetic analysis also showed that the species A. cryaerophilus is composed by 4 genomovars, which represent genomic species that could not be phenotypically differentiated. Finally, the phylogenetic analysis of the genomes of all the species of the genus, together with the calculation of different genomic indexes (ANI, isDDH, AAI, POCP and RSCU) allowed us to discover that the genus Arcobacter is actually formed by at least 7 genera, differentiable genetically and with a combination of phenotypic tests.
The genus Arcobacter belongs to the family Campylobacteraceae and includes species considered emergent pathogens because they can produce infections in humans and animals. The species of the genus are widely distributed worldwide and the consumption of contaminated food or water is considered the source of the infection. There are several tools for the epidemiological characterization of the strains that could help to clarify the routes of infection. However, the mechanisms of action of these bacteria are still poorly understood and there is no standardized treatment. The number of species of the genus has increased considerably in recent years and the use of new isolation techniques has led to the discovery of other new species. In this thesis, it was demonstrated that the epidemiological analysis using the Multilocus Sequence Typing (MLST) technique is not precise. In addition, the high resistance to certain antibiotics suggested the need for introducing changes in the treatments used in Arcobacter infections. A total of 4 new species were described using phenotypic characterization, Multilocus Phylogenetic Analysis (MLPA) of 5 genes (atpA, gyrA, gyrB, hsp60 and rpoB) and information extracted from the sequenced genomes of these species and the phylogenetically close ones. The use of genomes and their comparison and phylogenetic analysis also showed that the species A. cryaerophilus is composed by 4 genomovars, which represent genomic species that could not be phenotypically differentiated. Finally, the phylogenetic analysis of the genomes of all the species of the genus, together with the calculation of different genomic indexes (ANI, isDDH, AAI, POCP and RSCU) allowed us to discover that the genus Arcobacter is actually formed by at least 7 genera, differentiable genetically and with a combination of phenotypic tests.