title: Uncoupling between core genome and virulome in extraintestinal pathogenic Escherichia coli.
abstract: Extraintestinal pathogenic Escherichia coli (ExPEC) are among the most frequently isolated bacterial pathogens in hospitals. They are considered opportunistic pathogens and are found mostly in urinary and bloodstream infections. They are genetically diverse, and many studies have sought associations between genotypes or virulence genes and infection site, severity, or outcome, with varied, often contradictory, results. To understand these difficulties, we have analyzed the diversity patterns in the core genomes and virulomes of more than 500 ExPEC isolates from 5 different collections. The core genome was analyzed using a multilocus sequence type-based single-nucleotide polymorphism (SNP) pyrosequencing approach, while the virulence gene content (the virulome) was studied by polymerase chain reaction detection of 25 representative genes. SNP typing showed a similar population structure in the different collections: half of the isolates belong to a few sequence types (5 to 8), while the other half is composed of a large diversity of sequence types that are found once or twice. Sampling analysis by rarefaction plots of SNP profiles showed saturation curves indicative of a limited diversity. Contrary to this, the virulome shows an extremely high diversity, with almost as many gene profiles as isolates, and linear, nonsaturating, rarefaction plots, even within sequence types. These data show that genetic exchange rates are very heterogeneous along the chromosome, being much higher in the virulome fraction of the genome than in the core genome.
authors.affiliation: a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain.
authors.forename: Natalia
authors.initials: N
authors.lastname: Fernández-Romero
authors.affiliation: a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain.
authors.forename: María Pilar
authors.initials: MP
authors.lastname: Romero-Gómez
authors.affiliation: b Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Mora-Rillo
authors.affiliation: c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.|d Departamento de Medicina, Universidad de Sevilla, Spain.|e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Rodríguez-Baño
authors.affiliation: c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.|e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.|f Departamento de Microbiología, Universidad de Sevilla, Spain.
authors.forename: Lorena
authors.initials: L
authors.lastname: López-Cerero
authors.affiliation: c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.|e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.|f Departamento de Microbiología, Universidad de Sevilla, Spain.
authors.forename: Álvaro
authors.initials: Á
authors.lastname: Pascual
authors.affiliation: a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain.|e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Mingorance
mesh_terms: D004926:Escherichia coli / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity*; D004927:Escherichia coli Infections / Q000382:microbiology*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D058885:Multilocus Sequence Typing; D020641:Polymorphism, Single Nucleotide; D014774:Virulence
chemical_list: D029968:Escherichia coli Proteins
keywords: Escherichia coli; ExPEC; core genome; génome commun; pangenome; pangénome; virulome