A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia.

IMPORTANCE: The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.

Severity of Escherichia coli bacteraemia is independent of the intrinsic virulence of the strains assessed in a mouse model.

Extraintestinal pathogenic Escherichia coli (ExPEC) strains, a major cause of bacteraemia, typically belong to phylogenetic group B2 and express diverse accessory traits that contribute to virulence in mouse infection models. However, their high genomic diversity obscures the relationship between virulence factors and severity of infection in patients. In this study, we analysed concomitantly the strain's expression of virulence in a mouse model, genomic determinants and the clinical severity of infection in 60 bacteraemic patients. We show that bacterial virulence based on an animal model study and virulence factor determination is not correlated with pejorative outcome of E. coli human blood infections.