Clinical microbiology has long relied on growing bacteria in culture to determine
antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic …

Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient
populations in hospitals around the world. Intensive care unit (ICU) patients are particularly …

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging
technologies capable of producing reads tens of kilobases long. Assembling complete …

Recombination is an important evolutionary force in bacteria, but it remains challenging to
reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present …

Fast and accurate identification and typing of pathogens are essential for effective
surveillance and outbreak detection. The current routine procedure is based on a variety of …

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology,
surveillance and infection control, yet routine use of whole genome sequencing (WGS) for …

Whole-genome sequencing has opened the way for investigating the dynamics and
genomic evolution of bacterial pathogens during the colonization and infection of humans …

Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based
method for identifying clonal relationships among bacteria. Today, in the whole-genome era …

Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities
worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon …

Background It has been thought that Clostridium difficile infection is transmitted
predominantly within health care settings. However, endemic spread has hampered …