Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial
evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can …

Background Whole genome sequence (WGS)-based strain typing finds increasing use in the
epidemiologic analysis of bacterial pathogens in both public health as well as more …

Fully exploiting the wealth of data in current bacterial population genomics datasets requires
synthesizing and integrating different types of analysis across millions of base pairs in …

The emergence of new sequencing technologies has facilitated the use of bacterial whole
genome alignments for evolutionary studies and outbreak analyses. These datasets, of …

Some bacteria can transfer to new host species, and this poses a risk to human health.
Indeed, an estimated 60% of all human pathogens have originated from other animal …

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant
(MDR) clone responsible for a high proportion of urinary tract and bloodstream infections …

Identifying structure in collections of sequence data sets remains a common problem in
genomics. hierBAPS, a popular algorithm for identifying population structure in haploid …

Extensive genomic diversity within coexisting members of a microbial species has been
revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by …

Enterococcus faecium, natively a gut commensal organism, emerged as a leading cause of
multidrug-resistant hospital-acquired infection in the 1980s. As the living record of its …

Abstract Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for
which a commercial vaccine for humans is not available. Employing the advantages of high …