No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typin...

BACKGROUND Infants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates a...

The aim of this study was to investigate sequence-based genotyping methods to distinguish 27 Riemerella anatipestifer isolates from ducklings in South Korea. The 16S rRNA sequences of the 27 R. anatipestifer isolates showed 99�100% similarities to each other and to reference sequences from Genbank (AY871822.2, AY871834.2, CP002562.1, EU715016.1, EU016548.1, EU715000.1, EU715008.1 and EU715011.1...

Phylogenetic reconstruction of three highly conserved proteins involved in bacterial conjugation (relaxase, coupling protein and a type IV secretion system ATPase) allowed the classification of transmissible elements in relaxase MOB families and mating pair formation MPF groups. These evolutionary studies point to the existence of a limited number of module combinations in transmissible element...

Background: Escherichia coli (E. coli) is one of the most important infectious agents in patients undergoing prostate biopsy. It belongs to a large family of gram-negative rods, Enterobacteriaceae. This family includes members of the normal flora of the intestine that are only occasionally pathogenic. Recent considerations of rectal colonization with fluoroquinolone-resistant E. coli shows the ...

The perfect phylogeny model for haplotype evolution has been successfully applied to haplotype resolution from genotype data. In this study we explore the application of the perfect phylogeny model to other problems in the design and analysis of genetic studies. We consider a novel type of data, xor-genotypes, which distinguish heterozygote from homozygote sites but do not identify the homozygo...

Extraintestinal pathogenic Escherichia coli (ExPEC) strains of human and avian origin show similarities that suggest that the avian strains potentially have zoonotic properties. However, the phylogenetic relationships between avian and human ExPEC strains are poorly documented, so this possibility is difficult to assess. We used PCR-based phylotyping and multilocus sequence typing (MLST) to det...

Paracoccidioides brasiliensis is the etiological agent of paracoccidioidomycosis, an important human systemic mycosis in Latin America. Recently, the existence of three different phylogenetic species (S1, PS2, and PS3) of P. brasiliensis was demonstrated. Despite being genetically isolated, all three species were capable of inducing disease in both humans and animals, although lower virulence h...