background escherichia coli is one of the most causative pathogen of urinary tract infection. urinary tract infections (utis) are the second most common cause of morbidity and remain a serious health concern among the clinicians. the severity of uti caused by uropathogenic e. coli (upec) is due to the expression of a wide spectrum of virulent factors such as adhesin coding operons. little is kn...

Recent isolation of Pseudomonas aeruginosa strains from the open ocean and subsequent pulsed-field gel electrophoresis analyses indicate that these strains have a unique genotype (N. H. Khan, Y. Ishii, N. Kimata-Kino, H. Esaki, T. Nishino, M. Nishimura, and K. Kogure, Microb. Ecol. 53:173-186, 2007). We hypothesized that ocean P. aeruginosa strains have a unique phylogenetic position relative t...

Repetitive-element PCR (rep-PCR) fingerprinting is a promising molecular typing tool for Escherichia coli, including for discriminating between pathogenic and nonpathogenic clones, but is plagued by irreproducibility. Using the ERIC2 and BOXA1R primers and 15 E. coli strains from the ECOR reference collection (three from each phylogenetic group, as defined by multilocus enzyme electrophoresis [...

background and objectives: diarrheagenic escherichia coli (dec) strains are a major cause of intestinal syndromes in the developing countries. the aim of this study was to determine the prevalence of enterotoxigenic e. coli (etec) and enteroinvasive e. coli (eiec) in relation to phylogenetic background from patients with diarrhea. materials and methods: a total of 110 e. coli isolates were obta...

BACKGROUND Multi-drug-resistant, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, constitute an emerging public-health concern. Little data on the molecular epidemiology of ESBL producing Escherichia coli is available in Germany. Here we describe the prevalence and molecular epidemiology of ESBL producing-Escherichia coli isolates at a German University hospital. METHODS ...

OBJECTIVES To characterize bla(CTX-M-15)-carrying plasmids and lineages of nine strains of Escherichia coli from cattle. METHODS Plasmid DNA was analysed using PCR-based replicon typing and plasmid sub-typing schemes, restriction fragment length polymorphism, S1 nuclease-PFGE and Southern hybridization. Strains were characterized by PFGE, multilocus sequence typing, phylogenetic grouping and ...

Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2 and D). Characterization of phylogenetic groups is of clinical interest, as group A and B1 generally associated with commensals, whereas most enteropathogenic isolates are assigned to group D, and group B2 is associated with extra-intestinal pathotype. One hundred E. coli strains recove...

The Shigella genus has historically been separated into four species, based on biochemical assays. The classification within each species relies on serotyping. Recently, genome sequencing and DNA assays, in particular the multilocus sequence typing (MLST) approach, greatly improved the current knowledge of the origin and phylogenetic evolution of Shigella spp. The Shigella and Escherichia gener...

The spa gene occurs in all strains of Staphylococcus aureus (S. aureus), can function as a genetic marker and might be used distinguish strains at the species level. Hence, due to these advantages, we used spa typing and the Based Upon Repeat Pattern (BURP) to assign the clonal and phylogenetic relationships of S. aureus strains. The sensitivity of S. aureus strains to methicillin was determine...

Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherich...