ABSTRACT
To assess the distribution of phylogroups and O25/ST131 in the Netherlands, we performed a real-time polymerase chain reaction (PCR) on a collection of 108 wild-type Escherichia coli (WT-EC) and 134 extended-spectrum ß-lactamase-producing E. coli (ESBL-EC). Phylogroup B2 was predominant, but ESBL-EC were less likely to belong to this phylogroup (48.5%) than were WT-EC (66.7%; p = 0.005). In WT-EC, phylogroups B2 and D seem to be more virulent, having a higher prevalence among midstream urine isolates and blood culture isolates, than in catheter-related urine isolates (83.3% and 87.9% vs. 61.9%; p 0.048). O25/ST131 is associated with ESBL production, being almost absent among phylogroup B2 WT-EC (61.5% vs. 5.6%; p < 0.001).
Subject(s)
Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Escherichia coli/classification , Escherichia coli/genetics , Genotype , Adult , Aged , Aged, 80 and over , Escherichia coli/isolation & purification , Female , Humans , Male , Middle Aged , Netherlands/epidemiology , Prevalence , Prospective Studies , Real-Time Polymerase Chain Reaction , Retrospective Studies , Serogroup , beta-Lactamases/metabolismABSTRACT
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) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.
Subject(s)
Disease Outbreaks , Drug Resistance, Bacterial , Escherichia coli Infections/epidemiology , Escherichia coli/genetics , High-Throughput Nucleotide Sequencing/methods , Molecular Typing/methods , beta-Lactamases/genetics , Cluster Analysis , Cross-Sectional Studies , Escherichia coli/classification , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Infections/diagnosis , Genes, Bacterial , Humans , Microbial Sensitivity Tests/methods , Molecular Epidemiology/methods , Netherlands/epidemiology , Nursing Homes , PhylogenyABSTRACT
Seven international laboratories tested the recently proposed single-locus typing strategy for Aspergillus fumigatus subtyping for interlaboratory reproducibility. Comparative sequence analyses of portions of the locus AFUA_3G08990, encoding a putative cell surface protein (denoted CSP), was performed with a panel of Aspergillus isolates. Each laboratory followed very different protocols for extraction of DNA, PCR, and sequencing. Results revealed that the CSP typing method was a reproducible and portable strain typing method.
Subject(s)
Aspergillus fumigatus/classification , Aspergillus fumigatus/genetics , DNA, Fungal/genetics , Mycological Typing Techniques/methods , Mycological Typing Techniques/standards , Sequence Analysis, DNA/methods , Sequence Analysis, DNA/standards , Genotype , Reproducibility of ResultsABSTRACT
Andreas Vesalius was born in Brussels on December 31, 1514 from a long line of physicians. He died in Zante in 1564. He was a typical son of the Renaissance. In 1543, his two most important books were published: De Humani Corporis Fabrica, Libri Septum and the Epitome. The former was a book of over 700 pages with several illustrations, highly systematically composed and fully indexed. Andreas Vesalius was the first modern anatomist who based his anatomical descriptions on personal observation. The kidney was a fascinating organ to Vesalius, whose function, particularly regarding the production of urine, he did not fully grasp. He makes short work of the 'perforated membrane theory' which was the current conception of the origin of urine in the kidney. Andreas Vesalius broke with the established rigid and fabricated way of teaching anatomy, and introduced the modern concept of learning based on personal observations, using illustration combined with a critical spirit and sense of experiment.
