Geogenomic segregation and temporal trends of human pathogenic Escherichia coli o157:H7, Washington, USA, 2005-2014

The often-noted and persistent increased incidence of Escherichia coli O157:H7 infections in rural areas is not well understood. We used a cohort of E. coli O157:H7 cases reported in Washington, USA, during 2005–2014, along with phylogenomic characterization of the infecting isolates, to identify geographic segregation of and temporal trends in specific phylogenetic lineages of E. coli O157:H7. Kernel estimation and generalized additive models demonstrated that pathogen lineages were spatially segregated during the period of analysis and identified a focus of segregation spanning multiple, predominantly rural, counties for each of the main clinical lineages, Ib, IIa, and IIb. These results suggest the existence of local reservoirs from which humans are infected. We also noted a secular increase in the proportion of lineage IIa and IIb isolates. Spatial segregation by phylogenetic lineage offers the potential to identify local reservoirs and intervene to prevent continued transmission

Chapter Three. EED library as a basis for systematic reviews

3.1 Defining Systematic Review Question Priorities 3.2 Determining Relevance to the Systematic Review 3.3 Acquisition of References and Copyright Fair Use Compliance 3.4 Documenting Relevance to the Systematic Review 3.5 Data Extraction for the Systematic Review 3.6 EED Library: Search Results Overview 3.7 Quality Control 3.8 EED Library Statushttps://digitalcommons.wustl.edu/tropicalenteropathybook/1004/thumbnail.jp

Chapter Five. Systematic review results by biomarker classifications

5.1 Markers of Absorption and Permeability Overview 5.2 Markers of Absorption 5.3 Markers of Permeability 5.4 Markers of Digestion 5.5 Markers of Intestinal Inflammation and Intestinal Immune Activation 5.6 Markers of Systemic Inflammation and Systemic Immune Activation 5.7 Markers of Microbial Drivers 5.8 Markers of Nonspecific Intestinal Injury 5.9 Markers of Extra-Small Intestinal Function 5.10 Relationships Between Markers of EED, Including Histopathology 5.11 Relationships between EED Biomarkers and Growth or Other Outcomes of Interesthttps://digitalcommons.wustl.edu/tropicalenteropathybook/1006/thumbnail.jp

Droplet digital PCR quantifies host inflammatory transcripts in feces reliably and reproducibly

AbstractThe gut is the most extensive, interactive, and complex interface between the human host and the environment and therefore a critical site of immunological activity. Non-invasive methods to assess the host response in this organ are currently lacking. Feces are the available analyte which have been in proximity to the gut tissue.We applied a method of concentrating host transcripts from fecal specimens using a existing bead-based affinity separation method for nucleic acids and quantified transcripts using droplet digital PCR (ddPCR) to determine the copy numbers of a variety of key transcripts in the gut immune system. ddPCR compartmentalizes the reaction in a small aqueous droplet suspended in oil, and counts droplets as either fluorescent or non-fluorescent. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used to normalize transcript concentration.This method was applied to 799 fecal samples from rural Malawian children, and over 20,000 transcript concentrations were quantified. Host mRNA was detected in >99% samples, a threshold for target detection was established at an average expression of 0.02 copies target/GAPDH, above which correlation coefficient between duplicate measurements is >0.95. Quantities of transcript detected using ddPCR were greater than standard qPCR. Fecal sample preservation at the time of collection did not require immediate freezing or the addition of buffers or enzymes. Measurements of transcripts encoding immunoactive proteins correlated with a measure of gut inflammation in the study children, thereby substantiating their relevance. This method allows investigators to interrogate gene expression in the gut

Chapter Six. Conclusions and future implications

6.1 Summary of Findings 6.2 Future Biomarker and Diagnostics Researchhttps://digitalcommons.wustl.edu/tropicalenteropathybook/1007/thumbnail.jp

Enteric pathogen testing importance for children with acute gastroenteritis: A modified Delphi study

The application of clinical diagnostics for gastroenteritis in children has implications for a broad collection of stakeholders, impacting clinical care, communicable disease control, and laboratory utilization. To support diagnostic stewardship as gastroenteritis testing options continue to advance, it is critical to understand which enteropathogens constitute priorities for testing across stakeholder groups. Using a modified Delphi technique, we elicited opinions of subject matter experts to determine clinical and public health testing priorities. There was a high level of overall agreement (≥80%) among stakeholders (final roun

Electron impact ionization cross section of metastable N2(A Σu+)

Journal ArticleExtensive studies of electron impact cross sections have been carried out both experimentally and theoretically for a number of ground state atoms and molecules.1 In general, as the electron energy is increased, such cross sections rise from a threshold at the ionization potential to a peak at an electron energy roughly 4-6 times the threshold energy, before falling monotonically

Adaptation, Legal Resiliency, and the U.S. Army Corps of Engineers: Managing Water Supply in a Climate-Altered World

There are existing legal systems that embody planned resiliency. One of these is the multiple-use paradigm, which instructs resource managers to manage resources to maximize their multiple uses. Despite this built-in resiliency into practice. One of these agencies, the United States Army Corps of Engineers, is charged with managing water storage throughout much of the United States for multiple purposes, including human needs, agriculture, transportation, recreation, electricity generation, habitat, and the environment. This Article examines the Corps\u27 history in managing this water storage and shows that the Corps is currently ill equipped to administer its requirements with resilience. Given the expected demographic growth and climate-changed future, these problems are only going to grow worse. This Article analyzes the potential obstacles to effective, resilient management and makes suggestions about how the Corps, and ultimately other agencies, can effectively make their administrative systems more adaptive and thus better suited to meet new demands

TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders

Background: Plant resistance (R) gene products recognize pathogen effector molecules. Many R genes code for proteins containing nucleotide binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. NBS-LRR proteins can be divided into two groups, TIR-NBS-LRR and non-TIR-NBS-LRR, based on the structure of the N-terminal domain. Although both classes are clearly present in gymnosperms and eudicots, only non-TIR sequences have been found consistently in monocots. Since most studies in monocots have been limited to agriculturally important grasses, it is difficult to draw conclusions. The purpose of our study was to look for evidence of these sequences in additional monocot orders. Findings: Using degenerate PCR, we amplified NBS sequences from four monocot species (C. blanda, D. marginata, S. trifasciata, and Spathiphyllum sp.), a gymnosperm (C. revoluta) and a eudicot (C. canephora). We successfully amplified TIR-NBS-LRR sequences from dicot and gymnosperm DNA, but not from monocot DNA. Using databases, we obtained NBS sequences from additional monocots, magnoliids and basal angiosperms. TIR-type sequences were not present in monocot or magnoliid sequences, but were present in the basal angiosperms. Phylogenetic analysis supported a single TIR clade and multiple non-TIR clades. Conclusion: We were unable to find monocot TIR-NBS-LRR sequences by PCR amplification or database searches. In contrast to previous studies, our results represent five monocot orders (Poales, Zingiberales, Arecales, Asparagales, and Alismatales). Our results establish the presence of TIR-NBS-LRR sequences in basal angiosperms and suggest that although these sequences were present in early land plants, they have been reduced significantly in monocots and magnoliids