The use of multiple hypothesis-generating methods in an outbreak investigation of Escherichia coli O121 infections associated with wheat flour, Canada 2016-2017.

A Canadian outbreak investigation into a cluster of Escherichia coli O121 was initiated in late 2016. When initial interviews using a closed-ended hypothesis-generating questionnaire did not point to a common source, cases were centrally re-interviewed using an open-ended approach. The open-ended interviews led cases to describe exposures with greater specificity, as well as food preparation activities. Data collected supported hypothesis generation, particularly with respect to flour exposures. In March 2017, an open sample of Brand X flour from a case home, and a closed sample collected at retail of the same brand and production date, tested positive for the outbreak strain of E. coli O121. In total, 76% (16/21) of cases reported that they used or probably used Brand X flour or that it was used or probably was used in the home during their exposure period. Crucial hypothesis-generating techniques used during the course of the investigation included a centralised open-ended interviewing approach and product sampling from case homes. This was the first outbreak investigation in Canada to identify flour as the source of infection.

Demonstration of Machine Learning-Based Model-Independent Stabilization of Source Properties in Synchrotron Light Sources.

Synchrotron light sources, arguably among the most powerful tools of modern scientific discovery, are presently undergoing a major transformation to provide orders of magnitude higher brightness and transverse coherence enabling the most demanding experiments. In these experiments, overall source stability will soon be limited by achievable levels of electron beam size stability, presently on the order of several microns, which is still 1-2 orders of magnitude larger than already demonstrated stability of source position and current. Until now source size stabilization has been achieved through corrections based on a combination of static predetermined physics models and lengthy calibration measurements, periodically repeated to counteract drift in the accelerator and instrumentation. We now demonstrate for the first time how the application of machine learning allows for a physics- and model-independent stabilization of source size relying only on previously existing instrumentation. Such feed-forward correction based on a neural network that can be continuously online retrained achieves source size stability as low as 0.2 µm (0.4%) rms, which results in overall source stability approaching the subpercent noise floor of the most sensitive experiments.

Methods for generating hypotheses in human enteric illness outbreak investigations: a scoping review of the evidence.

Enteric illness outbreaks are complex events, therefore, outbreak investigators use many different hypothesis generation methods depending on the situation. This scoping review was conducted to describe methods used to generate a hypothesis during enteric illness outbreak investigations. The search included five databases and grey literature for articles published between 1 January 2000 and 2 May 2015. Relevance screening and article characterisation were conducted by two independent reviewers using pretested forms. There were 903 outbreaks that described hypothesis generation methods and 33 papers which focused on the evaluation of hypothesis generation methods. Common hypothesis generation methods described are analytic studies (64.8%), descriptive epidemiology (33.7%), food or environmental sampling (32.8%) and facility inspections (27.9%). The least common methods included the use of a single interviewer (0.4%) and investigation of outliers (0.4%). Most studies reported using two or more methods to generate hypotheses (81.2%), with 29.2% of studies reporting using four or more. The use of multiple different hypothesis generation methods both within and between outbreaks highlights the complexity of enteric illness outbreak investigations. Future research should examine the effectiveness of each method and the contexts for which each is most effective in efficiently leading to source identification.

Outbreaks of Salmonella illness associated with frozen raw breaded chicken products in Canada, 2015-2019.

Frozen raw breaded chicken products (FRBCP) have been identified as a risk factor for Salmonella infection in Canada. In 2017, Canada implemented whole genome sequencing (WGS) for clinical and non-clinical Salmonella isolates, which increased understanding of the relatedness of Salmonella isolates, resulting in an increased number of Salmonella outbreak investigations. A total of 18 outbreaks and 584 laboratory-confirmed cases have been associated with FRBCP or chicken since 2017. The introduction of WGS provided the evidence needed to support a new requirement to control the risk of Salmonella in FRBCP produced for retail sale.

Outbreak of Salmonella Reading in persons of Eastern Mediterranean origin in Canada, 2014-2015.

BACKGROUND: Salmonella Reading (S. Reading) is a rare serotype of Salmonella subspecies (spp.) in Canada with less than nine cases reported each year (2011-2013). An increase in S. Reading was identified in several Canadian provinces in early 2015, prompting the initiation of a national outbreak investigation. OBJECTIVES: To describe a multi-provincial S. Reading outbreak in Canada that affected over 30 people. METHODS: Cases were defined as laboratory-confirmed S. Reading with related pulsed-field gel electrophoresis (PFGE) patterns. Onset dates were between November 2014 and September 2015.​: Early in the investigation, investigators noted cases were predominantly of Eastern Mediterranean origin, mainly Afghan and Lebanese and many of those affected had consumed food items not typically captured on standard enteric outbreak hypothesis-generating questionnaires. An open-ended three day food consumption survey was conducted with a convenience sample of community informants to better understand food preferences of the affected ethnocultural populations. Results of the survey were used to design a focused questionnaire for case re-interviews and subsequent outbreak cases. Public health investigators obtained food samples from case homes and relevant food premises. Food safety authorities conducted traceback of suspected food items and collected food samples for laboratory testing. RESULTS: There were 31 confirmed cases (Ontario=23, Alberta=7, New Brunswick=1) and three probable (Ontario=2, Alberta=1) cases of S. Reading identified as part of the outbreak. The median age was 31 years (range less than one to 85 years) and 53% (18/34) of cases were female. Seven cases were hospitalized. No deaths were reported. Most cases were of Eastern Mediterranean origin (n=23) or had reported consuming Eastern Mediterranean foods (n=3). The predominant ethnic origins reported by cases were Afghan in Ontario (n=12) and Lebanese in Alberta (n=3). Genetic similarity of clinical isolates was further confirmed using whole genome sequencing.​: Three ethnic bakeries were identified as possible common exposures for the cases; however, traceback of foods of interest from these bakeries did not identify a common supplier and the source of the illness was not identified. In total, 227 food samples from retail premises (n=142), restaurants (n=13) and case homes (n=72) were tested; two food samples, kalonji seeds and tahini, were positive for S. Ruiru and S. Meleagridis. These products were recalled from the marketplace. CONCLUSION: Despite extensive epidemiological, microbiological and food traceback investigations, a common source was not identified for this S. Reading outbreak. Challenges included lack of familiarity with the food items consumed in affected ethnocultural groups, as well as a lack of background data on expected food exposures in the outbreak population. Engaging local partners helped build understanding of food preferences in affected communities. Given Canada's ethnic and cultural diversity, culturally competent approaches to enteric outbreak investigations and food consumption surveys may be useful.

Summary: Canada's Food-borne Illness Outbreak Response Protocol.

BACKGROUND: The burden of illness due to food-borne pathogens each year in Canada is significant. Investigations of food-borne illness outbreaks, particularly those with cases in more than one jurisdiction, are complex. Accordingly, efficient outbreak response requires the coordination and collaboration of many investigative partners. OBJECTIVE: To highlight the Public Health Agency of Canada's Food-borne Illness Outbreak Response Protocol (FIORP), the primary guidance document for investigations of multi-jurisdictional food-borne illness outbreaks in Canada. APPROACH: The current version of the FIORP was developed in 2010 by the Public Health Agency of Canada following consultation with Health Canada, the Canadian Food Inspection Agency, and provincial and territorial stakeholders. RESULTS: The FIORP outlines guiding principles and operating procedures to enhance collaboration and coordination among multiple investigative partners in response to multi-jurisdictional food-borne illness outbreaks. It has provided guidance for the conduct of 22 such investigations led by the Public Health Agency of Canada's Centre for Food-borne, Environmental and Zoonotic Infectious Diseases between 2011 and 2013. Furthermore, it has also served as a guide for the development of provincial protocols. CONCLUSION: The timely and effective investigation of and response to multi-jurisdictional food-borne illness outbreaks in Canada is facilitated and enhanced by the FIORP.

Outbreak of E. coli O157:H7 associated with lettuce served at fast food chains in the Maritimes and Ontario, Canada, Dec 2012.

BACKGROUND: Identification and control of multi-jurisdictional foodborne illness outbreaks can be complex because of their multidisciplinary nature and the number of investigative partners involved. OBJECTIVE: To describe the multi-jurisdictional outbreak response to an E. coli O157:H7 outbreak in Canada that highlights the importance of early notification and collaboration and the value of centralized interviewing. METHODS: Investigators from local, provincial and federal jurisdictions, using a national outbreak response protocol to clarify roles and responsibilities and facilitate collaboration, conducted a rapid investigation that included centralized re-interview of cases, descriptive methods, binomial probability, and traceback findings to identify the source of the outbreak. RESULTS: There were 31 laboratory confirmed cases identified in New Brunswick, Nova Scotia, and Ontario. Thirteen cases (42%) were hospitalized and one case (3%) developed hemolytic uremic syndrome; there were no deaths. Due to early notification a coordinated investigation was initiated before laboratory subtyping was available. Re-interview of cases identified 10 cases who had not initially reported exposure to the source of the outbreak. Less than one week after the Outbreak Investigation Coordinating Committee was formed, consumption of shredded lettuce from a fast food chain was identified as the likely source of the illnesses and the implicated importer/processor initiated a precautionary recall the same day. CONCLUSION: This outbreak investigation highlights the importance of early notification, prompt re-interviewing and collaboration to rapidly identify the source of an outbreak.

Soft x-ray scattering facility at the Advanced Light Source with real-time data processing and analysis.

We present the development and characterization of a dedicated resonant soft x-ray scattering facility. Capable of operation over a wide energy range, the beamline and endstation are primarily used for scattering from soft matter systems around the carbon K-edge (∼285 eV). We describe the specialized design of the instrument and characteristics of the beamline. Operational characteristics of immediate interest to users such as polarization control, degree of higher harmonic spectral contamination, and detector noise are delineated. Of special interest is the development of a higher harmonic rejection system that improves the spectral purity of the x-ray beam. Special software and a user-friendly interface have been implemented to allow real-time data processing and preliminary data analysis simultaneous with data acquisition.

Current-induced formation of gradient crystals in block copolymer electrolytes.

Conventional ordered phases such as crystals and liquid crystals have constant domain spacings. In this Letter, we report on the formation of coherently ordered morphologies wherein the domain spacing changes continuously along a specified direction. We have coined the term "gradient crystal" to refer to this structure, a signature of which is a small-angle X-ray scattering pattern that resembles a sundial. Gradient crystals composed of a gyroid morphology form spontaneously when ionic current is driven through a block copolymer electrolyte. We propose that this structure forms because it allows for a continuous change in domain spacing without requiring the introduction of defects. Previous studies have shown that applied electric fields ranging from 1000 to 40,000 V/mm can induce long-range structural order, alignment, and morphological transitions in block copolymers. Gradient crystals form under applied electric fields as low as 2.5 V/mm due to the presence of direct ionic currents that are absent in the aforementioned studies.

Investigation of antirelaxation coatings for alkali-metal vapor cells using surface science techniques.

Many technologies based on cells containing alkali-metal atomic vapor benefit from the use of antirelaxation surface coatings in order to preserve atomic spin polarization. In particular, paraffin has been used for this purpose for several decades and has been demonstrated to allow an atom to experience up to 10 000 collisions with the walls of its container without depolarizing, but the details of its operation remain poorly understood. We apply modern surface and bulk techniques to the study of paraffin coatings in order to characterize the properties that enable the effective preservation of alkali spin polarization. These methods include Fourier transform infrared spectroscopy, differential scanning calorimetry, atomic force microscopy, near-edge x-ray absorption fine structure spectroscopy, and x-ray photoelectron spectroscopy. We also compare the light-induced atomic desorption yields of several different paraffin materials. Experimental results include the determination that crystallinity of the coating material is unnecessary, and the detection of C[Double Bond]C double bonds present within a particular class of effective paraffin coatings. Further study should lead to the development of more robust paraffin antirelaxation coatings, as well as the design and synthesis of new classes of coating materials.

Monte Carlo study of crystalline order and defects on weakly curved surfaces.

We numerically study the ground states of particles interacting via a repulsive Yukawa potential on two rigid substrates shaped as isolated and periodically arranged bumps characterized by a spatially varying Gaussian curvature. Below a critical aspect ratio that describes the substrate deformation, the lattice is frustrated, but defect free. A further increase of the aspect ratio triggers defect unbinding transitions that lower the total potential energy by introducing dislocations either in isolation or within grain boundaries. In the presence of very strong deformations, isolated disclinations are nucleated. We show that the character and spatial distribution of defects observed in the ground state reflect the symmetries and periodicity of the two model surfaces investigated in this study.