Last data update: Sep 16, 2024. (Total: 47680 publications since 2009)
Records 1-3 (of 3 Records) |
Query Trace: Trees EK [original query] |
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Use of whole genome sequencing to complement characterisation of a typhoid fever outbreak among a Marshallese community: Oklahoma, 2015.
Burnsed LJ , Kovar LD , Angelo KM , Trees EK , Concepcion-Acevedo J , McDermott MD , Wagner D , Bradley KK . Epidemiol Infect 2018 147 1-7 Typhoid fever is an illness caused by Salmonella enterica serotype Typhi. In developing regions, it affects an estimated 20 million people annually, causing 200 000 deaths. Although uncommon, cases occur in the USA each year, predominantly due to international travel. During February 2015, the Oklahoma State Department of Health (OSDH) detected an outbreak of typhoid fever among residents of northwestern Oklahoma. OSDH conducted case-patient interviews to identify the source and symptomatic contacts. Whole genome sequencing (WGS) was performed to characterise the genetic relatedness of isolates among the four outbreak-associated pulsed-field gel electrophoresis (PFGE) patterns. We identified 38 cases, 25 confirmed and 13 probable, in two states. WGS revealed a 0-10 single-nucleotide polymorphism variation between isolates. Although we were unable to determine the source, almost all case-patients were members of the Marshallese community that attended a common event in Oklahoma, or were contacts to a confirmed case. This is the largest outbreak of typhoid fever in the USA since 1989, and first to apply WGS to complement interpretation of PFGE results during a typhoid fever outbreak investigation. This investigation illustrates the potential risk of outbreaks among communities comprised of international populations from regions where typhoid fever remains endemic. |
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.
Timme RE , Rand H , Shumway M , Trees EK , Simmons M , Agarwala R , Davis S , Tillman GE , Defibaugh-Chavez S , Carleton HA , Klimke WA , Katz LS . PeerJ 2017 2017 (10) e3893 Background. As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods. We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (referencebased SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and ``known'' phylogenetic trees in publiclyaccessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results. Our ``outbreak'' benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the ``known tree'' can be accurately called the ``true tree''. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion. These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools-we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines. |
Outbreak of Shiga-toxigenic Escherichia coli O157:H7 infections associated with rodeo attendance, Utah and Idaho, 2009
Lanier WA , Hall JM , Herlihy RK , Rolfs RT , Wagner JM , Smith LH , Hyytia-Trees EK . Foodborne Pathog Dis 2011 8 (10) 1131-3 OBJECTIVES: In summer 2009, the Utah Department of Health investigated an outbreak of Shiga-toxigenic Escherichia coli (STEC) O157:H7 (O157) illness associated with attendance at multiple rodeos. MATERIALS AND METHODS: Patients were interviewed regarding exposures during the week before illness onset. A ground beef traceback investigation was performed. Ground beef samples from patient homes and a grocery store were tested for STEC O157. Rodeo managers were interviewed regarding food vendors present and cattle used at the rodeos. Environmental samples were collected from rodeo grounds. Two-enzyme pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) were performed on isolates. RESULTS: Fourteen patients with primary STEC O157 illness were reported in this outbreak. Isolates from all patients were indistinguishable by PFGE. Isolates from nine patients had identical MLVA patterns (main outbreak strain), and five had minor differences. Thirteen (93%) patients reported ground beef consumption during the week before illness onset. Results of the ground beef traceback investigation and ground beef sampling were negative. Of 12 primary patients asked specifically about rodeo attendance, all reported having attended a rodeo during the week before illness onset; four rodeos were mentioned. All four rodeos had used bulls from the same cattle supplier. An isolate of STEC O157 identified from a dirt sample collected from the bullpens of one of the attended rodeos was indistinguishable by PFGE and MLVA from the main outbreak strain. DISCUSSION: Recommendations were provided to rodeo management to keep livestock and manure separate from rodeo attendees. This is the first reported STEC O157 outbreak associated with attendance at multiple rodeos. Public health officials should be aware of the potential for rodeo-associated STEC illness. |
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