Please let us know if you have presented PARE-related work and we will add it to our list. Corresponding authors are listed in bold. Journal Articles Genné-Bacon, E., Fux, M., Bove, S.A., Payne, F., Xenakis, G., Coley, J.D., and Bascom-Slack, C. (2024). Dipping your toe in the CURE pool: Longitudinal tracking of instructors suggests use
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Metagenomic bioinformatics module: PARE-Seq The metagenomic bioinformatics module, PARE-Seq, demonstrates how scientists can use total metagenomic DNA extracted from environmental samples to search for any antibiotic resistance genes that may be present, regardless of what organism carries them, and regardless of whether that organism is living or expressing (using) those genes. Unlike traditional bioinformatics teaching
Identification of tetracycline-resistance genes from total soil DNA Students test soil samples for the presence of different tetracycline-resistance genes. This module does not require handling of live organisms. Students extract genomic DNA directly from soil and subject to PCR followed by gel electrophoresis. Module Organization This module doesn’t require handling of biological organisms; however, the
Identification of clinically important resistance genes This module is currently in development. Students will use primers to detect genes representing antibiotic resistance types that are difficult to treat and recently emerging globally in patients with antibiotic resistant infections (e.g. blaNDM-1, mcr-1). The assumption is that these “emergent” genes are circulating in the environment before they
Isolation of TcR plasmid and transfer into E. coli Students learn about the genetics of plasmid transfer by isolating plasmids from a tetracycline-resistant (TcR) colony identified in the Core PARE module and then attempting to transform a tetracyline-sensitive strain of E. coli using the plasmid preparation. There is no assurance that TcR is harbored on
Kirby-Bauer testing TcR isolates Students assess colonies isolated in the core PARE module for resistance to other antibiotics using the Kirby-Bauer disk diffusion assay which relies on measurement of the zone of inhibition after microbial growth around an antibiotic impregnated filter disk. Since the Kirby-Bauer test is intended for use on isolates of known identity,
16S PCR from colony Students choose a colony isolated from the core PARE module for tentative phylogenetic characterization. Genomic DNA is isolated and used in PCR reactions to amplify the 16S rRNA gene. Amplification results are confirmed by gel electrophoresis, the amplified DNA cleaned and sent for sequencing. Sequences are compared to those in the
Environmental prevalence of TcR This is the flagship course-based research module of the Prevalence of Antibiotic-Resistant microbes in the Environment (PARE) program. It engages students in a crowdsourcing effort to provide environmental surveillance data that could lead to identification of “hotspots” or environmental resistance reservoirs. Students perform classic microbiological techniques such as serial dilution and
Tracing the course of antibiotic resistance using PCR This skill-building lab represents a fictional case study of a very real problem. Students are presented with information regarding an outbreak of food-borne infection that is resistant to treatment with antibiotics. They are tasked with using PCR and gel electrophoresis to establish whether farms are at risk from antibiotic resistant