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Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology.

ABSTRACT: The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance spread. Students work in groups to analyze outbreak data to identify the bacterial species and antibiotic resistance genes, to infer a phylogenetic tree examining relatedness among isolates, and to determine a possible source of the outbreak. Students then compile their results in individual reports and provide recommendations for preventing the further spread of antibiotic resistant organisms. In addition to providing genomic outbreak data, we include a teaching concepts guide discussing three integral components of the module: how evolutionary biology concepts of natural selection and competition impact antibiotic resistance; outbreak investigation information to aid in phylogenetic analysis and creation of recommendations; and instructions for the bioinformatics protocol. Completion of this module provides students an opportunity to think critically about the evolution of resistance, practice bioinformatics techniques, and relate evolutionary biology to current events.

SUBMITTER: Pierce AA

PROVIDER: S-EPMC6502480 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology.

Pierce Amanda A AA de Man Tom J B TJB

Journal of biological education 20180309 2

The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance ...[more]

PMID: 31073246

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Project description:BackgroundAlthough evolutionary theory is foundational and integrative in modern biology, there remains widespread lack of acceptance among U.S. residents. An interdisciplinary approach to teaching evolutionary theory at the undergraduate level has many advantages, such as giving students a context for learning about evolution and application of evolutionary theory to other academic disciplines and everyday life. While there are foundational examples of interdisciplinary approaches to teaching evolutionary theory, there are few examples of courses with application of evolutionary theory to issues of sustainability, such as conservation or global climate change. We build on the practical and theoretical work of others to create an interdisciplinary course on evolutionary theory for non-science majors, with ties to sustainability. Our course is taught in three modules, with extensive readings and hands-on lab activities. The first module is focused on honey bee biology, with hands-on beekeeping experiences; the second module on native plants and community education on sustainability; and the third module on the evolution of the subjective human experience of free will.ResultsWe found that students in our course experienced an increased acceptance of evolutionary theory. We found that students also met the course leaning objectives, of basic knowledge of evolutionary theory and application of evolutionary theory to other disciplines, assessed through group and individual major assignments. We also found that students had an expanded perspective on interdisciplinary application of evolutionary theory, assessed through closed-ended survey questions and analysis of open-ended writing.ConclusionsStudents in our course experienced an increase of acceptance of evolutionary theory and an expanded perspective on interdisciplinary application of evolutionary theory, despite the fact that many students were not science majors.Supplementary informationThe online version contains supplementary material available at 10.1186/s12052-023-00188-4.

Project description:Outbreak investigations are essential to control and prevent the dissemination of pathogens. This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. The protocol was developed using 42 methicillin-resistant Staphylococcus aureus (MRSA) isolates identified from former well-characterized outbreaks. The validation of the protocol was performed using Illumina technology (MiSeq, Illumina). Additionally, a real-time outbreak investigation of six clinical S. aureus isolates was conducted to test the ONT-based protocol. The suggested protocol includes: (1) a 20 h sequencing run; (2) identification of the sequence type (ST); (3) de novo genome assembly; (4) polishing of the draft genomes; and (5) phylogenetic analysis based on SNPs. After the sequencing run, it was possible to identify the ST in 2 h (20 min per isolate). Assemblies were achieved after 4 h (40 min per isolate) while the polishing was carried out in 7 min per isolate (42 min in total). The phylogenetic analysis took 0.6 h to confirm an outbreak. Overall, the developed protocol was able to at least discard an outbreak in 27 h (mean) after the bacterial identification and less than 33 h to confirm it. All these estimated times were calculated considering the average time for six MRSA isolates per sequencing run. During the real-time S. aureus outbreak investigation, the protocol was able to identify two outbreaks in less than 31 h. The suggested protocol enables identification of outbreaks in early stages using a portable and low-cost device along with a streamlined downstream analysis, therefore having the potential to be incorporated in routine surveillance analysis workflows. In addition, further analysis may include identification of virulence and antibiotic resistance genes for improved pathogen characterization.

Dataset Information

Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology.

Publications

Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology.

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