As a result of the ongoing Coronavirus pandemic, the 11th Annual CPS Research Symposium was conducted virtually over the course of five consecutive weeks in 2020.
Session 4 featured the use of genomics and metagenomics in three final project reports and one interim results presentation. These projects focus on the challenges of identifying new or revisited indicators and index testing-targets of human viral pathogens that may ultimately be used in the produce industry, the distribution and relatedness of Listeria species in the U.S. and the use of that information to better understand source-risk related to facilities and product, identification of competitors of Listeria monocytogenes that might control that organism in composts and build our knowledge base of bacterial pathogen persistence and rates of genetic diversification in the Yuma and Salinas vegetable production regions. These outstanding presentations and discussions generated the following executive summary and more lengthy Key Learnings.
These learnings are meant to inform and provoke thought with an eye towards inspiring readers to examine their own produce safety programs and to use the research to make improvements. They are not meant as a directive on what must be done to produce safe food.
This and other recordings of CPS webinars are available via CPS’s website. The latest information about specific research projects mentioned in this document is available via CPS’s website, including our extensive research database and other produce safety resources.
Key Learnings Executive Summary
- Genomics and metagenomics are important tools to help fill produce safety knowledge gaps. Genomics and metagenomics are powerful technologies being leveraged to address critical and biologically complex produce safety challenges. It is important to understand how these technologies can be used and what they will mean for the produce industry moving forward.
- Research builds better research. The four research projects highlighted in Session 4 all have their roots in previously funded CPS projects. Research is a process where the learnings from one project are leveraged to ask better questions and fuel development of new tools to address those questions.
- Potential indicators for human enteric viruses have been identified. The presence of crAssphage and six other indicator organisms have been correlated with the presence of various human enteric viruses in agricultural water influenced by or blended with reclaimed wastewater using genomic approaches to dissect the complex microbial community associated with these water sources.
- Listeria spp. distribution has been mapped throughout the U.S. 31-percent of soil samples, collected from non-production public sites, were positive for Listeria and 12-percent were positive for Listeria monocytogenes (Lm). 14 known and 5 new Listeria species were identified. The greatest occurrence of Listeria spp. was found in the Mississippi River Basin.
- Listeria whole genome sequencing data can be leveraged in source tracking. Soil isolates of Lm collected from these natural environments were sequenced, compared to a public database, and some clinical isolates were found to be closely related. These sequence data can be used to provide context for interpreting whole genome sequencing results during outbreak source tracking and indicate that low single nucleotide polymorphism (SNP) differences (evidence of high similarity) between human, food, facility, or regionally obtained environmental isolates do not necessarily imply a causal link to a firm’s product.
- Composts contain competitor bacteria that demonstrate lab-based anti-Lm properties. Genomic and metagenomic approaches were used to dissect the diverse microbial communities in dairy and poultry composts to identify competitive exclusion (CE) organisms with anti-Lm activity. When composts were inoculated with Lm, Bacillus strains, among others, demonstrated antimicrobial molecule production shown to be inhibitory to Lm. While long-term and speculative, CE may offer new opportunities for Lm control in farm inputs used by organic and conventional systems.
This is the Key Learnings Executive Summary only. See the PDF link for more extensive information.