A Schema for Digitized Surface Swab Site Metadata in Open-Source DNA Sequence Databases.

Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens by swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata that are associated with the swab site locations. However, the swab site location information is currently collected in a single, free-text, "isolation source", field-promoting generation of poorly detailed descriptions with various word order, granularity, and linguistic errors, making automation difficult and reducing machine-actionability. We assessed 1,498 free-text swab site descriptions that were generated during routine foodborne pathogen surveillance. The lexicon of free-text metadata was evaluated to determine the informational facets and the quantity of unique terms used by data collectors. Open Biological Ontologies (OBO) Foundry libraries were used to develop hierarchical vocabularies that are connected with logical relationships to describe swab site locations. 5 informational facets that were described by 338 unique terms were identified via content analysis. Term hierarchy facets were developed, as were statements (called axioms) about how the entities within these five domains are related. The schema developed through this study has been integrated into a publicly available pathogen metadata standard, facilitating ongoing surveillance and investigations. The One Health Enteric Package was available at NCBI BioSample, beginning in 2022. The collective use of metadata standards increases the interoperability of DNA sequence databases and enables large-scale approaches to data sharing and artificial intelligence as well as big-data solutions to food safety. IMPORTANCE The regular analysis of whole-genome sequence data in collections such as NCBI's Pathogen Detection Database is used by many public health organizations to detect outbreaks of infectious disease. However, isolate metadata in these databases are often incomplete and of poor quality. These complex, raw metadata must often be reorganized and manually formatted for use in aggregate analyses. These processes are inefficient and time-consuming, increasing the interpretative labor needed by public health groups to extract actionable information. The future use of open genomic epidemiology networks will be supported through the development of an internationally applicable vocabulary system with which swab site locations can be described.

Ability of Two Strains of Lactic Acid Bacteria To Inhibit Listeria monocytogenes by Spot Inoculation and in an Environmental Microbiome Context.

We evaluated the ability of two strains of lactic acid bacteria (LAB) to inhibit L. monocytogenes using spot inoculation and environmental microbiome attached-biomass assays. LAB strains (PS01155 and PS01156) were tested for antilisterial activity toward 22 phylogenetically distinct L. monocytogenes strains isolated from three fruit packing environments (F1, F2, and F3). LAB strains were tested by spot inoculation onto L. monocytogenes lawns (108 and 107 CFU/mL) and incubated at 15, 20, 25, or 30°C for 3 days. The same LAB strains were also cocultured at 15°C for 3, 5, and 15 days in polypropylene conical tubes with L. monocytogenes and environmental microbiome suspensions collected from F1, F2, and F3. In the spot inoculation assay, PS01156 was significantly more inhibitory toward less concentrated L. monocytogenes lawns than more concentrated lawns at all the tested temperatures, while PS01155 was significantly more inhibitory toward less concentrated lawns only at 15 and 25°C. Furthermore, inhibition of L. monocytogenes by PS01156 was significantly greater at 15°C than higher temperatures, whereas the temperature did not have an effect on the inhibitory activity of PS01155. In the assay using attached environmental microbiome biomass, L. monocytogenes concentration was significantly reduced by PS01156, but not PS01155, when cocultured with microbiomes from F1 and F3 and incubated for 3 days at 15°C. Attached biomass microbiota composition was significantly affected by incubation time but not by LAB strain. This study demonstrates that LAB strains that may exhibit inhibitory properties toward L. monocytogenes in a spot inoculation assay may not maintain antilisterial activity within a complex microbiome. IMPORTANCE Listeria monocytogenes has previously been associated with outbreaks of foodborne illness linked to consumption of fresh produce. In addition to conventional cleaning and sanitizing, lactic acid bacteria (LAB) have been studied for biocontrol of L. monocytogenes in food processing environments that are challenging to clean and sanitize. We evaluated whether two specific LAB strains, PS01155 and PS01156, can inhibit the growth of L. monocytogenes strains in a spot inoculation and in an attached-biomass assay, in which they were cocultured with environmental microbiomes collected from tree fruit packing facilities. LAB strains PS01155 and PS01156 inhibited L. monocytogenes in a spot inoculation assay, but the antilisterial activity was lower or not detected when they were grown with environmental microbiota. These results highlight the importance of conducting biocontrol challenge tests in the context of the complex environmental microbiomes present in food processing facilities to assess their potential for application in the food industry.