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Keystone Microtrack: Mapping Microbes and Pathogens in the Susquehanna River Basin

This project sought to characterize Salmonella in the Susquehanna River Basin, with a focus on both prevalence and which serovars were present. Additionally, we wanted to examine basic physical characteristics, as well as the bacterial communities, of those streams. Lastly, we collated this information and developed an open-source, interactive mapping tool (Keystone MicroTrack) to make these results publicly accessible.

All data were generated from samples collected during May and July of 2018 and 2019. 28 sites were sampled during each collection period, for a total of 112 samples. Briefly, from each site: 10 L of water were filtered through a modified-Moore swab for use with culturing, 125 mL of water was filtered thru a 0.22 µm for use for community profiling, and water quality (Conductivity, pH, salinity, and TDS) was collected.

Two selective enrichment broths (Rappaport-Vassiliadis and tetrathionate) were used for culturing. Suspected Salmonella colonies were confirmed by streaking onto different media (XLT-4 and HE+N). DNA was isolated from these cultures and processed for CRISPR analysis. All genes were also sequenced for use with phylogenetic analysis.

DNA was extracted from the filters and processed for 16S rRNA analysis, which was done through QIIME 2. Within sample (alpha) and between (sample) diversity were examined with samples grouped by Salmonella presence based on culturing results. Biomarker analysis was also performed to see which bacteria, if any, differed significantly in abundance according to that grouping.

In total, 56% of the samples were Salmonella-positive. Notably, Salmonella was much more prevalent in the spring (86% and 82%, 2018 and 2019 respectively) than in the summer (21% and 36%). Across all samples, 25 different serovars were identified, with 80% of samples having more than one. Serovar Give was the most prevalent serovar. Considering the top ten serovars, eight of them have previously been associated with huma illness. At least one serovar from the top 10 was present in over 70% of the samples that had Salmonella.

Significant differences in both alpha and beta diversity for the total bacterial communities were discovered when the samples were grouped by Salmonella presence. Furthermore, specific taxa were identified that had greatly differential abundance in association with Salmonella presence.

These data have been incorporated into the Keystone MicroTrack tool, which will is accessible to anyone online. This tool will be a valuable resource for public health officials, as well as for everyday citizens who live in the area.

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