Comparison of DNA-based Detection Methods for Wild Pigs in the San Juan Bay Estuary Area
Citation:
Parker, B., I. Cappielo Cosme, M. Cuebas Irizarry, AND M. Molina. Comparison of DNA-based Detection Methods for Wild Pigs in the San Juan Bay Estuary Area. 2024 American Society for Microbiology Annual Meeting, Atlanta, GA, June 13 - 17, 2024.
Impact/Purpose:
Fecal contamination of water with fecal material from wild pigs could be a public health concern because it has been demonstrated that wild pigs carry pathogenic enteric bacteria.Hence, it is key to have an assay that can easily detect this invasive species in the environment, especially after removal events, to determine eradication success and monitor for potential reestablishment. In this study we aimed to 1.) compare the sensitivity of eDNA and MST assays in detecting wild pigs in an estuarine system, 2.) analyze the viability of the MST assay as a detection method for wild pigs. Our results indicate that MST can be used as an alternative to eDNA as a molecular detection method for wild pigs.
Description:
Wild pigs are an invasive species found globally that pose significant economic impact and a serious risk to local ecosystems, agriculture, and public health. Fecal contamination of water is one of these public health concerns as wild pigs have been shown to carry pathogenic enteric bacteria. Despite previous attempts in the USA to remove wild pigs, their natural fecundity causes rapid re-dispersion into previously inhabited areas. Hence, it is key to have an assay that can easily detect this invasive species in the environment, especially after removal events, to determine eradication success and monitor for potential reestablishment. Environmental DNA (eDNA) found in water has previously been utilized as a molecular method to detect wild pigs however, microbial source tracking (MST) markers could be used as an alternative as it has the potential to be highly sensitive and specific. Unlike eDNA, MST solely detects fecal contamination, making it a better indicator for public health risks associated with the presence of pigs. In this study we aimed to 1.) compare the sensitivity of eDNA and MST assays in detecting wild pigs in an estuarine system, 2.) analyze the viability of the MST assay as a detection method for wild pigs and, 3.) assess the success of two wild pig removal events conducted in the San Juan Bay Estuary (SJBE) area between 2021 and 2022.Water samples were collected monthly across 16 locations in the SJBE from May 2021 thru December 2023 and filtered using a 0.45µm filter. Filters were subsequently extracted and screened for pig mitochondrial DNA (eDNA) and pig-specific Bacteroidales (MST) via qPCR. The MST assay was able to detect pigs at 8 sites compared to the eDNA assay which detected pigs at 4 sites. The 4 sites where the eDNA detected pigs were those that had the highest percent detection frequency (PDF) for the MST assay. There was a detectable drop in PDF between June 2021 (50% MST; 33% eDNA) and July 2021 (0% MST; 5% eDNA) following a wild pig removal event. PDF for both assays showed evidence of redispersal of wild pigs back into this system following this event. These results indicate that MST can be used as an alternative to eDNA as a molecular detection method for wild pigs. Further work will focus on testing more samples following the removal event of 2022 to better assess the effectiveness of the second removal event.