Genome-Wide Searching Single Nucleotide-Polymorphisms (SNPs) and SNPs-Targeting a Multiplex Primer for Identification of Common Salmonella Serotypes

Prevalence of Salmonella spp. and Escherichia coli in the feces of free-roaming wildlife throughout South Korea

Wildlife can carry pathogenic organisms, including viruses, bacteria, parasites, and fungi, which can spread to humans and cause mild to serious illnesses and even death. Spreading through animal feces, these pathogens significantly contributes to the global burden of human diseases. Therefore, the present study investigated the prevalence of zoonotic bacterial pathogens, such as Salmonella spp., Escherichia coli, and Shiga toxin-producing E. coli (STEC), in animal feces. Between September 2015 and August 2017, 699 wildlife fecal samples were collected from various agricultural production regions and mountainous areas in South Korea. Fecal samples were collected from wild mammals (85.26%, 596/699) and birds (14.73%, 103/699). Salmonella spp. and E. coli were present in 3% (21/699) and 45.63% (319/699) of the samples, respectively. Moreover, virulence genes stx1 and both stx1 and stx2 were detected in 13.30% (93/699) and 0.72% (5/699) of the samples, respectively. The 21 Salmonella spp. were detected in badgers (n = 5), leopard cats (n = 7), wild boars (n = 2), and magpies (n = 7); STEC was detected in roe deer, water deer, mice, and wild boars. Through phylogenetic and gene-network analyses, the Salmonella spp. isolates (n = 21 laboratory isolates, at least one isolate from each Salmonella-positive animal fecal sample, and n = 6 widely prevalent reference Salmonella serovars) were grouped into two major lineages: S. enterica subsp. enterica and S. enterica subsp. diarizonae. Similarly, 93 E. coli isolates belonged to stx1, including three major lineages (groups 1-3), and stx1 and stx2 detected groups. To the best of our knowledge, this is the first report of a wild leopard cat serving as a reservoir for Salmonella spp. in South Korea. The research findings can help manage the potential risk of wildlife contamination and improve precautionary measures to protect public health.

Development of Molecular-Based Species Identification and Optimization of Reaction Conditions for Molecular Diagnosis of Three Major Asian Planthoppers (Hemiptera: Delphacidae)

Asian planthoppers (Hemiptera: Delphacidae) that include brown planthoppers (BPH, Nilaparvata lugens, Stål), white-backed planthoppers (WBPH, Sogatella furcifera, Horváth), and small brown planthoppers (SBPH, Laodelphax striatellus, Fallén) are the primary sucking-type pests of rice. These three insects share morphological and sequence similarities. As insecticide resistance patterns and control strategies vary according to species, the accurate discrimination of these species is important. Here, we developed six species-specific primers based on partial mitochondrial genome sequences. The primers were successfully used in multiplex PCR, loop-mediated isothermal amplification (LAMP) assays, and conventional PCR. Here, we used genomic DNA obtained using the DNA-releasing technique (tissue samples were incubated at 95 °C for 5 min with 30 μL nuclease-free water, and the supernatant was used). We showed that multiplex PCR could analyze the density of each species following a mass collection in the field; the LAMP assay can diagnose the species within 40 min; conventional PCR can be widely applied to a large number of field samples, as well as individuals or mass collections. In conclusion, these results demonstrate the potential of the species-specific primers and DNA-releasing technique for accurate multiplex PCR and LAMP assays, which may assist the intensive field monitoring of integrated management of these species.