ABSTRACT
Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.
ABSTRACT
Background: Even though miRNAs play vital roles in developmental biology by regulating the translation of mRNAs, they are poorly studied in oomycetes, especially in the plant pathogen Phytophthora. Objective: The study aimed to predict and identify the putative miRNAs and their targets in Phytophthora infestans and Phytophthora cinnamomi. Methods: The homology-based comparative method was used to identify the unique miRNA sequences in P. infestans and P. cinnamomi with 148,689 EST and TSA sequences of these species. Secondary structure prediction of sRNAs for the 76 resultant sequences has been performed with the MFOLD tool, and their targets were predicted using psRNATarget. Results: Novel miRNAs, miR-8210 and miR-4968, were predicted from P. infestans and P. cinnamomi, respectively, along with their structural features. The newly identified miRNAs were identified to play important roles in gene regulation, with few of their target genes predicted as transcription factors, tumor suppressor genes, stress-responsive genes, DNA repair genes, etc. Conclusion: The miRNAs and their targets identified have opened new interference and editing targets for the development of Phytophthora resistant crop varieties.
