New York State Department of Agriculture and Markets

Salmonella is one of the most important foodborne pathogens worldwide. Therefore, this study was conducted to understand the importance of this microorganism in street food and the environment of an urban park in Quito, Ecuador. This research included phenotypic characterization and whole genome sequencing (WGS) analysis of isolates from different food matrices and fecal samples of dogs and pigeons. Salmonella was found in 10% (18/180) of the food samples, 3% (3/100) of the dog stool samples, and 5% (5/100) of the pigeon stool samples. These results also showed that meals containing any sauce or eggs were associated with a high probability of Salmonella isolation, regardless of other ingredients. All Salmonella isolates from food were identified as Salmonella enterica serovar Typhimurium (S. Typhimurium) while isolates from animal feces belonged to Salmonella enterica serovar Infantis (S. Infantis) and S. Typhimurium. WGS analysis showed that all S. Typhimurium strains belonged to ST19 and S. Infantis to ST32 according to the Multi-Locus Sequence Type (MLST) scheme. These strains were not related to Salmonella genomes of other origins when a Single Nucleotide Polymorphism (SNP) tree analysis was carried out. Antimicrobial resistance genes, such as blaCTX-M-65, were predominantly linked to the pESI-like plasmid found in S. Infantis. These results show the importance of urban fauna as a reservoir of S. Infantis and the impact these animals could have in terms of public health.

Cucurbit crops comprise ∼25% of the vegetable acreage in the mid-Atlantic and Northeastern United States. However, options for postemergence weed control in these crops are limited. Overlapping herbicides is a technique that involves sequential applications of soil-applied residual herbicides to lengthen herbicidal activity before the first herbicide dissipates. Residual herbicides such as S -metolachlor will not control emerged weeds, but weed control efficacy may be extended if these herbicides are applied after crop emergence, but before weed emergence occurs. Currently S- metolachlor is not labeled for broadcast applications over cucurbit crops. Greenhouse studies were conducted to evaluate pumpkin, cucumber, and summer squash variety response to varying S- metolachlor rates. S -metolachlor was applied at 1.42 and 2.85 lb/acre at the two-leaf stage of pumpkin and 0.71, 1.42, 2.85, and 5.7 lb/acre at the two-leaf stage of cucumber and summer squash. Cucumber showed a greater response to S- metolachlor with up to 67% injury observed at 5.70 lb/acre. S- metolachlor applications to pumpkin and summer squash resulted in less than 6% injury, regardless of application rate or crop variety. S- metolachlor applied at 2.85 lb/acre reduced pumpkin and cucumber dry weight 6% and 19%, respectively, but did not reduce squash dry weight. S- metolachlor reduced cucumber dry weight 78% for all varieties. Pumpkin varieties ‘Munchkin’ and ‘Baby Bear’ exhibited a 23% difference in dry weight, but no other differences were observed among other varieties because of S -metolachlor applications. Summer squash varieties ‘Respect’ and ‘Golden Glory’ exhibited a 31% difference in dry weight, but no other differences were observed among other varieties. Results show that pumpkin and summer squash demonstrated good crop safety when S- metolachlor was applied as a broadcast treatment after crop emergence. However, caution should be urged when applying this herbicide to cucumber.

PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI. SCOPE: to provide a standardized procedure to collect isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI. RESPONSIBILITIES- SOP Responsible Officials: Ruth Timme, Maria Balkey The GenomeTrakr Network Management will be responsible to monitor GenomeTrakr submissions processed through Bionumerics and ensure that all GT labs are familiar with the mandatory metadata fields required for submission of GenomeTrakr sequencing records to NCBI. V3: Added dropdown menus from controlled vocabulary to sequenced by and project name to metadata template PulseNet_Bionumerics_Isolate_Metadata V4: Changes in metadata template PulseNet_Bionumerics_Isolate_Metadata. - Added dropdown menus from controlled vocabulary to collected_by , SourceCountryState - Added fields: collected by, isolation source - Added mapping table of attribute names. - Remove requirement to send biosample update to NCBI to make changes on sequenced by and project name.

Abscisic acid (ABA) plays crucial regulatory roles in cold acclimation and deacclimation of grapevine, making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring. To understand the function of ABA, we conducted experiments during cold acclimation and deacclimation and evaluated the impact of exogenous ABA on the grapevine transcriptome. RNA-seq data were collected periodically hours or days after ABA treatment. Transcriptomic data were analyzed using principal component analysis (PCA), hierarchical clustering, unsupervised weighed gene co-expression network analysis (WGCNA), contrast-based differentially expressed genes (DEGs) identification and pre-ranked gene set enrichment analysis (GSEA). Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid (IAA) metabolism, galactose metabolism and ribosome biogenesis. We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes, suggesting the existence of a balancing system in response to excessive ABA. This balancing systems potentially eliminates the long-term negative effect on grapevine growing from using ABA in the field. These findings advance our understanding about the regulation of grapevine physiology during dormancy and supports the potential of applying ABA as a cultural practice to mitigate cold injury in winter and spring.

Powdery mildew (Podosphaera aphanis) is a destructive and widespread disease of strawberry (Fragaria × ananassa), especially when susceptible cultivars are grown in high plastic tunnels or glasshouses. Many powdery mildews thrive in humid environments but free water films on plant surfaces can inhibit conidial germination of some species. We hypothesized that P. aphanis might be directly suppressed by rain through the action of water films and meteoric water. In repeated experiments, the hydrophobic conidia of P. aphanis collected on the surface of water droplets, resulting in their removal when the droplets rolled over the leaf surfaces and fell to the ground. Meteoric water and water films also damaged conidiophores. Brief midday water mists applied in pulses lasting 1 min each four times per day were as effective as multiple fungicide treatments in suppressing powdery mildew. Rapid drying of the pulsed mists resulted in effective suppression of powdery mildew without consequent increases of fungal pathogens that might benefit from water films. The timing and duration of water sprinkling has been refined to the point where it can provide a commercially relevant degree of suppression of powdery mildew on strawberry in a high-tunnel production system.

Pathogen-tested foundation plant stocks are the cornerstone of sustainable specialty crop production. They provide the propagative units that are used to produce clean planting materials, which are essential as the first-line management option of diseases caused by graft-transmissible pathogens such as viruses, viroids, bacteria, and phytoplasmas. In the United States, efforts to produce, maintain, and distribute pathogen-tested propagative material of specialty crops are spearheaded by centers of the National Clean Plant Network (NCPN). Agricultural economists collaborated with plant pathologists, extension educators, specialty crop growers, and regulators to investigate the impacts of select diseases caused by graft-transmissible pathogens and to estimate the return on investments in NCPN centers. Economic studies have proven valuable to the NCPN in (i) incentivizing the use of clean planting material derived from pathogen-tested foundation plant stocks; (ii) documenting benefits of clean plant centers, which can outweigh operating costs by 10:1 to 150:1; (iii) aiding the development of disease management solutions that are not only ecologically driven but also profit maximizing; and (iv) disseminating integrated disease management recommendations that resonate with growers. Together, economic studies have reinforced efforts to safeguard specialty crops in the United States through the production and use of clean planting material.

Five strains of Salmonella enterica subsp. enterica serovar Infantis and two strains of S. enterica subsp. enterica serovar Kentucky isolated in 2017 from Ecuadorian layer poultry farms were sequenced using Illumina MiSeq technology. These isolates were collected on layer farms in central Ecuador, one of the most important areas of egg production in the country. The genome sequences of these isolates show valuable information for surveillance purposes.

The apple scab pathogen, Venturia inaequalis, is among the most economically important fungal pathogens that affects apples. Fungicide applications are an essential part of disease management. Implementation of cultural practices and genetic sources of resistance in the host are vital components of scab management. This is the first presentation of multiple, high quality, well-annotated genomes of four North American V. inaequalis isolates having both sensitive and multiple fungicide resistance phenotypes. We envision that these isolates will enable investigations into fungicide resistance mechanisms, exploring fungal virulence factors and delineating phylogenomic relationships among apple scab isolates from around the world.

Crop pathogens and pests reduce the yield and quality of agricultural production. They cause substantial economic losses and reduce food security at household, national and global levels. Quantitative, standardized information on crop losses is difficult to compile and compare across crops, agroecosystems and regions. Here, we report on an expert-based assessment of crop health, and provide numerical estimates of yield losses on an individual pathogen and pest basis for five major crops globally and in food security hotspots. Our results document losses associated with 137 pathogens and pests associated with wheat, rice, maize, potato and soybean worldwide. Our yield loss (range) estimates at a global level and per hotspot for wheat (21.5% (10.1-28.1%)), rice (30.0% (24.6-40.9%)), maize (22.5% (19.5-41.1%)), potato (17.2% (8.1-21.0%)) and soybean (21.4% (11.0-32.4%)) suggest that the highest losses are associated with food-deficit regions with fast-growing populations, and frequently with emerging or re-emerging pests and diseases. Our assessment highlights differences in impacts among crop pathogens and pests and among food security hotspots. This analysis contributes critical information to prioritize crop health management to improve the sustainability of agroecosystems in delivering services to societies.