Ecology and Detection of Human Pathogens in the Produce Production Continuum

<p>1:Elucidate biological factors and molecular mechanisms that enhance or reduce fitness characteristics related to survival and growth of enteric pathogens in the produce production continuum.(A)Phenotypic characterization of shiga toxin-producing E. coli O111 strains of environmental &amp; clinical origins &amp; (B)traits contributing to fitness of Salmonella strains on pre-harvest lettuce.(C)Evaluate formation of STEC persisters &amp; factors contributing to population size in produce production continuum.(D)Compare fitness &amp; physiology of different STEC serotypes &amp; associated indigenous microbiota on produce growing in conventional vs organic soil.(E)EcO157 biofilm formation under stress conditions in MAP lettuce.(F)Identify genes involved in attachment of L. monocytogenes to produce &amp; role of biofilm formation in survival on produce.(G)Evaluate interaction of EcO157 with various lettuce accessions.(H) Investigate evolution of EcO157 in MAP lettuce &amp; (I)interactions between norovirus &amp; native plant-associated bacteria. 2:Identify environmental factors that affect the persistence and transmission of enteric pathogens in the produce production environment for risk assessment.(A)Develop &amp; deploy quantitative assessment of enteric pathogens in surface water in several watersheds (WS)in Salinas region to enhance current incidence data supplied to FDA for risk assessment model.(B)Determine survival &amp; fitness characteristics of enteric pathogens in water &amp; sediment samples from central California coastal (cCc) produce production regions &amp; (C)the impact of indigenous microbial community on environmental persistence of STECs in sediment from WS locations often positive for STEC strains in Salinas region using metagenomics approach.(D)Comparative genomics &amp; transcriptomics applied to characterize environmental Shiga toxin-producing E. coli. (E)Investigate survival &amp; persistence of Salmonella &amp; L. monocytogenes in Central California WS to measure prevalence, identify subtypes &amp; regional traits.(F)Characterize F+ RNA Coliphages in water samples from cCc produce production regions &amp; determine feasibility as indicators for source-tracking enteric pathogens &amp; (G)enteric pathogens transported through aerosols &amp; determine seasonal fluctuations in cCc produce production regions.(H)Determine if wild pigs are hosts for human norovirus (HuNoV). 3:Develop methods for the detection and subtyping of enteric bacterial and viral pathogens from produce production environments; to aid epidemiological investigations and to distinguish pathogenic from non-pathogenic strains. (A)Develop FT-IR identification libraries for serotype analysis.(B)Improve STEC subtyping using sequence of CRISPR &amp; other hypervariable genes to augment existing MLVA method.(C)Examine bacterial &amp; produce-associated factors impacting genome &amp; STEC virulence evolution.(D)Develop better assay to determine inactivation status of Tulane virus (TV) &amp; HuNoV caused by viral genomic damage &amp; (E)accurate, fast, &amp; low-cost multi-amplicon in situ capture qRT-PCR assay determining HuNoV infectivity. 4:Study the ecology of Shiga toxin-producing E. coli (STEC) bacteriophages and its association with bacterial hosts.</p>