Location: Produce Safety and Microbiology Research2012 Annual Report
1. Sequencing and analysis of Campylobacter genomes. Some Campylobacter species cause human bacterial gastroenteritis and/or disease in food animals. Although most cases of Campylobacter associated food-borne illness are currently attributed to Campylobacter jejuni, emerging Campylobacter species have become linked increasingly to human illness. We have completed the genome sequences of 27 Campylobacter species, subspecies and biovars. Additionally, the genome sequences of multiple novel species, isolated from California agricultural regions, were also completed. Campylobacters colonize a wide variety of mammalian and avian hosts and can be isolated from meat, water, milk and shellfish. Comparative genomics of these completed Campylobacter genomes will provide further insights into the genetic basis of host association, pathogenicity and survival in the environment.
2. Sequencing of salmonella associated with multiple outbreaks. In 2009, shredded lettuce at restaurants seemed the likely source of an outbreak of Salmonella Typhimurium. This was followed in 2010-2011 by a Salmonella outbreak that occurred among students and workers in laboratories. To help elucidate the exact genetic relationship of these outbreak strains, we performed genome sequencing of five outbreak-associated clinical strains that were isolated across the United States between 2009 and 2010. Comparison of these sequences with the seven completed S. Typhimurium genomes revealed that all of these strains are nearly identical to the strain of S. Typhimurium used in clinical and research labs for over two decades. These results have raised concerns about 1) the 2009 shredded lettuce outbreak source, 2) the security of laboratory strains, and 3) persistence of S. Typhimurium strains from “field to fork”.
3. Development of rapid and inexpensive multiplex assay for STEC. The recent STEC outbreaks have emphasized the importance of developing rapid methods for genotyping virulent bacterial strains. An inexpensive colorimetric DNA microarray-based method was developed for simultaneous identification of multiple virulence genes in E. coli O157 and non-O157. This facilitated detection and characterization of STEC isolates recovered from multiple animal sources and environmental samples in agricultural regions in California. The efficiency of this method for STEC has led to collaboration in a major project on human noroviruses, which is the leading cause of human gastroenteritis worldwide.
4. Rapid top-down proteomic identification of shiga toxin variants. STEC are increasingly linked to severe outbreaks of foodborne illness in the US (spinach in 2006) and elsewhere (e.g. fenugreek seeds in 2011 in Germany and France). Toxicity of Stx vary by differences in primary amino acid sequences. We developed a rapid mass spectrometry-based top-down proteomic method to identify sequence-specific Stx variants. The method is simple and fast and can distinguish between highly similar sequence variants. An Stx variant can be identified within 1 to 2 hours after bacterial culturing using this technique and has potential as a rapid identification tool during an outbreak of foodborne illness as well as a powerful research tool.
5. Edible food compounds inactivate virulent bacterial and plant toxins. The increasing number of outbreaks worldwide has raised concern. Stx is the primary virulence factor of STEC, so decreasing active Stx in contaminated food is a strategy for minimizing illness. Stx virulence is based on the 3-D conformation of the protein. In collaborative studies, we discovered that (a) orally ingested Stx damages kidney, spleen, and thymus tissues in mice; (b) freshly prepared juice from Red Delicious apples inhibited the biological activity of Stx; (c) 4-hydroxytyrosol from olives inactivated Staphylococcus aureus and it’s enterotoxin; (d) olive powder inhibited multiple foodborne pathogens; and (e) reconstituted milk inhibited activity of ricin toxin (isolated from castor beans), a toxin similar in activity to Stx. These findings suggest that safe food-compatible compounds can inactivate toxins. The proposed strategies to overcome the virulence of toxins will benefit microbial food safety, animal and human health, food biosecurity, and the economy.
6. Incidence of pathogens in the environment. Thousands of strains of STEC, including O157:H7, Salmonella, Listeria monocytogenes and Campylobacter species have been isolated from > 15,000 environmental samples, and characterized for serotype, genotype and virulence factors. The epidemiology and ecology of pathogens in a major food production region has stimulated multiple interactions with regulatory agencies and industry. In addition to the microbial source tracking information provided for comparison to the field data obtained, these strains provide an unprecedented resource for addressing fundamental biology objectives related to comparative genomics, analysis of foodborne pathogens from multiple sources, and gene expression profiling of related strains from different sources.
Parker, C., Kyle, J.L., Huynh, S., Carter, M.Q., Brandl, M., Mandrell, R.E. 2012. Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak. Applied and Environmental Microbiology. 78:455-463.