Research Project: Ecology and Detection of Human Pathogens in the Produce Production Continuum

Location: Produce Safety and Microbiology Research

2019 Annual Report

Objectives
Objective 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. Sub-objective 1A-1I (Refer to uploaded Project Plan) Objective 2: Identify environmental factors that affect the persistence and transmission of enteric pathogens in the produce production environment for risk assessment. Sub-objective 2A-2H (Refer to uploaded Project Plan) Objective 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. Sub-objective 3A-3E (Refer to uploaded Project Plan) Objective 4: Study the ecology of Shiga toxin-producing E. coli (STEC) bacteriophages and its association with bacterial hosts. Objective 5: Development of immuno-, bacteriophage-, and mass spectrometry-based methods for rapid detection of foodborne pathogens.

Approach
Plant-microbe model systems in combination with population studies, ecology, molecular methods, genomics, and microbiology will be used to investigate the interaction of human bacterial and viral pathogens with plants and plant-associated bacteria, as well as to develop improved methods for detection and subtyping of human on produce. Pathogenic E. coli is a foodborne pathogen that has been linked to numerous outbreaks of foodborne illnesses, and the illnesses are primarily attributed to the ingestion of Shiga toxin-producing E. coli (STEC). Previous research has indicated the virulence markers such as stx genes, of STEC strains are conferred to stx-encoding bacteriophages and can be transduced into the susceptible bacterial hosts. In order to understand the interplay between STEC-specific phages and their bacterial hosts in the environment to enhance the safety of food products and the prevention of new emerging foodborne pathogens, the initial focuses of the phage research are to isolate, collect and characterize STEC phages and to understand the relationship between phages and their hosts in the environment. Efficient methods for isolation of STEC bacteriophages will be utilized. Characterization of STEC bacteriophages will be established using genomic sequencing and proteomic analyses. The association of fecal contamination with the population of STEC bacteriophages in the environment will be determined. Environmental factors that influence the geographical distribution of STEC bacteriophages will be identified. This will establish a foundation to study biological interactions between phages and their hosts and the association of phages with bacterial evolution as well as to utilize collected phages to develop biosensors and pre-harvest biological controls for STEC to improve the microbiological food safety of the food supplies.

Progress Report
Under Objective 1, we continued several studies on the fitness and survival of enteric pathogens in various produce production environments. For Sub-objectives 1A and 1H, investigations on sigma S (encoded by RpoS), the stationary phase sigma factor of RNA polymerase, were done in two different Shiga toxin-producing Escherichia coli (STEC) subtypes. Rpo-minus mutants constructed in STEC O111 and STEC O157 were able to utilize a wider range of nutrients, as shown by phenotypic microarrays, than their wild type counterparts. However, the mutants had lower competitive fitness when inoculated onto lettuce grown in Modified Atmosphere Packaging (MAP), suggesting that RpoS promotes leaf colonization at the population level. Sub-objective 1C dealt with studies of persister cells of E. coli. Persister cells of STEC tolerate stresses and could survive on produce to cause outbreaks. In investigations relevant to leafy green production, STEC O157 and STEC O104 persisters formed when the strains were incubated both in field water and in swash water from spinach leaves, and this work was accepted for publication in Food Microbiology. Further work indicates persisters of O145, O121, and O111 STEC subtypes form persister cells at a similar level as STEC O157 strains. Persistence populations of STEC strains that were inoculated onto romaine lettuce plants is under study. Data on persister cell formation of E. coli O157:H7 on romaine lettuce was used to develop a model to predict the switch rate from normal to persister cell. Using data from four published studies of STEC survival in the field, the switch rates computed by the model were similar in pathogen cells grown either in field grown lettuce or in laboratory grown lettuce, showing the relevance of laboratory models in this area. This work was submitted for publication. In support of Sub-objective 1D, research continued with University of California at Davis collaborators and studies of six different STEC serotypes in conventional and organic soils. A third year of soil studies again showed that there was suppression of STEC growth because of biological factors in organic soils compared to conventional soil. Metagenomic analysis of DNAs from organic and conventional soils with demonstrated differences in microbial activity and STEC suppression is ongoing using two different methods for identification of bacteria. Sub-objective 1F had been delayed due to technical problems, so the project is at the 24-month step. Genomic libraries of Listeria monocytogenes enriched for deficiencies in attachment to cantaloupe were constructed. Amplicon sequencing using the Illumina Mi-Seq is ongoing, and analysis of genes presumed to play a role in produce attachment has begun. Meanwhile biofilm formation of various strains on stainless steel, glass, and polystyrene is still being investigated. Sub-objective 1G involves the colonization of different lettuce varieties with E. coli O157:H7, and studies showed that the pathogen levels increased rapidly after inoculation onto cut leaves grown at 24 degrees Celsius (C), irrespective of MAP conditions, and declined at 6 degrees C in MAP at different rates, depending on the lettuce variety. Lettuce microbiome analysis from pre- through post-harvest environments showed compositional differences among varieties. In Human Norovirus (HuNoV) studies under Sub-objective 1I, ligands for HuNoV binding both to pig gastric mucin and to romaine lettuce leaves were isolated via use of bacteria engineered to display HuNoV capsid proteins. Analysis predicts the ligand is a chimera of Human Blood Group Antigen (HBGA) type A and Lewis A. HBGA-like molecules were identified also in some bacterial strains that naturally inhabit lettuce leaves, indicating multiple binding sites for HuNoV on lettuce. Three manuscripts were submitted on this work. Objective 2 deals with environmental factors that affect persistence and transmission of enteric pathogens, and under Sub-objective 2C, metagenomic analysis of sediment samples from the Salinas, California, region was completed with collaborators at the Georgia Institute of Technology. Sediments from six sample locations had metagenomes that were significantly different from each other, as indicated by principle component analysis. Due to the complexity of the samples STEC was not detected in the sequence data; however, STEC has been isolated from these sediments. Many antibiotic resistance genes and antibiotic production genes were found in the sediments, indicating that this environment is a reservoir for those genes. A manuscript is in preparation. Sub-objective 2D deals with comparative genomics of 12 environmental and two clinical STEC O145 strains. The 12 environmental strains are from the same region near Salinas, but they are genetically diverse. Six environmental strains were related to a strain responsible for a foodborne outbreak in Belgium. Analysis indicated that 957 coding sequences encoded strain-specific functions, which might explain strain variations in pathogenicity and persistence. Further work on DNA methylation pathways compared the novel PstI-RM DNA methylase system with the dam system and showed deficiencies in dam led to global impacts on cellular transcription, including regulation of Shiga toxin genes; whereas, the PstI-RM system only regulates a few genes, including some involved in iron acquisition and chemical resistance. Manuscripts are in preparation. Salmonella and L. monocytogenes isolates from the Salinas region continued to be characterized as part of Sub-objective 2E. In collaboration with the Food and Drug Administration (FDA), whole genome analysis and subtyping continues on nearly 1,300 L. monocytogenes strains. Most common clonal complexes include several hypervirulent ones responsible for several outbreaks including CC1, CC6, CC2, CC5, and CC4, as well as ST382, which has been responsible for three produce-related outbreaks in the last five years. Salmonella serotype analysis is ongoing for approximately 1,600 strains, with the top three serotypes being 6,8:d:- (Muenchen), Give, and Typhimurium. Manuscripts are in preparation. For Sub-objective 2H, 115 feral pig stool samples were collected from various regions in California to test for the prevalence of HuNoV and Porcine NoV. Nucleic acid sequencing is ongoing for positive samples. Under Objective 3, methodsare being developed to detect and subtype enteric pathogens. For Sub-objective 3B, sequence analysis of CRISPR regions in outer membrane protein genes lacked sufficient variation to be used to subtype STEC serotypes. Using Whole genome Multi-locus Sequence Typing (wgMLST), 120 STEC strains isolated from the Salinas region were analyzed. wgMLST gave improved, but similar resolution to previous Multi Locus Variable Number Tandem Repeat (MLVA) typing. Work continues to ensure proper criteria for the new wgMLST method, but data reveals transport of STEC pathogens in the Salinas region with long range transport occurring through domestic and wild animals. Under Sub-objective 3C, studies to examine produce-related factors that impact the genomes and virulence of STEC strains, bacteriophages that can transfer shiga toxin genes were identified. However, technical problems with recipient strains for the phage transduction resulted in an inability to measure the transduction efficiency. Optimization of the methods is ongoing. For Sub-objectives 3D and 3E and validation of PCR methods for HuNoV detection, the assays showed large variability, so results could not be validated. A new aptamer-based assay was developed, the primers and probes in the polymerase chain reaction (PCR) assays are being redesigned, and experiments continue. Manuscripts describing the work are in preparation. Objective 4 involves the study of STEC bacteriophages, and several lytic phages that are free of unwanted genes (virulence genes, antibiotic resistance genes, lysogenic genes) and specific to serogroups O26, O45, O103, O111, O145, and O157 were isolated and sequenced. Additional physiological characterization indicated that one phage (vB_EcoS-Ro145clw) infects STEC O145 and has a large burst size (192 phage/infected cell), can withstand a pH range of 3 – 10, and is not affected by temperature extremes (-80 degrees C – 73 degrees C). It could reduce the population of an outbreak strain of O145:H28 by five logs in four hours at 37 degrees C. This phage is a promising candidate for STEC O145 biocontrol, and characterization of other phages is ongoing. Objective 5 focuses on rapid methods for detection of enteric pathogens. Utilizing phage previously isolated by our group, a bacteriophage-based electrochemical biosensor using screen-printed carbon electrode (SPCE) chips for screening STEC strains of O26, O157, and O179 was developed. The chips were customized with the phages and were used for testing 50 microliter samples. The detection system was wirelessly connected via Bluetooth to an Android device and application for data processing and readouts. Extensive in-house trials show a limit of detection of 10-100 viable cells per 1 milliliter samples of apple juice and environmental water, or 1 gram of ground meat in less than 30 minutes. A patent application was filed, and ongoing work focuses on conversion of the detecting reagents to dry formats for commercialization. In additional work in Objective 5, 24 different monoclonal antibodies against entertoxin-B from Staphylococcus aureus (SEB) were generated. SEB is a heat stable toxin that causes food poisoning. The antibodies bind SEB protein and can function in a variety of immunoassay formats. Two antibodies were developed into a rapid, portable, lateral flow assay with SEB detection limit of 5 ng/ml with visual colorimetric positive results.

Accomplishments
1. Development of fast, efficient tests to detect Human Norovirus. Researchers in Albany, California, in collaboration with scientists at the Shanghai Jiao Tong University in China, developed two new assays for the rapid detection of Human Norovirus (HuNoV). One assay is based on binding of HuNoV to specific antibodies on a filter paper test strip (Immune-Chromatographic Assay, ICA), and the other is based on HuNoV binding to a DNA molecule (called an “aptamer”) engineered specifically to bind the virus. Testing 97 human, clinical samples, the ICA test kit was compared to standard PCR-based assays, and the ICA kit showed 85–100% agreement with the longer, more complicated PCR assay. The ICA test could be completed in 15 minutes, is predicted to have a two-year shelf life and can detect the clinically relevant GI and GII subtypes of HuNoV. The ICA greatly reduces the detection time for HuNoV and has sensitivity comparable to other immunological kits without using special equipment and reagents. The collaborative team expects to file a patent application for this new assay.

2. Determination of the minimum dose of sulfur dioxide fumigation to inactivate foodborne pathogens on table grapes. California produces 99 percent of the commercial table grapes in the U.S., and fumigation with sulfur dioxide at a single dose of 5,000 ppm-h is commonly used by the table grapes industry for field packaging of harvested product. The unit ppm-h is the product of the concentration of sulfur dioxide (SO2) in parts per million multiplied by the duration of the fumigation in hours. ARS researchers in Albany, California, determined the minimum dose needed to inactivate foodborne pathogens inoculated onto freshly harvested table grapes under field packaging conditions. They found that the standard SO2 dose was sufficient to kill all Salmonella enterica Thompson and E. coli O157:H7 cells when each of the pathogens were inoculated at levels of 10,000 cells per grape; however, this dose did not inactivate the pathogens when they were at levels of 1,000,000 cells per grape. Similar results were obtained when the grapes were placed into cold storage after dosing with SO2, indicating that when the pathogens were at higher levels on the grape surface that the standard method was not sufficient to completely inactivate S. enterica Thompson and E. coli O157:H7. The results are important for the improvement of intervention strategies to ensure the safety of table grapes and was communicated to the growers in California through the California Table Grape Commission, who requested this research.

3. A portable bacteriophage-based electrochemical biosensor for the detection of viable Shiga toxin-producing Escherichia coli (STEC). The global market of food analysis requires low-cost, reliable tools to evaluate the safety of food, and current laboratory-based microbial detection methods typically require 24 to 72 hours to generate test results. There is a need for new, low-cost assays that will shorten this detection time without compromising sensitivity and specificity. ARS researchers in Albany, California, developed a prototype sensitive, portable bacterial virus-based detection system for Shiga toxin-producing E. coli (STEC) rapid screening. Taking only 30 minutes to perform and costing only $3.28/test, this new biosensor is up to 88% less expensive than traditional culture-requiring, polymerase chain reaction (PCR)-based tests, and antibody tests, and yields results hours to days faster than existing tests. This prototype resulted in a patent application and improved the efficiency and cost of current screening for STEC conducted by regulatory agencies and industries.

4. Development of imGLAD, a new pipeline for the accurate detection of pathogens by metagenomics. Rapid and accurate detection of pathogens from food samples is critically needed by the food industry, and the cost of Whole Genome Sequencing (WGS) from bacterial samples continues to decrease. ARS scientists in Albany, California, in collaboration with scientists at the Georgia Institute of Technology, developed a technique called imGLAD (in-silico-metagenomics for genome low-abundance detection) to detect human foodborne pathogens in samples of mixed DNA extracted from environmental samples. Digitally analyzing mixed DNA sequences from environmental samples, the imGLAD tool uses the sequence-discrete population concept to discriminate between DNA sequences from target pathogens and co-occurring close relatives, while masking DNA sequences from regions of bacterial genomes that are not informative. imGLAD was validated by detecting pathogenic Escherichia coli O157:H7 cells inoculated into field-grown, organic, baby spinach leaves where the limit of detection was 100 cells/100 grams of spinach leaves. Not only is metagenomics-based detection of pathogens much faster than current culture-based methods of detection, but it also provides additional information that can be used for source-tracking foodborne outbreaks, which is essential information for public health investigations. This cutting-edge method is of interest to industries developing detection methods, growers, and public health agencies.

5. Presence of specific persister populations of Shiga toxin producing Escherichia coli (STEC) in leafy green production. Bacterial persistence is a phenomenon in which a subpopulation of cells become more resistant to environmental stresses, including antibiotics. Persister cells of Shiga toxin-producing E. coli (STEC) strains may be capable of surviving harsh environments to eventually cause human illness, but persistence has not been studied in conditions related to leafy green production where STEC has been demonstrated and infect consumers. ARS researchers in Albany, California, established that persister populations of STEC were enhanced when grown both in spinach wash water and field surface water, where they underwent limited multiplication. Considering the high tolerance of persister cells to antimicrobial treatments and their ability to revert to normal cells, these data indicate that STEC persister cells are likely common at several points throughout agricultural production and reveal a mechanism whereby STEC may survive on the farm to eventually cause foodborne illness. The presence of persister cells in a leafy green production environment may pose significant challenges in the development of effective control strategies to ensure the microbial safety of fresh produce. This information is essential to growers, regulatory agencies, and manufacturers to develop mitigation approaches to lower persister populations or to awaken persister cells so that they would be easier to kill.

6. Model to predict Escherichia coli O157:H7 persister cells on lettuce. Outbreaks of pathogenic E. coli O157:H7 infection linked to lettuce continue to impact public health and U.S. lettuce production, which is valued annually at nearly $2 billion. Studies show that this human pathogen has poor fitness on crops in the field, but little is known about the physiology of the few pathogen cells that survive on lettuce plants and contribute to outbreaks. In collaboration with scientists at Cleveland State University, Cleveland, Ohio, scientists at ARS, Albany, California, used laboratory-acquired data to develop a predictive model for the prevalence of E. coli O157:H7 persister cells on lettuce. Application of the model to field studies revealed that the rate of formation of such persister cells on lettuce matched that observed in the laboratory studies. The model provides an important tool to assess the survival of this pathogen on lettuce in the field and supports the value of laboratory-acquired information to improve produce safety in agricultural environments.

7. An effective biocontrol agent and antibiotic alternative to kill non-O157 Shiga toxin-producing Escherichia coli. The number of cases of Shiga toxin-producing Escherichia coli (STEC)-related foodborne infections increases each year, with an estimated 176,000 cases, 2,400 hospitalizations, and 20 deaths annually in the U.S. Next to STEC O157, STEC O145 is the most widespread pathogen among the top six non-O157 STEC serogroups associated with foodborne outbreaks in the U.S., and STEC O145 was responsible for a multistate outbreak associated with lettuce consumption in the U.S. in 2010. ARS researchers in Albany, California, isolated, identified, and genomically characterized a novel virus (bacteriophage) that specifically kills STEC O145. This lytic bacteriophage, called Phage Ro145clw, kills STEC O145 with a huge burst size, releasing many copies of itself after killing the bacterium, and shows strong lytic infection against both environmental and outbreak STEC O145 strains. With physiological features rendering it resistant to a wide range of pH and temperatures, this phage is a promising antimicrobial agent that can be used to combat pathogenic E. coli O145 under different environmental conditions, and its use in biocontrol efforts is of interest to growers and industry.

8. Reduction of Shiga toxin production in environmental Escherichia coli. Shiga toxins are the primary virulence factor associated with Shiga toxin producing E. coli (STEC). ARS scientists in Albany, California, collaborated to measure the amount of Shiga toxins produced by 45 STEC strains that were isolated from water, soil, and animal waste from areas of California where leafy green produce is grown. Although none of these strains were associated with outbreaks, the amount of Shiga toxin produced varied considerably by strain, and this variation was due to insertions of a specific DNA element, termed the 1203v insertion sequence (IS), into the Shiga toxin-producing genes. These results suggest that introducing the naturally occurring 1203v IS may be an effective way of naturally reducing the Shiga toxin production in the STEC found in the environments where green leafy vegetables are grown. This novel type of biocontrol for STEC is of interest to industries developing pre-harvest interventions to reduce the pathogen in the environment.

9. Curli fimbriae contribute to persistence of Shiga Toxin producing Escherichia coli in leafy green post-harvest environments. Curli fimbriae contribute to persistence of Shiga Toxin producing Escherichia coli (STEC) in leafy green post-harvest environments. STEC is one of the main causal agents of foodborne illness outbreaks linked to fresh leafy vegetables, and its survival within biofilms on produce and on surfaces enhances its survival and persistence. STEC within biofilms are difficult to remove from processing equipment, and they are more resistant to anti-bacterial washes used in the produce industry. ARS scientists in Albany, California, demonstrated that that curli fimbriae (a specific type of appendage that protrudes from the cell) of STEC promote the participation of the pathogen cells in mixed biofilms on stainless steel surfaces, likely through mediating the interaction between the pathogen cells and biofilm-proficient microorganisms naturally associated with spinach leaves. This work provides an understanding of the mechanism through which STEC joins biofilms, gains protection from stresses, and then becomes resistant to intervention measures on stainless steel food processing equipment. These published results provide information for developing methods to prevent STEC contamination of leafy green processing plants to food processors, researchers, and companies developing science-based interventions to aid postharvest food safety for processor rinses and equipment cleaning.

10. Identification of Human Norovirus binding sites on lettuce leaves. Human Norovirus (HuNoV) is the most common cause of diarrheal illness in the U.S., and HuNoV-contaminated lettuce has caused several outbreaks and sporadic illnesses. In humans, HuNoV binds to Human Blood Group Antigens (HBGA), but it is unclear how the virus attaches to and accumulates on pre-harvest lettuce leaves since HuNoV is very difficult to grow in the laboratory for direct studies. ARS researchers in Albany, California, in collaboration with scientists at Shanghai Jiao Tong University and Shanghai Institute of Technology, showed that bacteria engineered to carry the HuNoV capsid protein could bind both to compounds within pig gastric mucin (a more natural binding ligand) and to compounds on lettuce surfaces. The scientists identified an oligosaccharide on the lettuce responsible for HuNoV binding as well as molecules similar to HBGA that are produced by bacteria naturally present on the lettuce surface, which indicates that HuNoV has multiple binding sites on pre-harvest lettuce surfaces. This new information on HuNoV binding to produce surfaces provides data on these binding compounds that provide protection and a means of transmission for HuNoV to consumers. This research is important to public health professionals, growers, and researchers developing interventions to reduce HuNoV contamination.

11. Contribution of metabolic traits of Shiga toxin producing Escherichia coli (STEC) to persistence and virulence. Shiga toxin producing Escherichia coli (STEC) includes phenotypically diverse E. coli strains, some of which cause very mild to no illness, while others cause severe foodborne illness. ARS scientists in Albany, California, examined the population structure, virulence potential, and metabolic profile of environmental STEC serotype O121 strains isolated originally from a major produce production region in California and compared them with clinical STEC O121 strains from human patients. Generally, clinical STEC O121 strains displayed higher metabolic activities than environmental STEC O121 strains for several carbon substrates; however, there were some environmental isolates that shared the same enhanced metabolic potential as clinical isolates for several specific carbon sources. These data imply that variants of STEC O121 in the environment that have increased metabolic potential for such plant-derived carbohydrates, mucus-derived substrates, or secondary metabolites produced by indigenous microorganisms are selected in the preharvest environment and lead to the survival of STEC O121 there with increased potential to cause human illness. This published study indicates that metabolic potential is an important factor impacting the dissemination of this pathogen in agricultural environments. This study provides information for risk assessment modelers and public health agencies to assess the potential virulence of STEC strains in the environment.

Review Publications
Liao, Y., Sun, X., Quintela, I.A., Bridges, D.F., Liu, F., Zhang, Y., Salvador, A., Wu, V.C. 2019. Discovery of novel shiga toxin-producing Escherichia coli (STEC)- specific bacteriophages from non-fecal composts using genomic characterization. Frontiers in Microbiology. 10:627. https://doi.org/10.3389/fmicb.2019.00627.
Rong, S., Zhou, Y., Wang, M., Guan, S., Zhang, S., Cai, B., Wang, D., Tian, P., Li, Q. 2019. Characterization of conditions for bacteria-human norovirus capsid P protein complex (BPC) binding to and removal from Romaine lettuce extract. International Journal of Food Microbiology. 298:11-19. https://doi.org/10.1016/j.ijfoodmicro.2019.03.008.
Parker, C., Huynh, S., Bono, J.L., Miller, W.G., Cooley, M.B., Brandl, M. 2019. Complete genome sequences of three Shiga toxin-producing Escherichia coli O111:H8 strains exhibiting an aggregation phenotype. Microbiology Resource Announcements. 8(1):e01335-18. https://doi.org/10.1128/MRA.01335-18.
Silva, C.J., Lee, B.G., Yambao, J.C., Erickson-Beltran, M.L., Quiñones, B. 2019. Using nanospray liquid chromatography and mass spectrometry to quantitate Shiga toxin production in environmental Escherichia coli recovered from a major produce production region in California. Journal of Agricultural and Food Chemistry. 67(5):1554-1562. https://doi.org/10.1021/acs.jafc.8b05324.
Jayeola, V., Parsons, C., Gorski, L.A., Kathariou, S. 2019. Validation of an ampicillin selection protocol to enrich for mutants of Listeria monocytogenes unable to replicate on fresh produce. FEMS Microbiology Letters. 366(7):fnz076. https://doi.org/10.1093/femsle/fnz076.
Tran, T.D., Huynh, S., Parker, C., Han, R., Hnasko, R.M., Gorski, L.A., McGarvey, J.A. 2018. Complete genome sequence of Lactococcus lactis subsp. lactis strain 14B4, which inhibits the growth of Salmonella enterica serotype Poona in vitro. Microbiology Resource Announcements. 7(19):e01364-18. https://doi.org/10.1128/MRA.01364-18.
He, X., Ardissino, G., Patfield, S.A., Cheng, L.W., Silva, C.J., Brigotti, M. 2018. An improved method for the sensitive detection of Shiga toxin 2 in human serum. Toxins. 10(2):59. https://doi.org/10.3390/toxins10020059.
Silva, C.J. 2018. Food forensics: using mass spectrometry to detect foodborne protein contaminants as exemplified by Shiga toxin variants and prion strains. Journal of Agricultural and Food Chemistry. 66(32):8435-8450. https://doi.org/10.1021/acs.jafc.8b01517.
Silva, C.J., Brandon, D.L., Skinner, C.B., He, X. 2017. Shiga Toxins: a Review of Structure, Mechanism, and Detection. Cham, Switzerland: Springer International Publishing. 118 p.
Ni, P., Xu, Q., Yin, Y., Liu, D., Zhang, J., Wu, Q., Tian, P., Shi, X., Wang, D. 2017. Prevalence and characterization of Salmonella serovars isolated from farm products in Shanghai. Food Control. 85:269-275. https://doi.org/10.1016/j.foodcont.2017.10.009.
Quintela, I.A., De Los Reyes, B.G., Lin, C., Wu, V.C. 2019. Simultaneous colorimetric detection of a variety of Salmonella spp. in food and environmental samples by optical biosensing using oligonucleotide-gold nanoparticles. Frontiers in Microbiology. 10:1138. https://doi.org/10.3389/fmicb.2019.01138.
Liao, Y., Salvador, A., Harden, L.A., Liu, F., Lavenburg, V.M., Li, R.W., Wu, V.C. 2019. Characterization of a lytic bacteriophage as an antimicrobial agent for biocontrol of Shiga toxin-producing Escherichia coli O145 strains. Antibiotics. 8(2):74. https://doi.org/10.3390/antibiotics8020074.
Liao, Y., Liu, F., Wu, V.C. 2019. Complete genome sequence of a lytic T7-like phage, Escherichia phage vB_EcoP-Ro45lw, isolated from non-fecal compost samples. Microbiology Resource Announcements. 8:e00036-19. https://doi.org/10.1128/MRA.00036-19.
Carter, M.Q., Feng, D., Li, H. 2019. Curli fimbriae confer shiga toxin-producing Escherichia coli a competitive trait in mixed biofilms. Food Microbiology. 82:482-488. https://doi.org/10.1016/j.fm.2019.03.024.
Carter, M.Q., Tan, Z., Pham, A.C., Carychao, D.K., Cooley, M.B. 2019. A clonal shiga toxin-producing Escherichia coli O121:H19 population exhibits diverse carbon utilization patterns. Foodborne Pathogens and Disease. 16(6):384-393. https://doi.org/10.1089/fpd.2018.2567.
Castro, J.C., Rodriguez, L.M., Harvey, W.T., Weigland, M.R., Hatt, J.K., Carter, M.Q., Konstantinidis, K. 2018. imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ. 6:e5882. https://doi.org/10.7717/peerj.5882.
Carter, M.Q., Pham, A.C. 2018. Complete genome sequence of a natural Escherichia coli O145:H11 isolate that belongs to Phylo-group A. Genome Announcements. 6:e000349-18. https://doi.org/10.1128/genomeA.00349-18.
Carter, M.Q., Pham, A.C. 2018. Complete genome sequences of two atypical enteropathogenic Escherichia coli O145 environmental strains. Genome Announcements. 6:e00418-18. https://doi.org/10.1128/genomeA.00418-18.
Carter, M.Q., Pham, A.C., Huynh, S., He, X. 2017. Complete Genome Sequence of a Shiga toxin-producing Enterobacter cloacae Clinical Isolate. Genome Announcements. 5(37):e00883-17. https://doi.org/10.1128/genomeA.00883-17.
Thao, S., Brandl, M., Carter, M.Q. 2019. Enhanced formation of persister variants in shiga toxin-producing Escherichia coli under conditions relevant to fresh produce production. Food Microbiology. 84:103241. https://doi.org/10.1016/j.fm.2019.103241.
Liu, D., Zhang, Z., Jia, F., Wu, Q., Tian, P., Wang, D. 2018. Development and evaluation of a novel in situ target-capture approach for aptamer selection of human noroviruses. Talanta. 193:199-205. https://doi.org/10.1016/j.talanta.2018.09.084.
Quiñones, B., Yambao, J.C., Silva, C.J., Lee, B.G. 2019. Draft genome sequences of Shiga toxin-producing Escherichia coli O157:H7 strains recovered from a major production region for leafy greens in California. Microbiology Resource Announcements. 8(27):e00644-19. https://doi.org/10.1128/MRA.00644-19.
Lee, S., Chen, Y., Gorski, L.A., Ward, T.J., Osborne, J., Kathariou, S. 2018. Listeria monocytogenes source distribution analysis indicates regional heterogeneity and ecological niche preference among serotype 4b clones. mBio. 9(2):1-12. https://doi.org/10.1128/mBio.00396-18.
Tran, T., Huynh, S., Parker, C., Hnasko, R.M., Gorski, L.A., McGarvey, J.A. 2018. Complete genome sequences of three Bacillus amyloliquefaciens strains that inhibit the growth of Listeria monocytogenes in vitro. Genome Announcements. 6(25):e00579-18. https://doi.org/10.1128/genomeA.00579-18.
Liao, Y., Zhang, Y., Salvador, A., Wu, V.C. 2019. Genome sequence of a T4-like phage, Escherichia phage vB_EcoM-Sa45lw, infecting Shiga toxin-producing Escherichia coli strains. Microbiology Resource Announcements. 8:e00804-19. https://doi.org/10.1128/MRA.00804-19.
Liao, Y., Liu, F., Wu, V.C. 2018. Complete genome sequence of Escherichia Phage vB_EcoM-Pr121LW isolated from soil in an organic farm. Microbiology Resource Announcements. 7:e01236-18. https://doi.org/10.1128/MRA.01236-18.