Progress 10/01/14 to 09/30/17
Outputs
Target Audience:We have reached many target audiences in the course of our work over the last year including: Shellfish growers and distributors; shellfish consumers; local, national, and federal shellfish safety managers; investors and developers of food technologies; the public at large; and students and graduate students. Specific venues include participation at the NH Shellfish growers meeting in Fall 2016, oral presentations at the regional Northeast Shellfish Sanitation Association conference in April 2017 in Freeport Maine, an oral and poster presentation at the New England Food Forum in April, several oral presentations at the International conference for molluscan shellfish safety in May 2017 in Galway Ireland, and oral presenter and expert panelist at the Interstate Shellfish Sanitation Conference national workshop on Vibrio in September 2017 in Baltimore MD. The PI also attended and provided guidance to regulators in the state of New Hampshire at an interagency meeting on Vibrio in September 2017 where we helped guide the development of importation permitting processes and shellfish testing regimes to prevent the introduction of human pathogenic Vibrio parahaemolyticus into NH shellfish harvest areas. The project research was presented and included in experiments in an advanced undergraduate/graduate student course GEN 704 Genetics of Prokaryotic Microbes (enrollment 13 students). Two student presentations were also conducted during departmental seminars at UNH by Feng Xu where faculty and graduate students were in attendance. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the project, four M.S. students and one Ph.D. student contributed and received invaluable training while conducting different aspects of the research. Nearly every year, each graduate student presented posters and talks at national or regional conferences, and also participated in several workshops and working group meetings with managers and public health officials. The graduate students also engaged an impressive group of undergraduate (13) and high school (seven) students in the work during the academic year and summer. Six of the undergraduates prepared and presented posters at the College of Life Sciences Undergraduate Research Conference, and six of the high school students presented their work at the Seacoast School of Technology Biotechnology II program conference. How have the results been disseminated to communities of interest?Our primary communication venues to the professional community are through scientific publications, oral and poster presentations at scientific meetings, invited seminars at Universities, and participation in workshops and working groups. We also have had many opportunities to communicate our findings to growers and managers through our attendance shellfish grower meetings in MA and NH. We also presented at a national workshop for shellfish management (ISSC), and presented at a food technology forum in Boston MA. We have been particularly fortunate that our work has garnered interest in the media, as this is an outstanding opportunity to demonstrate the applications of basic research in addressing issues of importance to the public, and also interest in the work we do. Select media outlets include the following: Men's Journal 2017; http://www.mensjournal.com/food-drink/articles/should-a-rise-in-food-poisoning-worry-oyster-lovers-w468252 NBC Boston, 2017; http://www.nbcboston.com/news/local/New-Bacterial-Pathogen-Found-in-Seafood-Along-Coast-412612923.html Associated Press article picked up nationally (Feb. 8th 2017); http://www.vnews.com/New-Hampshire-looks-for-answers-behind-oyster-outbreaks-6678555; http://www.pressherald.com/2017/02/08/new-strain-of-bacteria-is-making-seafood-lovers-sick/ Associated Press article, with commentary by Rita Colwell; https://apnews.com/d94d4e96c5e04e1497d72a89480fbb87/new-hampshire-looks-answers-behind-oyster-outbreaks NH Public Radio, all things considered:http://nhpr.org/post/unh-researchers-hone-harmful-oyster-bacteria https://phys.org/news/2016-12-hampshire-oyster-outbreaks.html What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
As the rate of infections from Vibrio parahaemolyticus contaminated shellfish harvested from the Northeast has steeply risen in just the last five years, local managers and public health officials have sought tools and information to aid in their development of management practices to decrease the risks associated with local product to protect not only consumers of shellfish, but also the growing shellfish industry. To this end, public health agencies in the region have provided unprecedented access to strains from infected individuals and information about trace back sources of contaminated shellfish to our research team so that we can generate a high resolution map of the distribution of pathogenic types in harvest areas throughout the region. Through genome sequencing and comparisons, we have now identified all major pathogenic lineages with established populations in the region, identified shared and unique diagnostic and virulence traits of these pathogens, and developed targeted surveillance tools. We also identified genetic characteristics associated with invasive pathogenic strains that link them to specific harvest areas, allowing more accurate trace-back of ilnesses. These tools have been employed during surveillance in both New Hampshire and Massachusetts to track the presence and abundance of specific pathogenic strains that are most likely to cause infection. Simultaneously, the dynamics of these pathogens have been traced with infection trends and environmental conditions to help managers better understand conditions that promote pathogen abundance and represent higher risk to consumers. Ultimately, this data will inform the development of better predictive models for risk assessment. The impact of the project was realized in real time during the research and has already informed management policy in CT, MA, and NH, aiding managers in these states to decrease illnesses (CT and MA), or maintain low incidence (NH).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
F. Xu, N. Gonzalez-Escalona, R.P. Sebra, K. P. Dress, V.S. Cooper, S.H. Jones, C.A. Whistler. 2017. Parallel evolution of two clades of a major Atlantic endemic Vibrio parahaemolyticus pathogen lineage by independent acquisition of related pathogenicity islands. Applied and Environmental Microbiology. 83 (18) e01168-17
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
F. Xu, N. Gonzalez-Escalona, J. Haendiges, R.A. Myers, J. Ferguson, T. Stiles, E. Hickey, M. Moore, J.M. Hickey, C. Schillaci, L. Mank, K. DeRosia-Banick, N. Matluk, A. Robbins, R. P. Sebra, V.S. Cooper, S.H. Jones, and C.A. Whistler. 2017. Sequence Type 631 Vibrio parahaemolyticus, an emerging foodborne pathogen in North America. Journal of Clinical Microbiology. 55(2):645-648. Doi:10.1128/JCM.02162-16
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2017
Citation:
Dynamics and Interactions of Emergent and Invasive Pathogenic Lineages of Vibrio parahaemolyticus in the Northeastern U.S.
Xu, Feng. University of New Hampshire, ProQuest Dissertations Publishing, 2017. 10285612.
- Type:
Conference Papers and Presentations
Status:
Under Review
Year Published:
2017
Citation:
Xu F, J.A. Hall, M. Malanga, C.M. Hallee, S.H. Jones and C.A. Whistler. Detection assays for Atlantic endemic pathogenic lineages of Vibrio parahaemolyticus with distinct histories of pathogenicity island acquisition. Proceedings of the 10th International Conference on Molluscan Shellfish Safety.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Marcinkiewicz AL, B.M. Schuster, S.H. Jones, V.S. Cooper and C.A. Whistler. 2017. Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology. Heliyon Journal doi: https://doi.org/10.1101/156851
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Xu F., J. Sevigny, V.S. Cooper, S.H. Jones and C.A. Whistler. The major Atlantic pathogenic lineage of Vibrio parahaemolyticus evolved by lateral acquisition of DNA derived from a Pacific native population. Genome Biology and Evolution
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Undergraduate and graduate students, Scientists, Shellfish managers, public health professionals, Aquaculture professionals, Shellfish growers, recreational harvesters, the general public. Changes/Problems:One of the most significant changes to the project was that a Ph.D. student funded by the project decided to only complete a M.S. degree and her efforts were redirected to writing her thesis. Although there are several important research goals she was very committed to completing, these are still in progress and her efforts are not focussed on their completion since she is now employed. The second change in direction, already alluded to above, is that we determined that it was of highest importance to develop methods for specific detection of strain types that had emerged as causing the greatest rise in infection rates in the region, rather than develop methods to evalute general changes in population structure. Although we still intend to pursue method development for population structure, graduate student Feng Xu is now supported on the project, and has committed her efforts towards specific pathogen evolution and ecology, and detection strategies. What opportunities for training and professional development has the project provided?Two graduate students not only participated in several aspects of the research, but they were also given the opportunity to deliver the plennary talk at a local workshop, and meet with growers and managers in the region. Several undergraduate students have also taken part in research. How have the results been disseminated to communities of interest?We continue to give presentations at international, national and regional scientific meetings. More importantly, we present at regional workshops giving us more opportunity to meet with managers and growers and discuss with them thier concerns and needs. What do you plan to do during the next reporting period to accomplish the goals?Our last year of the project will focus on completion of assays for strain type, and evaluation of how environmental conditions influence pathogen abundance.
Impacts
What was accomplished under these goals?
Illnesses caused by Vibrio parahaemolyticus have risen steeply in the region and have been linked to shellfish product harvested from multiple Northeast shellfish growing areas from Long Island Sound and the Gulf of Maine. This trend has triggered implementation of Vibrio control plans and changes in shellfish management and grower practices throughout the region, but illnesses continue despite these measures. This is largely due to a lack of understanding of the specific risk factors that lead to increased pathogen abundance in the region, and inadequate tools for the proactive monitoring of pathogen populations that is necessary to inform management policies. Managers, public health officials, and especially growers are in need of tools for the proactive monitoring of pathogens in order to inform regulatory policies that ensure food safety but that do not overburden growers and managers. Ultimately, these tools and the data generated by their use will protect consumers of shellfish from the regions, and ensure the growing aquaculture industry is minimally harmed by the climate-driven increase in disease causing organisms in local harvest areas. Objective 1: We continue to refine our genetic 'map' of pathogen types in the region. We have determined that in addition to the invasive ST36 strain that nationally causes the most infections, two related lineages that are both strain type ST631 have arisen and established populations along the entire Atlantic coast of North America. This strain causes an estimated 17% of infections. We now have a letter in press to the Journal of Clinical Microbiology on this finding. Several additional strains contribute infections including ST674, ST34, ST1127, ST636, and ST110. Objective 2:We have completed genomics comparisons on the major pathogen lineages described above for objective 1, and identified unique diagnostic genome content for most of these strains. Remarkably, we identified that nearly every pathogen lineage in the region has acquired the same piece of DNA that confers virulence, and we have designed detection assays to identify this DNA. Finally, we have developed and piloted quantitative methods for the enumeration of ST36 and ST631, which combined may cause up to 70% of all local source infections. We have begun development of an assay that will detect nearly every pathogen lineage in the region. Objective 3:At the onset of our project, which pre-dates the arrival of the invasive and highly virulent ST36 in the region which precipitated a remarkable increase in infections, we were going to apply a method for assessing population diversity with regard to seasonality as a model for assessing climate driven population dynamics. However, since we now know the strains of most threat in the region, we deemed it more important for translational science to develop sensitive enumeration methods for the pathogenic strains. These methods are currently being optimized for analysis of environmental samples collected during 2015 and 2016.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
E. Urquhart, S.H. Jones, J. Yu, B.M. Schuster, A.L. Marcinkiewicz, C.A. Whistler, V.S. Cooper. 2016. Environmental conditions associated with elevated risk conditions for Vibrio parahaemolyticus in Great Bay Estuary, NH. PLoS One 11(5): e0155018. Doi:10.137/journal.pone.0155018
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2016
Citation:
Marcinkiewicz, A.L. BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Jones S, Urquhart E, Hartwick M, Whistler C, Cooper V. 2016. Empirical Modeling of Vibrio parahaemolyticus Presence and Concentration in New Hampshire Shellfish, p. 21. In Blogoslawski WJ, Milke L, editors. 2016. 36th Milford Aquaculture Seminar. US Dept of Commerce, Northeast Fish Sci Cent Ref Doc. 16-06; 52 p. Available from: National Marine Fisheries Service, 166 Water Street, Woods Hole, MA 02543-1026, or online at http://www.nefsc.noaa.gov/publications/ 2015
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Feng Xu, Ashley L. Marcinkiewicz, Malachi L. Hallee, Kevin Drees, Jeffery Hall, Vaughn S. Cooper, Stephen H. Jones, and Cheryl A. Whistler.Dynamics of Emergent and Invasive Pathogen Lineages in the Northeast. INVITED plenary presentation at the Northeast Vibrio Forecasting Workshop, Sheldon CT, November 17, 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
C. Whistler, F. Xu, A. Marcinkiewicz, J. Hall, K. Drees, M. Halee, V. Cooper, S. Jones. Know Thy Enemy: How Analysis of the Northeastern Pathogenic Population of Vibrio parahaemolyticus Can Improve Pathogen Identification and Risk Assessment. Co-Chair of Vibrio session at the World Aquaculture Society/National Shellfisheries Association annual meeting, Las Vegas, NV. February 23, 2016.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
S. Jones, E. Urquhart, M. Hartwick, V. Cooper, C. Whistler. Empirical Modeling of Vibrio parahaemolyticus Presence and Concentration in New Hampshire Shellfish. World Aquaculture Society/National Shellfisheries Association annual meeting, Las Vegas, NV. February 23, 2016.
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:.We presented our continuing work to shellfish growers and managers at the Northeast Regional Aquaculture Conference and workshop in Feb 2015, and to a working group meeting for MA public health and marine fisheries managers as experts in May 2015. We also presented this work as part of the NH Sea Grant symposium in Jan 2015 at the UNH campus. Several graduate student seminars were presented on the UNH campus, and there were three presentations by undergraduates at the Undergraduate Research Conference in May. Two poster presentations were delivered at the national meeting for the American Society for Microbiology. The work was also discussed and integrated as part of an undergraduate/graduate course, GEN 704. Finally, several undergraduate students, including a McNair Scholar, participated in independent research projects, earning BMS795 or INCO795 credit for research or BCHM 799 for honors thesis. Changes/Problems:Ashley Marcinkiewicz has decided not to continue with her Ph.D studies and instead will complete a M.S. degree this year. This is a loss to the project and we hope to recruit a new student to work on the project in its final year of funding but training will undoubtedly slow progress. What opportunities for training and professional development has the project provided?The project has contributed to the training of four undergraduate, and two graduate students. How have the results been disseminated to communities of interest?We continue to participate in as many discussions with growers and managers as possible. We have also spoken with several companies that do local testing of shellfish to share with them what we have learned about strain detection and are developing partnerships with them to apply the methods under development. Upon publication of our major research findings this year, the PI also gave several interviews with the press, and was featured on All things considered on NH public Radio: http://nhpr.org/post/unh-researchers-hone-harmful-oyster-bacteria. A list of the media (newspaper and internet) are as follows: http://unhmagazine.unh.edu/w14/research.html http://www.nsf.gov/news/news_summ.jsp?cntn_id=134966&WT.mc_id=USNSF_195&WT.mc_ev=click http://www.brightsurf.com/news/headlines/109208/UNH_researchers_discover_new_method_to_detect_most_common_bacteria_contaminating_oysters_.html http://www.seacoastonline.com/article/20150422/NEWS/150429688 http://www.unh.edu/news/releases/2015/04/lw22oysters.cfm http://www.nzhealthtec.com/researchers-make-breakthrough-in-detecting-most-common-bacteria-contaminating-oysters/ http://www.thefishsite.com/fishnews/25530/new-method-to-detects-harmful-oyster-disease/ http://www.molecularbiologynews.org/Novel-PCR-Method-Detects-Shellfish-Disease http://www.fosters.com/article/20150422/NEWS/150429777/-1/breaking_ajax?utm_source=getresponse&utm_medium=email&utm_campaign=nhbr&utm_content=NHBR+Business+News+Browser http://innovations.oceanhub.com/science-breakthrough-in-shellfish-management/ http://socialnewslatino.com/unh-investigadores-encuentran-un-nuevo-metodo-para-detectar-las-bacterias-mas-comunes-que-infectan-las-ostras/ http://aquaculturenorthamerica.com/News/breakthrough-in-detecting-bacteria-contaminating-oysters/ http://www.asknature.org/strategy/fbb742afcf6e6c33bd2ea66940b3bc7c What do you plan to do during the next reporting period to accomplish the goals?We have work to do on developing and piloting the allele specific sequencing protocol, on further refinement of the qPCR assays, and developing conditions to assess competitiveness of strains in laboratory conditions. We have entered into new collaboration with industry partners, FDA scientists, and NH state shellfish management and their combined interest and resources will advance the research.
Impacts
What was accomplished under these goals?
Vibrio diseases are an important problem for shellfish harvesting and processing to ensure safety for consumers and economic viability for the growing shellfish aquaculture industry in New England. For this reason, research that improves our ability to identify and reduce the risk to consumers is relevant to food safety and shellfish aquaculture, and is a very high priority for the Northeast region. The shellfish aquaculture industry has suffered increasingly more frequent vibrio-associated disease outbreaks linked to shellfish consumption, both on a national, and very recently on a regional scale. These outbreaks and even individual cases of disease have had a widespread and cumulatively devastating impact on markets. Concerns about shellfish safety for the public has preempted discussion about implementation of further restrictions on the marketing of live fresh shellfish from certain at risk regions that could be economically crippling to the shellfish industry. Because of this, the top priority of the east coast shellfish growers industry is to reduce food-borne illnesses associated with their products. The overly simplistic use of seawater temperature as a predictor for risk, and application of post-harvest strategies of rapid cooling has reduced, but not prevented cases of shellfish food poisoning from V. parahaemolyticus. Shellfish managers recognize the most successful modelling and management must be tailored to the region and based on regional data that is currently lacking. The impact of this Hatch project is the development of regional detection strategies to inform management practices that reduce infections. Objective 1: Examine the relatedness of local pathogens to each other and to endemic populations. Using our collections of clinical isolates obtained from public health agencies in the region, expanded from our early collections from NH/MA to include those from ME and CT, we have now identified five pathogen strain types, called sequence types (ST) that have caused the majority of infections from local sources and are either confirmed or presumed resident in various harvest areas. Of these, most infections have been caused by ST36, an invasive strain endemic to the Pacific which is now resident in harvest areas of the Mid and North Atlantic and has been isolated from MA harvest area closed this last summer due to illnesses traced to shellfish. This strain is particularly problematic in Duxbury and Katama Bay MA, but has not been traced to other harvest areas of MA (although it is resident in Long Island Sound). ST631 is the next most frequent strain in clinical sources, and this strain has been resident for some time, especially in harvest areas of Cape Cod MA, including Dennis, but potentially Wellfleet. ST34 and 674 are both resident in NH and MA, but have caused relatively fewer infections, and it is unclear whether all strains are pathogenic. Finally, ST1127 has caused four infections traced locally, but no isolates were identified from our collections from the environment, so this strain type may not be local. Objective 2: Complete whole genome comparisons, and develop a diagnostic method for strain types based on allele frequencies. We have sequenced more than 200 genomes of local environmental and clinical V. parahaemolyticus isolates and performed whole genome comparisons to identify unique attributes of each strain. As there was an immediate need for detection of strains in shellfish management, we focused our efforts on first developing binary PCR for strain typing and also quantitative PCR assays to detect the five strain types presumed resident in the northeast for surveillance to use in management. The typing methods for ST36 and ST631 were applied in shellfish monitoring in cooperation with the Massachusetts Division of Marine Fisheries (MADMF) across all major harvest areas in MA and also applied in NH surveillance for the summer of 2015. Additionally, we quite remarkably identified population specific markers for the invasive strain ST36 that can identify the exact area that the shellfish was harvested from, and we developed a PCR based trace back assay. When applied to clinical isolates from MA, we were able, within 24 hour, to notify MADMF of traceback population which correlated 100% with harvest site. We also have identified a unique architecture of the pathogenicity island shared by both ST36 and ST631, and are in the process of developing a PCR based detection that could identify either of these strain types as part of the FDA approved MPN enumeration assay. Transition to the allele frequency sequencing based approach is ongoing this winter before the next harvest season. GRA Ashley Marcinkiewicz applied typing methods from intensive sampling done in Barnstable and Dennis. Objective 3: Pilot typing method and quantify strain abundance in experimental populations to identify factors that can influence strain dominance. Laboratory experiments to analyze competitive dominance of strain types using fluorescence and binary PCR have been completed with several strain types. In particular, graudate student, Ashley Marcinkiewicz with several undergraduate researchers completed analysis of competitiveness with cool and warm water isolates, with strains with different hemolysin genotypes, and between strains harboring diagnostic phage (virus) islands. None of the experimental conditions tested favored hemolysin producers, and the phage, although associated with particular shellfish areas, does not appear to influence competitiveness in rich medium. She is currently evaluating more natural conditions. CHANGE IN KNOWLEDGE We now know which strain types have caused regional infections. We have developed capacity for not only identification/trace back of these strains, but rapid enumeration from environmental samples using quantitative PCR and Most Probable Number MPN methods approved by the Food and Drug Agency (FDA).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
F. Xu, S. Ilyas, J. Hall, S. Jones, V. Cooper and C.A. Whistler. 2015. Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast US reveals emerging resident and non-indigenous pathogen lineages. Frontiers in Microbiology. 6:272. Doi: 10.3389/fimcb.2015.00272
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
C.A. Whistler, J. Hall, F. Xu, S. Ilyas, P. Siwakoti, V. Cooper, S. Jones. 2015. Use of Whole Genome Phylogeny and Comparisons in the Development of an Improved Multiplex-PCR Assay to Identify Sequence Type 36 Vibrio parahaemolyticus. Journal of Clinical Microbiology. Pii:JCM.00034-15.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
CA Whistler. Population Dynamics of Vibrio parahaemolyticus in the Northeast. presented to the MA Department of Marine Fisheries, and Department of Public Health working group meeting Hinton State Lab, Jamaica Plain Boston MA, May 19, 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
F Xu and CA. Whistler. Characterization of clinical and environmental Vibrio parahaemolyticus from New England reveals emerging resident and invasive pathogen lineages. NACE, Feb. 2015. Portland ME.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
J. Hall and C.A. Whistler. Identification of Endemic Lineages of Vibrio Parahaemolyticus Causing Regional Outbreaks and Their Occurrence in New Hampshire Shellfish Waters. New Hampshire Sea Grant Program Research Symposium. UNH Jan. 30, 2015
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
A. Marcinkiewicz, F Xu, J. Hall, V. Cooper, C. Whistler. Using Phylogenetic Relationships and Phage Content to Elucidate Invasion of Vibrio parahaemolyticus Sequence Type 36 into the United States North Atlantic Coast. presented at the American Society for Microbiology general meeting, Boston MA, June 2015.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
F. Xu, J. Hall, S.H. Jones, V.S. Cooper and C.A. Whistler. Phylogenetic and Comparative Genomic Analysis of Resident Pathogenic Vibrio parahaemolyticus Strains from the Atlantic of the United States. Presented at the American Society for Microbiology general meeting, Boston MA June 2015
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