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Ayache N, Bill BD, Brosnahan ML, Campbell L, Deeds JR, Fiorendino JM, Gobler CJ, Handy SM, Harrington N, Kulis DM, McCarron P, Miles CO, Moore SK, Nagai S, Trainer VL, Wolny JL, Young CS, Smith JL. A survey of Dinophysis spp. and their potential to cause diarrhetic shellfish poisoning in coastal waters of the United States. J Phycol 2023; 59:658-680. [PMID: 36964950 DOI: 10.1111/jpy.13331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Multiple species of the genus Dinophysis produce diarrhetic shellfish toxins (okadaic acid and Dinophysis toxins, OA/DTXs analogs) and/or pectenotoxins (PTXs). Only since 2008 have DSP events (illnesses and/or shellfish harvesting closures) become recognized as a threat to human health in the United States. This study characterized 20 strains representing five species of Dinophysis spp. isolated from three US coastal regions that have experienced DSP events: the Northeast/Mid-Atlantic, the Gulf of Mexico, and the Pacific Northwest. Using a combination of morphometric and DNA-based evidence, seven Northeast/Mid-Atlantic isolates and four Pacific Northwest isolates were classified as D. acuminata, a total of four isolates from two coasts were classified as D. norvegica, two isolates from the Pacific Northwest coast were identified as D. fortii, and three isolates from the Gulf of Mexico were identified as D. ovum and D. caudata. Toxin profiles of D. acuminata and D. norvegica varied by their geographical origin within the United States. Cross-regional comparison of toxin profiles was not possible with the other three species; however, within each region, distinct species-conserved profiles for isolates of D. fortii, D. ovum, and D. caudata were observed. Historical and recent data from various State and Tribal monitoring programs were compiled and compared, including maximum recorded cell abundances of Dinophysis spp., maximum concentrations of OA/DTXs recorded in commercial shellfish species, and durations of harvesting closures, to provide perspective regarding potential for DSP impacts to regional public health and shellfish industry.
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Affiliation(s)
- Nour Ayache
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, Virginia, 23062, USA
| | - Brian D Bill
- Environmental and Fisheries Science Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Michael L Brosnahan
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Lisa Campbell
- Department of Oceanography and Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
- Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
| | - Jonathan R Deeds
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - James M Fiorendino
- Department of Oceanography and Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, New York, 11968, USA
| | - Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Neil Harrington
- Department of Natural Resources, Jamestown S'Klallam Tribe, Sequim, Washington, 98382, USA
| | - David M Kulis
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Pearse McCarron
- Biotoxin Metrology, National Research Council Canada, Halifax, Nova Scotia, B3H 3Z1, Canada
| | - Christopher O Miles
- Biotoxin Metrology, National Research Council Canada, Halifax, Nova Scotia, B3H 3Z1, Canada
| | - Stephanie K Moore
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Vera L Trainer
- Olympic Natural Resources Center, School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, Washington, 98195, USA
| | - Jennifer L Wolny
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Craig S Young
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, New York, 11968, USA
| | - Juliette L Smith
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, Virginia, 23062, USA
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Literman R, Windsor AM, Bart HL, Hunter ES, Deeds JR, Handy SM. Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus). Mol Phylogenet Evol 2023; 182:107715. [PMID: 36707011 DOI: 10.1016/j.ympev.2023.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/03/2022] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing ('genome skimming'). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species' native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data. These sites were used to classify Ictiobus spp. samples with genome-skim data, along with a larger set (n = 67) where ultraconserved elements (UCEs) were sequenced. Analyses of whole mitochondrial data revealed more limited signal. Nearly all samples matched their purported species based on morphologic identification, but two Missouri samples morphologically identified as I. niger grouped with samples of I. bubalus, albeit with significant enrichment of I. niger SNPs. To our knowledge this is the first report of a DNA-based tool to reliably discriminate these three morphologically distinct species.
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Affiliation(s)
- Robert Literman
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA.
| | - Amanda M Windsor
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Henry L Bart
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Elizabeth Sage Hunter
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
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Kirk R, Rosario ME, Oblie N, Jouaneh TMM, Carro MA, Wu C, Kim AM, Leibovitz E, Hunter ES, Literman R, Handy SM, Rowley DC, Bertin MJ. Screening the PRISM Library against Staphylococcus aureus Reveals a Sesquiterpene Lactone from Liriodendron tulipifera with Inhibitory Activity. ACS Omega 2022; 7:35677-35685. [PMID: 36249352 PMCID: PMC9558601 DOI: 10.1021/acsomega.2c03539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Infections caused by the bacterium Staphylococcus aureus continue to pose threats to human health and put a financial burden on the healthcare system. The overuse of antibiotics has contributed to mutations leading to the emergence of methicillin-resistant S. aureus, and there is a critical need for the discovery and development of new antibiotics to evade drug-resistant bacteria. Medicinal plants have shown promise as sources of new small-molecule therapeutics with potential uses against pathogenic infections. The principal Rhode Island secondary metabolite (PRISM) library is a botanical extract library generated from specimens in the URI Youngken Medicinal Garden by upper-division undergraduate students. PRISM extracts were screened for activity against strains of methicillin-susceptible S. aureus (MSSA). An extract generated from the tulip tree (Liriodendron tulipifera) demonstrated growth inhibition against MSSA, and a bioassay-guided approach identified a sesquiterpene lactone, laurenobiolide, as the active constituent. Intriguingly, its isomers, tulipinolide and epi-tulipinolide, lacked potent activity against MSSA. Laurenobiolide also proved to be more potent against MSSA than the structurally similar sesquiterpene lactones, costunolide and dehydrocostus lactone. Laurenobiolide was the most abundant in the twig bark of the tulip tree, supporting the twig bark's historical and cultural usage in poultices and teas.
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Affiliation(s)
- Riley
D. Kirk
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Margaret E. Rosario
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Nana Oblie
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Terra Marie M. Jouaneh
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Marina A. Carro
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Christine Wu
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Andrew M. Kim
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Elizabeth Leibovitz
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Elizabeth Sage Hunter
- Center
for Food Safety and Applied Nutrition, Office of Regulatory Science, United States Food and Drug Administration, College Park, Maryland 20740, United States
| | - Robert Literman
- Center
for Food Safety and Applied Nutrition, Office of Regulatory Science, United States Food and Drug Administration, College Park, Maryland 20740, United States
| | - Sara M. Handy
- Center
for Food Safety and Applied Nutrition, Office of Regulatory Science, United States Food and Drug Administration, College Park, Maryland 20740, United States
| | - David C. Rowley
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Matthew J. Bertin
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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Deeds JR, Literman RA, Handy SM, Klontz KC, Swajian KA, Benner RA, Bart HL. Haff disease associated with consumption of buffalofish ( Ictiobus spp.) in the United States, 2010-2020, with confirmation of the causative species. Clin Toxicol (Phila) 2022; 60:1087-1093. [PMID: 36200989 DOI: 10.1080/15563650.2022.2123815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND In the United States, buffalofish (Ictiobus spp.) are sporadically associated with sudden onset muscle pain and weakness due to rhabdomyolysis within 24 h of fish consumption (Haff disease). Previous genetic analyses of case-associated samples were unable to distinguish the three species of buffalofish that occur in the US, Ictiobus cyprinellus (bigmouth buffalo), Ictiobus bubalus (smallmouth buffalo), and Ictiobus niger (black buffalo). METHODS Ten events were investigated between 2010 and 2020 and demographic and clinical information was collected for 24 individuals. Meal remnants were collected from 5 of 10 events with additional associated samples (n = 24) collected from another five of 10 events. Low-coverage whole-genome sequencing (genome skimming) was used to identify meal remnants. RESULTS Patients (26-75 years of age) ranged from 1-4 per event, with 90% involving ≥2 individuals. Reported symptoms included muscle tenderness and weakness, nausea/vomiting, and brown/tea-colored urine. Median incubation period was 8 h. Ninety-six percent of cases were hospitalized with a median duration of four days. The most commonly reported laboratory finding was elevated creatine phosphokinase and liver transaminases. Treatment was supportive including intravenous fluids to prevent renal failure. Events occurred in California (1), Illinois (2), Louisiana (1), New York (1), Mississippi (1), Missouri (2), New Jersey (1), and Texas (1) with location of harvest, when known, being Illinois, Louisiana, Mississippi, Missouri, Texas, and Wisconsin. Meal remnants were identified as I. bubalus (n = 4) and I. niger (n = 1). Associated samples were identified as I. bubalus (n = 16), I. cyprinellus (n = 5), and I. niger (n = 3). DISCUSSION Time course, presentation of illness, and clinical findings were all consistent with previous domestic cases of buffalofish-associated Haff disease. In contrast to previous reports that I. cyprinellus is the causative species in US cases, data indicate that all three buffalofish species are harvested but I. bubalus is most often associated with illness.
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Affiliation(s)
- Jonathan R Deeds
- Division of Analytical Chemistry, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, MD, USA
| | - Robert A Literman
- Division of Analytical Chemistry, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, MD, USA
| | - Sara M Handy
- Division of Analytical Chemistry, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, MD, USA
| | - Karl C Klontz
- Division of Public Health Information and Analytics, Center for Food Safety and Applied Nutrition, Office of Analytics and Outreach, US Food and Drug Administration, College Park, MD, USA
| | - Karen A Swajian
- Division of Seafood Safety, Center for Food Safety and Applied Nutrition, Office of Food Safety, US Food and Drug Administration, College Park, MD, USA
| | - Ronald A Benner
- Division of Seafood Science and Technology, Center for Food Safety and Applied Nutrition, Office of Food Safety, US Food and Drug Administration, Dauphin Island, AL, USA
| | - Henry L Bart
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
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Parveen I, Techen N, Handy SM, Li J, Wu C, Chittiboyina AG, Khan IA. The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species. Planta Med 2022; 88:985-993. [PMID: 34544191 DOI: 10.1055/a-1618-6496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Morphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 - 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.
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Affiliation(s)
- Iffat Parveen
- National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
| | - Natascha Techen
- National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
| | - Jing Li
- Botanical Review Team, Immediate Office, Office of New Drug Product, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Charles Wu
- Botanical Review Team, Immediate Office, Office of New Drug Product, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Amar G Chittiboyina
- National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research; School of Pharmacy, University of Mississippi, University, MS, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, USA
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Lu Z, Handy SM, Zhang N, Quan Z, Xu Q, Ambrose M, Giancaspro G, Sarma ND. Development and Validation of a Species-specific PCR Method for the Identification of Ginseng Species Using Orthogonal Approaches. Planta Med 2022; 88:1004-1019. [PMID: 34388833 DOI: 10.1055/a-1478-9143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
When testing botanical ingredients of herbal medicines and dietary supplements, the complexity of botanical matrixes often requires the use of orthogonal methods to establish identification procedures suitable for quality control purposes. Genomic-based botanical identification methods are evolving and emerging as useful quality control tools to complement traditional morphological and chemical identification methods. Species-specific polymerase chain reaction methods are being evaluated for botanical quality control and as a cost-effective approach to identify and discriminate between closely related botanical species. This paper describes orthogonal identification of Panax ginseng, P. quinquefolius, and P. notoginseng materials in commerce as an example of the development and validation of a set of species-specific polymerase chain reaction methods to establish botanical identity in ginseng roots. This work also explored the possibility of extending the application of species-specific polymerase chain reaction methods to provide species identity information for processed materials, such as steamed roots and hydroalcoholic extracts, and showed success with this approach. Finally, the paper provides recommendations for an out-of-specification investigation of samples that may pass some of the orthogonal tests and fail others.
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Affiliation(s)
- Zhengfei Lu
- United States Pharmacopeia (USP) Project Team on Botanical Library for Identification using DNA-based Methods, Rockville, MD, USA
- Herbalife International of America, Inc., Corporate Center of Excellence Quality Laboratory, Torrance, CA, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
| | - Ning Zhang
- United States Pharmacopeia (USP), Rockville, MD, USA
- Currently at TopEdit Author Services, Gaithersburg, MD, USA
| | - Zheng Quan
- United States Pharmacopeia (USP) Project Team on Botanical Library for Identification using DNA-based Methods, Rockville, MD, USA
- Herbalife International of America, Inc., Corporate Center of Excellence Quality Laboratory, Torrance, CA, USA
| | - Qun Xu
- United States Pharmacopeia (USP), Rockville, MD, USA
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Mutebi RR, Ario AR, Nabatanzi M, Kyamwine IB, Wibabara Y, Muwereza P, Eurien D, Kwesiga B, Bulage L, Kabwama SN, Kadobera D, Henderson A, Callahan JH, Croley TR, Knolhoff AM, Mangrum JB, Handy SM, McFarland MA, Sam JLF, Harris JR, Zhu BP. Large outbreak of Jimsonweed (Datura stramonium) poisoning due to consumption of contaminated humanitarian relief food: Uganda, March-April 2019. BMC Public Health 2022; 22:623. [PMID: 35354446 PMCID: PMC8969350 DOI: 10.1186/s12889-022-12854-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
Background Jimsonweed (Datura stramonium) contains toxic alkaloids that cause gastrointestinal and central nervous system symptoms when ingested. This can be lethal at high doses. The plant may grow together with leguminous crops, mixing with them during harvesting. On 13 March 2019, more than 200 case-patients were admitted to multiple health centres for acute gastrointestinal and neurologic symptoms. We investigated to determine the cause and magnitude of the outbreak and recommended evidence-based control and prevention measures. Methods We defined a suspected case as sudden onset of confusion, dizziness, convulsions, hallucinations, diarrhoea, or vomiting with no other medically plausible explanations in a resident of Napak or Amudat District from 1 March—30 April 2019. We reviewed medical records and canvassed all villages of the eight affected subcounties to identify cases. In a retrospective cohort study conducted in 17 villages that reported the earliest cases, we interviewed 211 residents about dietary history during 11–15 March. We used modified Poisson regression to assess suspected food exposures. Food samples underwent chemical (heavy metals, chemical contaminants, and toxins), proteomic, DNA, and microbiological testing in one national and three international laboratories. Results We identified 293 suspected cases; five (1.7%) died. Symptoms included confusion (62%), dizziness (38%), diarrhoea (22%), nausea/vomiting (18%), convulsions (12%), and hallucinations (8%). The outbreak started on 12 March, 2–12 h after Batch X of fortified corn-soy blend (CSB +) was distributed. In the retrospective cohort study, 66% of 134 persons who ate CSB + , compared with 2.2% of 75 who did not developed illness (RRadj = 22, 95% CI = 6.0–81). Samples of Batch X distributed 11–15 March contained 14 tropane alkaloids, including atropine (25-50 ppm) and scopolamine (1-10 ppm). Proteins of Solanaceae seeds and Jimsonweed DNA were identified. No other significant laboratory findings were observed. Conclusion This was the largest documented outbreak caused by food contamination with tropane alkaloids. Implicated food was immediately withdrawn. Routine food safety and quality checks could prevent future outbreaks.
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Affiliation(s)
- Ronald R Mutebi
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda.
| | - Alex R Ario
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda.,Ministry of Health, Kampala, Uganda
| | - Maureen Nabatanzi
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Irene B Kyamwine
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Yvette Wibabara
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Peter Muwereza
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Daniel Eurien
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Benon Kwesiga
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Lilian Bulage
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Steven N Kabwama
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Daniel Kadobera
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Alden Henderson
- Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John H Callahan
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Timothy R Croley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Ann M Knolhoff
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - John B Mangrum
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Melinda A McFarland
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Jennifer L Fong Sam
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Julie R Harris
- Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA.,US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Bao-Ping Zhu
- Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA.,US Centers for Disease Control and Prevention, Kampala, Uganda
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Literman RA, Ott BM, Wen J, Grauke LJ, Schwartz RS, Handy SM. Reference-free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids. Appl Plant Sci 2022; 10:e11455. [PMID: 35228913 PMCID: PMC8861591 DOI: 10.1002/aps3.11455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
PREMISE DNA-based species identification is critical when morphological identification is restricted, but DNA-based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome-wide single-nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data. METHODS Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus Carya, isolating sites where genetic variation was restricted to a single Carya species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid Carya specimens, even at very low sequencing depths. RESULTS We identified between 46,000 and 476,000 species-identifying SNPs for each of eight diploid Carya species, and all species identifications were concordant with the species of record. For all putative F1 hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses. DISCUSSION Bioinformatics pipelines that use only short-read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non-model clades alike.
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Affiliation(s)
- Robert A. Literman
- Office of Regulatory Science, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
| | - Brittany M. Ott
- Office of Food Additive Safety, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
| | - Jun Wen
- Department of Botany, National Museum of Natural HistorySmithsonian InstitutionWashington, D.C.USA
| | - L. J. Grauke
- United States Department of Agriculture (USDA)–Agricultural Research Service Pecan Breeding and GeneticsSomervilleTexasUSA
| | - Rachel S. Schwartz
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sara M. Handy
- Office of Regulatory Science, Center for Food Safety and Applied NutritionU.S. Food and Drug AdministrationCollege ParkMarylandUSA
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Hunter ES, Literman R, Handy SM. Utilizing Big Data to Identify Tiny Toxic Components: Digitalis. Foods 2021; 10:1794. [PMID: 34441571 PMCID: PMC8391216 DOI: 10.3390/foods10081794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022] Open
Abstract
The botanical genus Digitalis is equal parts colorful, toxic, and medicinal, and its bioactive compounds have a long history of therapeutic use. However, with an extremely narrow therapeutic range, even trace amounts of Digitalis can cause adverse effects. Using chemical methods, the United States Food and Drug Administration traced a 1997 case of Digitalis toxicity to a shipment of Plantago (a common ingredient in dietary supplements marketed to improve digestion) contaminated with Digitalis lanata. With increased accessibility to next generation sequencing technology, here we ask whether this case could have been cracked rapidly using shallow genome sequencing strategies (e.g., genome skims). Using a modified implementation of the Site Identification from Short Read Sequences (SISRS) bioinformatics pipeline with whole-genome sequence data, we generated over 2 M genus-level single nucleotide polymorphisms in addition to species-informative single nucleotide polymorphisms. We simulated dietary supplement contamination by spiking low quantities (0-10%) of Digitalis whole-genome sequence data into a background of commonly used ingredients in products marketed for "digestive cleansing" and reliably detected Digitalis at the genus level while also discriminating between Digitalis species. This work serves as a roadmap for the development of novel DNA-based assays to quickly and reliably detect the presence of toxic species such as Digitalis in food products or dietary supplements using genomic methods and highlights the power of harnessing the entire genome to identify botanical species.
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Affiliation(s)
| | | | - Sara M. Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD 20740, USA; (E.S.H.); (R.L.)
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10
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Handy SM, Pawar RS, Ottesen AR, Ramachandran P, Sagi S, Zhang N, Hsu E, Erickson DL. HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea. Planta Med 2021; 87:314-324. [PMID: 33445185 DOI: 10.1055/a-1336-1685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing "finished" products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Rahul S Pawar
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Andrea R Ottesen
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Satyanarayanaraju Sagi
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Ning Zhang
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Erica Hsu
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
| | - David L Erickson
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
- DNA4 Technologies LLC, Halethorpe, Maryland, United States
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11
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Handy SM, Ott BM, Hunter ES, Zhang S, Erickson DL, Wolle MM, Conklin SD, Lane CE. Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States. J Agric Food Chem 2020; 68:15516-15525. [PMID: 33334103 DOI: 10.1021/acs.jafc.0c03734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Brittany M Ott
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
| | - Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
| | - Shu Zhang
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - Mesay Mulugeta Wolle
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Sean D Conklin
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
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12
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Villacrés-Vallejo J, Aranda-Ventura J, Wallis A, Cagle R, Handy SM, Davis J, Reed E, Zhang S, Strain E, Pava-Ripoll M, Erickson D, Ramachandran P, Ottesen A. Using full chloroplast genomes of 'red' and 'yellow' Bixa orellana (achiote) for kmer based identification and phylogenetic inference. BMC Genomics 2020; 21:544. [PMID: 32762642 PMCID: PMC7430826 DOI: 10.1186/s12864-020-06916-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/15/2020] [Indexed: 11/18/2022] Open
Abstract
Background Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choice for DNA based taxonomic annotation of plants. Bixa orellana, commonly known as “achiote” and “annatto” is a plant used for both human and animal foods and was thus identified for full chloroplast sequencing for the Center for Veterinary Medicine (CVM) Complete Chloroplast Animal Feed database. This work was conducted in collaboration with the Instituto de Medicina Tradicional (IMET) in Iquitos, Peru. There is a wide range of color variation in pods of Bixa orellana for which genetic loci that distinguish phenotypes have not yet been identified. Here we apply whole chloroplast genome sequencing of “red” and “yellow” individuals of Bixa orellana to provide high quality reference genomes to support kmer database development for use identifying this plant from complex mixtures using shotgun data. Additionally, we describe chloroplast gene content, synteny and phylogeny, and identify an indel and snp that may be associated with seed pod color. Results Fully assembled chloroplast genomes were produced for both red and yellow Bixa orellana accessions (158,918 and 158,823 bp respectively). Synteny and gene content was identical to the only other previously reported full chloroplast genome of Bixa orellana (NC_041550). We observed a 17 base pair deletion at position 58,399–58,415 in both accessions, relative to NC_041550 and a 6 bp deletion at position 75,531–75,526 and a snp at position 86,493 in red Bixa orellana. Conclusions Our data provide high quality reference genomes of individuals of red and yellow Bixa orellana to support kmer based identity markers for use with shotgun sequencing approaches for rapid, precise identification of Bixa orellana from complex mixtures. Kmer based phylogeny of full chloroplast genomes supports monophylly of Bixaceae consistent with alignment based approaches. A potentially discriminatory indel and snp were identified that may be correlated with the red phenotype.
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Affiliation(s)
- Jorge Villacrés-Vallejo
- Seguro Social de Salud, Instituto de Medicina Tradicional, Iquitos, Peru.,Universidad Nacional de la Amazonía Peruana, Facultad de Agronomía, Iquitos, Peru
| | | | - Anna Wallis
- Department of Plant Pathology, Cornell University, Ithaca, NY, USA
| | - Robin Cagle
- Department of Plant Pathology, Cornell University, Ithaca, NY, USA
| | - Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, FDA, College Park, MD, USA
| | - Jeffery Davis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, USA
| | - Elizabeth Reed
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, FDA, College Park, MD, USA
| | - Shu Zhang
- DNA4 Technologies LLC, Baltimore, MD, USA
| | - Errol Strain
- Office of Research, Center for Veterinary Medicine, FDA, Laurel, MD, USA
| | - Monica Pava-Ripoll
- Office of Food Safety, Center for Food Safety and Applied Nutrition, FDA, College Park, MD, USA
| | - David Erickson
- Joint Institute for Food Safety and Applied Nutrition, College Park, MD, USA
| | - Padmini Ramachandran
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, FDA, College Park, MD, USA
| | - Andrea Ottesen
- Office of Research, Center for Veterinary Medicine, FDA, Laurel, MD, USA. .,Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, USA.
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13
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Carlos KS, Conrad SM, Handy SM, de Jager LS. Investigation of food products containing garlic or onion for a false positive sulphite response by LC-MS/MS. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2020; 37:723-730. [PMID: 32160133 DOI: 10.1080/19440049.2020.1727965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In the US, sulphites must be declared on the label if they are present in concentrations greater than 10 mg/kg (determined as) SO2 because an allergic-like response has been reported in a small subset of the population upon consumption of sulphite-containing products. The most widely used method for sulphite determination, the optimised Monier-Williams (OMW), produces false positive results with vegetables from the Allium (garlic) and Brassica (cabbage) genera due to extraction conditions that are thought to cause endogenous sulphur compounds to release SO2. Recently, an LC-MS/MS method was developed for sulphites but has only been tested with samples that are 100% Allium or Brassica. Since regulatory samples may contain these vegetables as ingredients, additional investigations were necessary to determine the potential extent of false positives. Four blank matrices, chips, phyllo shells, hummus, and quinoa were spiked with various concentrations of onion and garlic powders. The sulphite concentrations were determined using an LC-MS/MS method. The matrix is extracted with a buffered formaldehyde solution, converting free and reversibly bound sulphite to the stable formaldehyde adduct, hydroxymethylsulfonate (HMS). It was determined that even at concentrations up to 8% garlic powder or 2% onion powder, the measured sulphite concentration was below the 10 mg/kg SO2 labelling threshold. Commercial dried garlic powders were evaluated to determine the variation in responses that might be encountered in future regulatory samples. Recovery studies were conducted to determine if these methods would detect added sulphite. The ability to eliminate false positives due to these ingredients will result in a greater reliability in the accurate determination of added sulphite to ensure compliance with labelling requirements.
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Affiliation(s)
- Katherine S Carlos
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Stephen M Conrad
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Lowri S de Jager
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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14
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Wolny JL, Egerton TA, Handy SM, Stutts WL, Smith JL, Whereat EB, Bachvaroff TR, Henrichs DW, Campbell L, Deeds JR. Characterization of Dinophysis spp. (Dinophyceae, Dinophysiales) from the mid-Atlantic region of the United States 1. J Phycol 2020; 56:404-424. [PMID: 31926032 DOI: 10.1111/jpy.12966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Due to the increasing prevalence of Dinophysis spp. and their toxins on every US coast in recent years, the need to identify and monitor for problematic Dinophysis populations has become apparent. Here, we present morphological analyses, using light and scanning electron microscopy, and rDNA sequence analysis, using a ~2-kb sequence of ribosomal ITS1, 5.8S, ITS2, and LSU DNA, of Dinophysis collected in mid-Atlantic estuarine and coastal waters from Virginia to New Jersey to better characterize local populations. In addition, we analyzed for diarrhetic shellfish poisoning (DSP) toxins in water and shellfish samples collected during blooms using liquid-chromatography tandem mass spectrometry and an in vitro protein phosphatase inhibition assay and compared this data to a toxin profile generated from a mid-Atlantic Dinophysis culture. Three distinct morphospecies were documented in mid-Atlantic surface waters: D. acuminata, D. norvegica, and a "small Dinophysis sp." that was morphologically distinct based on multivariate analysis of morphometric data but was genetically consistent with D. acuminata. While mid-Atlantic D. acuminata could not be distinguished from the other species in the D. acuminata-complex (D. ovum from the Gulf of Mexico and D. sacculus from the western Mediterranean Sea) using the molecular markers chosen, it could be distinguished based on morphometrics. Okadaic acid, dinophysistoxin 1, and pectenotoxin 2 were found in filtered water and shellfish samples during Dinophysis blooms in the mid-Atlantic region, as well as in a locally isolated D. acuminata culture. However, DSP toxins exceeded regulatory guidance concentrations only a few times during the study period and only in noncommercial shellfish samples.
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Affiliation(s)
- Jennifer L Wolny
- Maryland Department of Natural Resources, Resource Assessment Service, Annapolis, Maryland, 21401, USA
| | - Todd A Egerton
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Whitney L Stutts
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, USA
| | - Juliette L Smith
- Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, 23062, USA
| | - Edward B Whereat
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, Delaware, 19958, USA
| | - Tsvetan R Bachvaroff
- Institute for Marine and Environmental Technology, University of Maryland Center for Environmental Sciences, Baltimore, Maryland, 21202, USA
| | - Darren W Henrichs
- Department of Oceanography, Texas A&M University, College Station, Texas, 77843, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, Texas, 77843, USA
| | - Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, USA
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15
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Handy SM, Deeds JR, Ivanova NV, Hebert PDN, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF. A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance. J AOAC Int 2019. [DOI: 10.1093/jaoac/94.1.201] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5′ end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.
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Affiliation(s)
- Sara M Handy
- U.S. Food and Drug Administration, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Jonathan R Deeds
- U.S. Food and Drug Administration, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Natalia V Ivanova
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Paul D N Hebert
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Robert H Hanner
- University of Guelph, Department of Integrative Biology, 50 Stone Rd East, Guelph, ON, Canada, N1G 2W1
| | - Andrea Ormos
- Smithsonian Institution, National Museum of Natural History, Laboratories of Analytical Biology, MRC 534, Washington, DC 20013-7012, USA
| | - Lee A Weigt
- Smithsonian Institution, National Museum of Natural History, Laboratories of Analytical Biology, MRC 534, Washington, DC 20013-7012, USA
| | - Michelle M Moore
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Northwest, Applied Technology Center, 22201 23rd Dr SE, Bothell, WA 98021-4421, USA
| | - Haile F Yancy
- U.S. Food and Drug Administration, Office of Research, Center for Veterinary Medicine, 8401 Muirkirk Rd, Laurel, MD 20708
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16
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Puente-Lelievre C, Zhang N, Handy SM, Eischeid AC. Using Chloroplast Genomes for the Development of DNA-based Methods for Allergenic Plants. Am J Transl Res 2018. [DOI: 10.1055/s-0038-1644949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- C Puente-Lelievre
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States
| | - N Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States
| | - SM Handy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States
| | - AC Eischeid
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States
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17
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Pawar RS, Handy SM, Cheng R, Shyong N, Grundel E. Assessment of the Authenticity of Herbal Dietary Supplements: Comparison of Chemical and DNA Barcoding Methods. Planta Med 2017; 83:921-936. [PMID: 28454189 DOI: 10.1055/s-0043-107881] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
About 7 % of the U. S. population reports using botanical dietary supplements. Increased use of such supplements has led to discussions related to their authenticity and quality. Reports of adulteration with substandard materials or pharmaceuticals are of concern because such substitutions, whether inadvertent or deliberate, may reduce the efficacy of specific botanicals or lead to adverse events. Methods for verifying the identity of botanicals include macroscopic and microscopic examinations, chemical analysis, and DNA-based methods including DNA barcoding. Macroscopic and microscopic examinations may fail when a supplement consists of botanicals that have been processed beyond the ability to provide morphological characterizations. Chemical analysis of specific marker compounds encounters problems when these compounds are not distinct to a given species or when purified reference standards are not available. Recent investigations describing DNA barcoding analysis of botanical dietary supplements have raised concerns about the authenticity of the supplements themselves as well as the appropriateness of using DNA barcoding techniques with finished botanical products. We collected 112 market samples of frequently consumed botanical dietary supplements of ginkgo, soy, valerian, yohimbe, and St. John's wort and analyzed each for specific chemical markers (i.e., flavonol glycosides, total isoflavones, total valerenic acids, yohimbine, and hypericins, respectively). We used traditional DNA barcoding techniques targeting the nuclear ITS2 gene and the chloroplast gene psbA-trnH on the same samples to determine the presence of DNA of the labelled ingredient. We compared the results obtained by both methods to assess the contribution of each in determining the identity of the samples.
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Affiliation(s)
- Rahul S Pawar
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
| | - Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
| | - Raymond Cheng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
| | - Nicole Shyong
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
| | - Erich Grundel
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
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18
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Zhang N, Erickson DL, Ramachandran P, Ottesen AR, Timme RE, Funk VA, Luo Y, Handy SM. An analysis of Echinacea chloroplast genomes: Implications for future botanical identification. Sci Rep 2017; 7:216. [PMID: 28303008 PMCID: PMC5428300 DOI: 10.1038/s41598-017-00321-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/21/2017] [Indexed: 12/14/2022] Open
Abstract
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.
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Affiliation(s)
- Ning Zhang
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
| | - David L Erickson
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Andrea R Ottesen
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-0166, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
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19
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Eischeid AC, Stadig SR, Handy SM, Fry FS, Deeds J. Optimization and evaluation of a method for the generation of DNA barcodes for the identification of crustaceans. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.06.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Garber EAE, Parker CH, Handy SM, Cho CY, Panda R, Samadpour M, Reynaud DH, Ziobro GC. Presence of Undeclared Food Allergens in Cumin: The Need for Multiplex Methods. J Agric Food Chem 2016; 64:1202-1211. [PMID: 26769163 DOI: 10.1021/acs.jafc.5b05497] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Beginning in the autumn of 2014, millions of dollars of food and over 675 products were recalled in the United States due to the presence of undeclared peanut, attributed to cumin used in the manufacture of the products. Initial analyses also indicated the presence of almond. Subsequent research showed that the presence of peanut and almond did not fully explain the analytical results for the cumin samples. Using a combination of mass spectrometry, DNA-based methods (i.e., PCR and Sanger DNA Sequencing), microscopy, and antibody-based technologies (i.e., ELISA, Western blot analysis, and a novel xMAP multiplex assay) the presence of peanut was confirmed. Screening for secondary sources of adulteration (e.g., tree nuts, mahleb, peach, and cherry) supported the assessment that the cumin contained multiple contaminants. These results demonstrate the limitations of single analyte-specific assays and the need for orthogonal multiplex methods to detect food allergens irrespective of varietal or other differences.
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Affiliation(s)
- Eric A E Garber
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Christine H Parker
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Chung Y Cho
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Rakhi Panda
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Mansour Samadpour
- IEH Laboratories and Consulting Group, Inc. , Lake Forest Park, Washington 98155, United States
| | - Danica H Reynaud
- AuthenTechnologies LLC , Richmond, California 94806, United States
| | - George C Ziobro
- Office of Food Safety, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
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21
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Shokralla S, Hellberg RS, Handy SM, King I, Hajibabaei M. A DNA Mini-Barcoding System for Authentication of Processed Fish Products. Sci Rep 2015; 5:15894. [PMID: 26516098 PMCID: PMC4626862 DOI: 10.1038/srep15894] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/05/2015] [Indexed: 02/07/2023] Open
Abstract
Species substitution is a form of seafood fraud for the purpose of economic gain. DNA barcoding utilizes species-specific DNA sequence information for specimen identification. Previous work has established the usability of short DNA sequences-mini-barcodes-for identification of specimens harboring degraded DNA. This study aims at establishing a DNA mini-barcoding system for all fish species commonly used in processed fish products in North America. Six mini-barcode primer pairs targeting short (127-314 bp) fragments of the cytochrome c oxidase I (CO1) DNA barcode region were developed by examining over 8,000 DNA barcodes from species in the U.S. Food and Drug Administration (FDA) Seafood List. The mini-barcode primer pairs were then tested against 44 processed fish products representing a range of species and product types. Of the 44 products, 41 (93.2%) could be identified at the species or genus level. The greatest mini-barcoding success rate found with an individual primer pair was 88.6% compared to 20.5% success rate achieved by the full-length DNA barcode primers. Overall, this study presents a mini-barcoding system that can be used to identify a wide range of fish species in commercial products and may be utilized in high throughput DNA sequencing for authentication of heavily processed fish products.
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Affiliation(s)
- Shadi Shokralla
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Microbiology, Mansoura University, Mansoura 35516, Egypt
| | - Rosalee S. Hellberg
- Chapman University, Schmid College of Science and Technology, Orange, CA 92866, USA
| | - Sara M. Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Ian King
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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22
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Hamade AK, Deglin SE, McLaughlin JB, Deeds JR, Handy SM, Knolhoff AM. Suspected Palytoxin Inhalation Exposures Associated with Zoanthid Corals in Aquarium Shops and Homes - Alaska, 2012-2014. MMWR Morb Mortal Wkly Rep 2015; 64:852-5. [PMID: 26270061 PMCID: PMC4584591 DOI: 10.15585/mmwr.mm6431a4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
On August 12, 2014, an Anchorage hospital notified the Alaska Section of Epidemiology (SOE) that a middle-aged male resident of Anchorage (patient A) had arrived in the emergency department with possible palytoxin exposure. Patient A complained of a bitter metallic taste, fever, weakness, cough, and muscle pain 7-8 hours after introduction of live zoanthid coral into his home aquarium. Palytoxin, a potent toxin known to produce the reported effects, is contained in zoanthid marine corals.
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Affiliation(s)
- Ali K. Hamade
- Section of Epidemiology, Division of Public Health, State of Alaska
- Corresponding author: Ali Hamade,
| | | | | | - Jonathan R. Deeds
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration
| | - Sara M. Handy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration
| | - Ann M. Knolhoff
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration
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Deeds JR, Handy SM, Fry F, Granade H, Williams JT, Powers M, Shipp R, Weigt LA. Protocol for building a reference standard sequence library for DNA-based seafood identification. J AOAC Int 2015; 97:1626-33. [PMID: 25230794 DOI: 10.5740/jaoacint.14-111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the recent adoption of a DNA sequencing-based method for the species identification for seafood products by the U.S. Food and Drug Administration (FDA), a library of standard sequences derived from reference specimens with authoritative taxonomic authentication was required. Provided here are details of how the FDA and its collaborators are building this reference standard sequence library that will be used to confirm the accurate labeling of seafood products sold in interstate commerce in the United States. As an example data set from this library, information for 117 fish reference standards, representing 94 species from 43 families in 15 orders, collected over a 4-year period from the Gulf of Mexico, U.S., that are now stored at the Smithsonian Museum Support Center in Suitland, MD, are provided.
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Cole JB, Heegaard WG, Deeds JR, McGrath SC, Handy SM. Tetrodotoxin poisoning outbreak from imported dried puffer fish--Minneapolis, Minnesota, 2014. MMWR Morb Mortal Wkly Rep 2015; 63:1222-1225. [PMID: 25551594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
On June 13, 2014, two patients went to the Hennepin County Medical Center Emergency Department in Minneapolis, Minnesota, with symptoms suggestive of tetrodotoxin poisoning (i.e., oral paresthesias, weakness, and dyspnea) after consuming dried puffer fish (also known as globefish) purchased during a recent visit to New York City. The patients said two friends who consumed the same fish had similar, although less pronounced, symptoms and had not sought care. The Minnesota Department of Health conducted an investigation to determine the source of the product and samples were sent to the Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition for chemical and genetic analysis. Genetic analysis identified the product as puffer fish (Lagocephalus lunaris) and chemical analysis determined it was contaminated with high levels of tetrodotoxin. A traceback investigation was unable to determine the original source of the product. Tetrodotoxin is a deadly, potent poison; the minimum lethal dose in an adult human is estimated to be 2-3 mg. Tetrodotoxin is a heat-stable and acid-stable, nonprotein, alkaloid toxin found in many species of the fish family Tetraodontidae (puffer fish) as well as in certain gobies, amphibians, invertebrates, and the blue-ringed octopus. Tetrodotoxin exerts its effects by blocking voltage-activated sodium channels, terminating nerve conduction and muscle action potentials, leading to progressive paralysis and, in extreme cases, to death from respiratory failure. Because these fish were reportedly purchased in the United States, they pose a substantial U.S. public health hazard given the potency of the toxin and the high levels of toxin found in the fish.
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25
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Handy SM, Chizhikov V, Yakes BJ, Paul SZ, Deeds JR, Mossoba MM. Microarray chip development using infrared imaging for the identification of catfish species. Appl Spectrosc 2014; 68:1365-1373. [PMID: 25356840 DOI: 10.1366/14-07505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Several families of catfish species are extensively aquacultured around the world; however, only those from the family Ictaluridae can be labeled as catfish in the United States. Non-Ictalurid catfish species that are marketed as "catfish" in the USA are considered misbranded. Misbranding in general has led to an increased interest in developing deoxyribonucleic acid (DNA)-based methods such as DNA barcoding, polymerase chain reaction restriction fragment length polymorphism, and DNA microarrays with fluorescence detection for the identification of fish species. In this proof-of-concept study, DNA microarrays coupled with a newly developed mid-infrared imaging detection method were applied to the identification of seven species of catfish for the first time. Species-specific DNA probes targeting three regions per species of the cytochrome c oxidase 1 (barcoding) gene were developed and printed as microarrays on glass slides. Deoxyribonucleic acid targets labeled with biotin were hybridized to their complementary probes using a strategy that allowed the selective formation of a silver layer on hybridized spots needed for detection. Using this three-probe format, the seven species were all identified correctly, even when a limited number of false positive spots were observed. Raman spectroscopy was employed to further characterize the arrays.
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Affiliation(s)
- Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740 USA
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Kwegyir-Afful EE, Dejager LS, Handy SM, Wong J, Begley TH, Luccioli S. An investigational report into the causes of pine mouth events in US consumers. Food Chem Toxicol 2013; 60:181-7. [PMID: 23891758 DOI: 10.1016/j.fct.2013.07.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 07/03/2013] [Accepted: 07/15/2013] [Indexed: 11/18/2022]
Abstract
Between July 2008 and June 2012, the US Food and Drug Administration received 501 consumer reports of prolonged taste disturbances consistent with pine mouth syndrome. Consumers consistently reported a delayed bitter or metallic taste beginning hours to days following consumption of pine nuts that recurred with intake of any food or meal. This dysgeusia lasted in some cases up to a few weeks, but would eventually resolve without serious health consequences. To evaluate these reports, a questionnaire was developed to address various characteristics of the pine nuts consumed, pertinent medical history of complainants and other dysgeusia-related factors. Pine nut samples associated with 15 complaints were collected for analysis. The investigation of reports found no clear evidence of an underlying medical cause or common trigger that could adequately explain the occurrence of dysgeusia in complainants. Rather, the results of our investigation suggest that the occurrence of "pine mouth syndrome" in US consumers is correlated with the consumption of the pine nut species Pinus armandii.
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Affiliation(s)
- Ernest E Kwegyir-Afful
- Office of Food Additive Safety, CFSAN, College Park 20740, United States; Office of the Commissioner, Office of Science and Innovation, FDA, White Oak, United States.
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Handy SM, Timme RE, Jacob SM, Deeds JR. Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia. J Agric Food Chem 2013; 61:1060-1066. [PMID: 23311709 DOI: 10.1021/jf304223a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent work has shown that the presence of the species Pinus armandii , even when occurring as species mixtures of pine nuts, is correlated with taste disturbance (dysgeusia), also referred to as "pine mouth". Because of this known possibility of pine nut mixtures, a need was identified for a rapid streamlined assay to detect the presence of this species in the presence of other types of pine nuts. A locked nucleic acid probe was employed in a real-time polymerase chain reaction (RT-PCR) format to detect a single nucleotide polymorphism (SNP) unique to this species. This assay was able to detect P. armandii in homogenates down to ∼1% concentration (the lowest level tested) in the presence of several commonly co-occurring and closely related species of pine and should prove to be a useful tool for the detection of this species in food products.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, United States Food and Drug Administration-U.S. FDA, College Park, Maryland 20740, USA.
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28
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Fardin-Kia AR, Handy SM, Rader JI. Characterization of pine nuts in the U.S. market, including those associated with "pine mouth", by GC-FID. J Agric Food Chem 2012; 60:2701-2711. [PMID: 22339292 DOI: 10.1021/jf205188m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Taste disturbances following consumption of pine nuts, referred to as "pine mouth", have been reported by consumers in the United States and Europe. Nuts of Pinus armandii have been associated with pine mouth, and a diagnostic index (DI) measuring the content of Δ5-unsaturated fatty acids relative to that of their fatty acid precursors has been proposed for identifying nuts from this species. A 100 m SLB-IL 111 GC column was used to improve fatty acid separations, and 45 pine nut samples were analyzed, including pine mouth-associated samples. This study examined the use of a DI for the identification of mixtures of pine nut species and showed the limitation of morphological characteristics for species identification. DI values for many commercial samples did not match those of known reference species, indicating that the majority of pine nuts collected in the U.S. market, including those associated with pine mouth, are mixtures of nuts from different Pinus species.
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Affiliation(s)
- Ali Reza Fardin-Kia
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20740, United States.
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29
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Handy SM, Parks MB, Deeds JR, Liston A, de Jager LS, Luccioli S, Kwegyir-Afful E, Fardin-Kia AR, Begley TH, Rader JI, Diachenko GW. Use of the chloroplast gene ycf1 for the genetic differentiation of pine nuts obtained from consumers experiencing dysgeusia. J Agric Food Chem 2011; 59:10995-11002. [PMID: 21932798 DOI: 10.1021/jf203215v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Pine nuts are a part of traditional cooking in many parts of the world and have seen a significant increase in availability/use in the United States over the past 10 years. The U.S. Food and Drug Administration (US FDA) field offices received 411 complaints from U.S. consumers over the past three years regarding taste disturbances following the consumption of pine nuts. Using analysis of fatty acids by gas chromatography with flame ionization detection, previous reports have implicated nuts from Pinus armandii (Armand Pine) as the causative species for similar taste disturbances. This method was found to provide insufficient species resolution to link FDA consumer complaint samples to a single species of pine, particularly when samples contained species mixtures of pine nuts. Here we describe a DNA based method for differentiating pine nut samples using the ycf1 chloroplast gene. Although the exact cause of pine nut associated dysgeusia is still not known, we found that 15 of 15 samples from consumer complaints contained at least some Pinus armandii, confirming the apparent association of this species with taste disturbances.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, Maryland 20740, United States.
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30
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Deeds JR, Handy SM, White KD, Reimer JD. Palytoxin found in Palythoa sp. zoanthids (Anthozoa, Hexacorallia) sold in the home aquarium trade. PLoS One 2011; 6:e18235. [PMID: 21483745 PMCID: PMC3070722 DOI: 10.1371/journal.pone.0018235] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 02/23/2011] [Indexed: 11/19/2022] Open
Abstract
Zoanthids (Anthozoa, Hexacorallia) are colonial anemones that contain one of the deadliest toxins ever discovered, palytoxin (LD(50) in mice 300 ng/kg), but it is generally believed that highly toxic species are not sold in the home aquarium trade. We previously showed that an unintentionally introduced zoanthid in a home aquarium contained high concentrations of palytoxin and was likely responsible for a severe respiratory reaction when an individual attempted to eliminate the contaminant colonies using boiling water. To assess the availability and potential exposure of palytoxin to marine aquarium hobbyists, we analyzed zoanthid samples collected from local aquarium stores for palytoxin using liquid chromatography and high resolution mass spectrometry and attempted to identify the specimens through genetic analysis of 16S and cytochrome c oxidase 1 (COI) markers. We found four specimens of the same apparent species of zoanthid, that we described previously to be responsible for a severe respiratory reaction in a home aquarium, to be available in three aquarium stores in the Washington D.C. area. We found all of these specimens (n = 4) to be highly toxic with palytoxin or palytoxin-like compounds (range 0.5-3.5 mg crude toxin/g zoanthid). One of the most potent non-protein compounds ever discovered is present in dangerous quantities in a select species of zoanthid commonly sold in the home aquarium trade.
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Affiliation(s)
- Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, United States of America.
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31
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Rasmussen Hellberg RS, Naaum AM, Handy SM, Hanner RH, Deeds JR, Yancy HF, Morrissey MT. Interlaboratory evaluation of a real-time multiplex polymerase chain reaction method for identification of salmon and trout species in commercial products. J Agric Food Chem 2011; 59:876-884. [PMID: 21214178 DOI: 10.1021/jf103241y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This interlaboratory study evaluated a real-time multiplex polymerase chain reaction (PCR) method for identification of salmon and trout species in a range of commercial products in North America. Eighty salmon and trout products were tested with this method by three independent laboratories. Samples were collected in the United States and Canada, and only the collecting institution was aware of the species declaration. Following analysis with real-time PCR, all three laboratories were able to identify species in 79 of the 80 products, with 100% agreement on species assignment. A low level of fraud was detected, with only four products (5%) found to be substituted or mixtures of two species. The results for two of the fraudulent products were confirmed with alternate methods, but the other two products were heavily processed and could not be verified with methods other than real-time PCR. Overall, the results of this study show the usefulness and versatility of this real-time PCR method for the identification of commercial salmon and trout species.
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32
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Handy SM, Deeds JR, Ivanova NV, Hebert PDN, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF. A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 2011; 94:201-210. [PMID: 21391497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5' end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.
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Affiliation(s)
- Sara M Handy
- U.S. Food and Drug Administration, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA.
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Abstract
Dinoflagellates have unique nuclei and intriguing genome characteristics with very high DNA content making complete genome sequencing difficult. In dinoflagellates, many genes are found in multicopy gene families, but the processes involved in the establishment and maintenance of these gene families are poorly understood. Understanding the dynamics of gene family evolution in dinoflagellates requires comparisons at different evolutionary scales. Studies of closely related species provide fine-scale information relative to species divergence, whereas comparisons of more distantly related species provides broad context. We selected the actin gene family as a highly expressed conserved gene previously studied in dinoflagellates. Of the 142 sequences determined in this study, 103 were from the two closely related species, Dinophysis acuminata and D. caudata, including full length and partial cDNA sequences as well as partial genomic amplicons. For these two Dinophysis species, at least three types of sequences could be identified. Most copies (79%) were relatively similar and in nucleotide trees, the sequences formed two bushy clades corresponding to the two species. In comparisons within species, only eight to ten nucleotide differences were found between these copies. The two remaining types formed clades containing sequences from both species. One type included the most similar sequences in between-species comparisons with as few as 12 nucleotide differences between species. The second type included the most divergent sequences in comparisons between and within species with up to 93 nucleotide differences between sequences. In all the sequences, most variation occurred in synonymous sites or the 5' UnTranslated Region (UTR), although there was still limited amino acid variation between most sequences. Several potential pseudogenes were found (approximately 10% of all sequences depending on species) with incomplete open reading frames due to frameshifts or early stop codons. Overall, variation in the actin gene family fits best with the "birth and death" model of evolution based on recent duplications, pseudogenes, and incomplete lineage sorting. Divergence between species was similar to variation within species, so that actin may be too conserved to be useful for phylogenetic estimation of closely related species.
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Affiliation(s)
- Sunju Kim
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
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Handy SM, Bachvaroff TR, Timme RE, Wayne Coats D, Kim S, Delwiche CF. PHYLOGENY OF FOUR DINOPHYSIACEAN GENERA (DINOPHYCEAE, DINOPHYSIALES) BASED ON rDNA SEQUENCES FROM SINGLE CELLS AND ENVIRONMENTAL SAMPLES(1). J Phycol 2009; 45:1163-1174. [PMID: 27032361 DOI: 10.1111/j.1529-8817.2009.00738.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dinoflagellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. We examined the phylogeny of several dinophysiacean dinoflagellates using samples collected from four Atlantic sites. As a rule, 3.5 kb of sequence including the nuclear ribosomal genes SSU, 5.8S, LSU, plus their internal transcribed spacer (ITS) 1 and 2 regions were determined for 26 individuals, including representatives of two genera for which molecular data were previously unavailable, Ornithocercus F. Stein and Histioneis F. Stein. In addition, a clone library targeting the dinophysiacean ITS2 and LSU sequences was constructed from bulk environmental DNA from three sites. Three phylogenetic trees were inferred from the data, one using data from this study for cells identified to genus or species (3.5 kb, 28 taxa); another containing dinoflagellate SSU submissions from GenBank and the 12 new dinophysiacean sequences (1.9 kb, 56 taxa) from this study; and the third tree combing data from identified taxa, dinophysiacean GenBank submissions, and the clone libraries from this study (2.1 kb, 136 taxa). All trees were congruent and indicated a distinct division between the genera Phalacroma F. Stein and Dinophysis Ehrenb. The cyanobionts containing genera Histioneis and Ornithocercus were also monophyletic. This was the largest molecular phylogeny of dinophysoid taxa performed to date and was consistent with the view that the genus Phalacroma may not be synonymous with Dinophysis.
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Affiliation(s)
- Sara M Handy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
| | - Tsvetan R Bachvaroff
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
| | - Ruth E Timme
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
| | - D Wayne Coats
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
| | - Sunju Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USASmithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland 21037, USADepartment of Cell Biology and Molecular Genetics and the Maryland Agricultural Experiment Station, University of Maryland, College Park, Maryland 20742, USA
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Hoppenrath M, Bachvaroff TR, Handy SM, Delwiche CF, Leander BS. Molecular phylogeny of ocelloid-bearing dinoflagellates (Warnowiaceae) as inferred from SSU and LSU rDNA sequences. BMC Evol Biol 2009; 9:116. [PMID: 19467154 PMCID: PMC2694157 DOI: 10.1186/1471-2148-9-116] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 05/25/2009] [Indexed: 11/23/2022] Open
Abstract
Background Dinoflagellates represent a major lineage of unicellular eukaryotes with unparalleled diversity and complexity in morphological features. The monophyly of dinoflagellates has been convincingly demonstrated, but the interrelationships among dinoflagellate lineages still remain largely unresolved. Warnowiid dinoflagellates are among the most remarkable eukaryotes known because of their possession of highly elaborate ultrastructural systems: pistons, nematocysts, and ocelloids. Complex organelles like these are evolutionary innovations found only in a few athecate dinoflagellates. Moreover, the taxonomy of warnowiids is extremely confusing and inferences about the evolutionary history of this lineage are mired by the absence of molecular phylogenetic data from any member of the group. In this study, we provide the first molecular phylogenetic data for warnowiids and couple them with a review of warnowiid morphological features in order to formulate a hypothetical framework for understanding character evolution within the group. These data also enabled us to evaluate the evolutionary relationship(s) between warnowiids and the other group of dinoflagellates with complex organelles: polykrikoids. Results Molecular phylogenetic analyses of SSU and LSU rDNA sequences demonstrated that warnowiids form a well-supported clade that falls within the more inclusive Gymnodinium sensu stricto clade. These data also confirmed that polykrikoids are members of the Gymnodinium sensu stricto clade as well; however, a specific sister relationship between the warnowiid clade and the polykrikoid clade was unresolved in all of our analyses. Nonetheless, the new DNA sequences from different isolates of warnowiids provided organismal anchors for several previously unidentified sequences derived from environmental DNA surveys of marine biodiversity. Conclusion Comparative morphological data and molecular phylogenetic data demonstrate that the polykrikoid and the warnowiid clade are closely related to each other, but the precise branching order within the Gymnodinium sensu stricto clade remains unresolved. We regard the ocelloid as the best synapomorphy for warnowiids and infer that the most recent common ancestor of polykrikoids and warnowiids possessed both nematocysts and photosynthetic plastids that were subsequently lost during the early evolution of warnowiids. Our summary of species and genus concepts in warnowiids demonstrate that the systematics of this poorly understood group is highly problematic and a comprehensive revision is needed.
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Affiliation(s)
- Mona Hoppenrath
- Departments of Botany and Zoology, University of British Columbia, Vancouver, Canada.
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Demir E, Coyne KJ, Doblin MA, Handy SM, Hutchins DA. Assessment of microzooplankton grazing on Heterosigma akashiwo using a species-specific approach combining quantitative real-time PCR (QPCR) and dilution methods. Microb Ecol 2008; 55:583-94. [PMID: 17609846 DOI: 10.1007/s00248-007-9263-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 04/17/2007] [Indexed: 05/16/2023]
Abstract
Delaware's Inland Bays (DIB) are subject to numerous mixed blooms of harmful raphidophytes each year, and Heterosigma akashiwo is one of the consistently occurring species. Often, Chattonella subsalsa, C. cf. verruculosa, and Fibrocapsa japonica co-occur with H. akashiwo, indicating a dynamic consortium of raphidophyte species. In this study, microzooplankton grazing pressure was assessed as a top-down control mechanism on H. akashiwo populations in mixed communities. Quantitative real-time polymerase chain reaction (QPCR) with species-specific primers and probes were used in conjunction with the dilution method to assess grazing pressure on H. akashiwo and other raphidophytes. As a comparison, we measured changes in chlorophyll a (chl a) to determine whole community growth and mortality caused by grazing. We detected grazing on H akashiwo using QPCR in samples where chl a analyses indicated little or no grazing on the total phytoplankton community. Overall, specific microzooplankton grazing pressure on H akashiwo ranged from 0.88 to 1.88 day(-1) at various sites. Experiments conducted on larger sympatric raphidophytes (C. subsalsa, C. cf. verruculosa and F japonica) demonstrated no significant microzooplankton grazing on these species. Grazing pressure on H akashiwo may provide a competitive advantage to other raphidophytes such as Chattonella spp. that are too large to be consumed at high rates by microzooplankton and help to shape the dynamics of this harmful algal bloom consortium. Our results show that QPCR can be used in conjunction with the dilution method for evaluation of microzooplankton grazing pressure on specific phytoplankton species within a mixed community.
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Affiliation(s)
- Elif Demir
- College of Marine and Earth Studies, University of Delaware, Lewes, DE 19958, USA
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Ouellette AJA, Handy SM, Wilhelm SW. Toxic Microcystis is widespread in Lake Erie: PCR detection of toxin genes and molecular characterization of associated cyanobacterial communities. Microb Ecol 2006; 51:154-65. [PMID: 16435169 DOI: 10.1007/s00248-004-0146-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2004] [Accepted: 01/01/2005] [Indexed: 05/06/2023]
Abstract
During the past decade, algae blooms, which include the toxic cyanobacterium Microcystis, have reoccurred in the Laurentian Great Lakes, most commonly in the western basin of Lake Erie. Whereas the western basin is the most impacted by toxic Microcystis in Lake Erie, there has historically been little effort focused on identifying the spatial distribution of Microcystis throughout this lake. To address this lack of knowledge, we have employed a polymerase-chain-reaction-based detection of genes required for synthesis of the toxin microcystin (mcyD and mcyB), as well as 16S rDNA fragments specific to either all Microcystis or all cyanobacteria. Using a multiplex approach, we tested 21 samples from 13 field stations and found that toxigenic Microcystis were present in the western and eastern basins in the summers of 1999, 2000, and 2002 and the central basin in 1999 and 2002. This is the most extensive distribution of Microcystis reported in Lake Erie. Clone libraries (16S rDNA) of these cyanobacterial communities were generated from 7 of the 13 field stations (representing all three basins) to partially characterize this microbial community. These libraries were shown to be dominated by sequences assigned to the Synechococcus and Cyanobium phylogenetic cluster, indicating the importance of picoplankton in this large lake system.
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