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Stracke K, Adisakwattana P, Phuanukoonnon S, Yoonuan T, Poodeepiyasawat A, Dekumyoy P, Chaisiri K, Roth Schulze A, Wilcox S, Karunajeewa H, Traub RJ, Jex AR. Effective low-cost preservation of human stools in field-based studies for helminth and microbiota analysis. Int J Parasitol 2021; 51:741-748. [PMID: 33774039 DOI: 10.1016/j.ijpara.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/16/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022]
Abstract
Molecular studies of gastrointestinal infections or microbiotas require either rapid sample processing or effective interim preservation. This is difficult in remote settings in low-income countries, where the majority of the global infectious disease burden exists. Processing or freezing of samples immediately upon collection is often not feasible and the cost of commercial preservatives is prohibitive. We compared fresh freezing (the 'gold standard' method), with low-cost chemical preservation in (i) a salt-based buffer consisting of DMSO, EDTA and NaCl (DESS) or (ii) 2.5% potassium dichromate (PD), for soil-transmitted helminth detection and microbiota characterisation in pre-school and school-aged children from north-western Thailand. Fresh frozen samples were frozen at -20°C on collection and maintained at -80°C within ~3 days of collection until molecular analysis, with international shipping on dry ice. In contrast, chemically preserved samples were collected and stored at ~4°C, transported on wet ice and only stored at -20°C on arrival in Australia ~8 weeks after collection, with international shipping on wet ice. DESS and PD provided better sensitivity for STH diagnosis, estimating higher infection rates (>80% for Ascaris lumbricoides and >60% for Trichuris trichiura; versus 56% and 15% for these parasites in fresh frozen samples) and egg abundance (inferred as gene copy number estimates). All methods performed similarly for microbiota preservation, showing no significant differences in alpha-diversity based on overall richness or inverted Simpson's Index. All three methods performed similarly for RNA and protein preservation in a small subset of samples. Overall, DESS provided the best performance, with the added benefit of being non-toxic, compared with PD, hence making it particularly applicable for studies in remote and resource-poor settings.
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Affiliation(s)
- Katharina Stracke
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medical Biology, The Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Poom Adisakwattana
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Suparat Phuanukoonnon
- Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippayarat Yoonuan
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Akkarin Poodeepiyasawat
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paron Dekumyoy
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Harin Karunajeewa
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medicine - Western Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca J Traub
- Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron R Jex
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
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