Molecular Detection of in Two Main Types of Farm Soil Using Real-Time PCR Assays and Method Modification for Commercial Potting Mix

Overview

Journal Microorganisms

Specialty Microbiology

Date 2023 Jun 28

PMID 37375008

Authors

Joseph Arida

Alicia Shipley

Sonia Almeria

Affiliations

Soon will be listed here.

Abstract

is a foodborne protozoan parasite that causes outbreaks of diarrheal illness (cyclosporiasis) with clear seasonality worldwide. In the environment, oocysts are very robust, and contact with contaminated soil may serve as an important vehicle in the transmission of this organism, and it is considered a risk factor for this infection. The present study evaluated a flotation concentration method, previously shown to provide the best detection results when compared with DNA isolation directly from soil samples, in two main types of farm soil, silt loam soil and sandy clay loam, as well as in commercial potting mix samples inoculated with different numbers of oocysts. The flotation method was able to detect as few as 10 oocysts in 10 g of either type of farm soil without modifications, but needed an extra wash and samples of reduced size for the processing of the commercial potting mix to be able to detect 20 oocysts/5 g. A recently modified real-time PCR method for the detection of based on a mitochondrial gene target was also evaluated using selected samples of each type of soil. This comparative study confirmed that the concentration of oocysts in soil samples by flotation in high-density sucrose solutions is a sensitive method that can detect low numbers of oocysts in different types of soil.

Citing Articles

: A Perspective (2020-2023) with Emphasis on Epidemiology and Detection Methods.

Almeria S, Chacin-Bonilla L, Maloney J, Santin M Microorganisms. 2023; 11(9).

PMID: 37764015 PMC: 10536660. DOI: 10.3390/microorganisms11092171.

References

Sathyanarayanan L, Ortega Y . Effects of temperature and different food matrices on Cyclospora cayetanensis oocyst sporulation. J Parasitol. 2006; 92(2):218-22. DOI: 10.1645/GE-630R.1. View

Almeria S, da Silva A, Blessington T, Cloyd T, Cinar H, Durigan M . Evaluation of the U.S. Food and Drug Administration validated method for detection of Cyclospora cayetanensis in high-risk fresh produce matrices and a method modification for a prepared dish. Food Microbiol. 2018; 76:497-503. DOI: 10.1016/j.fm.2018.07.013. View

Almeria S, Cinar H, Dubey J . and Cyclosporiasis: An Update. Microorganisms. 2019; 7(9). PMC: 6780905. DOI: 10.3390/microorganisms7090317. View

Sidstedt M, Jansson L, Nilsson E, Noppa L, Forsman M, Radstrom P . Humic substances cause fluorescence inhibition in real-time polymerase chain reaction. Anal Biochem. 2015; 487:30-7. DOI: 10.1016/j.ab.2015.07.002. View

Resendiz-Nava C, Orozco-Mosqueda G, Mercado-Silva E, Flores-Robles S, Silva-Rojas H, Nava G . A Molecular Tool for Rapid Detection and Traceability of in Fresh Berries and Berry Farm Soils. Foods. 2020; 9(3). PMC: 7142967. DOI: 10.3390/foods9030261. View

Chacin-Bonilla L, Sanchez Y, Cardenas R . Factors associated with Cyclospora infection in a Venezuelan community: extreme poverty and soil transmission relate to cyclosporiasis. Trans R Soc Trop Med Hyg. 2022; 117(2):83-90. DOI: 10.1093/trstmh/trac070. View

Chacin-Bonilla L . Transmission of Cyclospora cayetanensis infection: a review focusing on soil-borne cyclosporiasis. Trans R Soc Trop Med Hyg. 2007; 102(3):215-6. DOI: 10.1016/j.trstmh.2007.06.005. View

Escotte-Binet S, Malik Da Silva A, Cances B, Aubert D, Dubey J, La Carbona S . A rapid and sensitive method to detect Toxoplasma gondii oocysts in soil samples. Vet Parasitol. 2019; 274:108904. DOI: 10.1016/j.vetpar.2019.07.012. View

Murphy H, Lee S, da Silva A . Evaluation of an Improved U.S. Food and Drug Administration Method for the Detection of Cyclospora cayetanensis in Produce Using Real-Time PCR. J Food Prot. 2017; 80(7):1133-1144. DOI: 10.4315/0362-028X.JFP-16-492. View

10.

Ortega Y, Sanchez R . Update on Cyclospora cayetanensis, a food-borne and waterborne parasite. Clin Microbiol Rev. 2010; 23(1):218-34. PMC: 2806662. DOI: 10.1128/CMR.00026-09. View

11.

Totton S, OConnor A, Naganathan T, Martinez B, Vriezen E, Torrence M . A scoping review of the detection, epidemiology and control of with an emphasis on produce, water and soil. Epidemiol Infect. 2021; 149:e49. PMC: 8060822. DOI: 10.1017/S0950268821000200. View

12.

Sagar K, Singh S, Goutam K, Konwar B . Assessment of five soil DNA extraction methods and a rapid laboratory-developed method for quality soil DNA extraction for 16S rDNA-based amplification and library construction. J Microbiol Methods. 2013; 97:68-73. DOI: 10.1016/j.mimet.2013.11.008. View

13.

Assurian A, Murphy H, Shipley A, Cinar H, Da Silva A, Almeria S . Assessment of Commercial DNA Cleanup Kits for Elimination of Real-Time PCR Inhibitors in the Detection of Cyclospora cayetanensis in Cilantro. J Food Prot. 2020; 83(11):1863-1870. DOI: 10.4315/JFP-20-139. View

14.

Bern C, Arrowood M, Eberhard M, Maguire J . Cyclospora in Guatemala: further considerations. J Clin Microbiol. 2002; 40(2):731-2. PMC: 153422. DOI: 10.1128/JCM.40.2.731-732.2002. View

15.

Steinbaum L, Kwong L, Ercumen A, Negash M, Lovely A, Njenga S . Detecting and enumerating soil-transmitted helminth eggs in soil: New method development and results from field testing in Kenya and Bangladesh. PLoS Negl Trop Dis. 2017; 11(4):e0005522. PMC: 5393894. DOI: 10.1371/journal.pntd.0005522. View

16.

Shipley A, Arida J, Almeria S . Comparative Evaluation of an Easy Laboratory Method for the Concentration of Oocysts and Commercial DNA Isolation Kits for the Molecular Detection of in Silt Loam Soil Samples. Microorganisms. 2022; 10(7). PMC: 9322252. DOI: 10.3390/microorganisms10071431. View

17.

Giangaspero A, Marangi M, Koehler A, Papini R, Normanno G, Lacasella V . Molecular detection of Cyclospora in water, soil, vegetables and humans in southern Italy signals a need for improved monitoring by health authorities. Int J Food Microbiol. 2015; 211:95-100. DOI: 10.1016/j.ijfoodmicro.2015.07.002. View

18.

Nunes C, Sinhorini I, Ogassawara S . Influence of soil texture in the recovery of Toxocara canis eggs by a flotation method. Vet Parasitol. 1994; 53(3-4):269-74. DOI: 10.1016/0304-4017(94)90190-2. View

19.

Lelu M, Gilot-Fromont E, Aubert D, Richaume A, Afonso E, Dupuis E . Development of a sensitive method for Toxoplasma gondii oocyst extraction in soil. Vet Parasitol. 2011; 183(1-2):59-67. DOI: 10.1016/j.vetpar.2011.06.018. View

20.

Maganira J, Mwangonde B, Kidima W, Mwita C, Nkwengulila G, Hoglund J . Validation of droplet digital Polymerase Chain Reaction for the detection and absolute quantification of Taenia solium eggs in spiked soil samples. Acta Trop. 2019; 200:105175. DOI: 10.1016/j.actatropica.2019.105175. View