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A Small Study on Clostridioides difficile in Spinach Field Soil and the Chemical and Microbial Factors that may Influence Prevalence

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Abstract

Clostridioides difficile is a human pathogen that is ubiquitous in soil. Despite increasing infection rates and evidence of foodborne transmission, there is limited data on prevalence in soil or which factors influence persistence. The aim of this study was to investigate the prevalence of these bacteria in soil from three different spinach fields and to examine the chemical composition (carbon, organic carbon, nitrogen, organic matter, minerals and pH) and microbiota to gain insight into the factors that may promote/inhibit C. difficile. The overall C. difficile prevalence (10%) was lower than expected (based on international studies) and a significantly (P < 0.05) higher prevalence was obtained in Field 3 (20%) as compared to Fields 1 and 2 (5% each). Analysis of the soil suggested that the pH as well as organic matter, calcium and phosphorus content directly and indirectly (via the microbiota) influenced the prevalence of C. difficile in adjacent fields, where other factors (eg. climate) are similar. Although further studies are required to validate our findings, the data provides the first step in developing potential soil based control strategies.

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Data Availability

Nucleotide sequence data reported are available in the GenBank database under the accession number PRJNA892487 and PRJNA884639.

References

  1. Symochko L, Bugyna L, Hafiiyak O (2021) Ecological aspects of biosecurity in modern agroecosystems. Int J Ecosyst Ecol Sci 11(1):181–186

    Article  Google Scholar 

  2. Fajardo C, Costa G, Nande M, Botías P, García-Cantalejo J, Martín M (2019) Pb, Cd, and Zn soil contamination: monitoring functional and structural impacts on the microbiome. Appl Soil Ecol 135:56–64

    Article  Google Scholar 

  3. Islam W, Noman A, Naveed H, Huang Z, Chen HYH (2020) Role of environmental factors in shaping the soil microbiome. Environ Sci Pollut Res 27(33):41225–41247

    Article  CAS  Google Scholar 

  4. Cao H, Chen R, Wang L, Jiang L, Yang F, Zheng S, Wang G, Lin X (2016) Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale. Sci Rep 6:25815

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ge Y, He JZ, Zhu YG, Zhang JB, Xu Z, Zhang LM, Zheng YM (2008) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2(3):254–264

    Article  CAS  PubMed  Google Scholar 

  6. Hemingway JD, Rothman DH, Grant KE, Rosengard SZ, Eglinton TI, Derry LA, Galy V (2019) Mineral protection regulates long-term global preservation of natural organic carbon. Nature 570(7760):228–231

    Article  CAS  Google Scholar 

  7. Fierer N (2017) Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579–590

    Article  CAS  PubMed  Google Scholar 

  8. Hu HW, Zhang LM, Dai Y, Di HJ, He JZ (2013) pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soils Sediments 13:1439–1449

    Article  Google Scholar 

  9. Russo SE, Legge R, Weber KA, Brodie EL, Goldfarb KC, Benson AK, Tan S (2012) Bacterial community structure of contrasting soils underlying Bornean rain forests: inferences from microarray and next-generation sequencing methods. Soil Biol Biochem 55:48–59

    Article  CAS  Google Scholar 

  10. Ulrich A, Becker R (2006) Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol 56:430–443

    Article  CAS  PubMed  Google Scholar 

  11. Pett-Ridge J, Firestone MK (2005) Redox fluctuation structures microbial communities in a wet tropical soil. Appl Environ Microbiol 71:6998–7007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Leschine SB (1995) Cellulose degradation in anaerobic environments. Annu Rev Microbiol 49:399–426

    Article  CAS  PubMed  Google Scholar 

  13. Kim J, Lee D, Lee K, Choi C, Kang K (2004) Distribution and antimicrobial susceptibility of Clostridium species in soil contaminated with domestic livestock feces of Korea. J Microbiol Biotechnol 14:401–410

    CAS  Google Scholar 

  14. Shivaperumal N, Chang BJ, Riley TV (2020) High prevalence of Clostridium difficile in home gardens in Western Australia. Appl Environ Microbiol J 87(1):e01572-e1620

    Article  Google Scholar 

  15. Warriner K, Xu C, Habash M, Sultan S, Weese SJ (2016) Dissemination of Clostridium difficile in food and the environment: significant sources of C. difficile community acquired infection? J Appl Microbiol 122:542–555

    Article  PubMed  Google Scholar 

  16. Tkalec V, Janezica S, Skoka B, Simonica T, Mesarica S, Vrabica T, Rupnik M (2019) High Clostridium difficile contamination rates of domestic and imported potatoes compared to some other vegetables in Slovenia. Food Microbiol 78:194–200

    Article  PubMed  Google Scholar 

  17. Marcos P, Whyte P, Rogers T, McElroy M, Fanning S, Frias J, Bolton D (2021) The prevalence of Clostridioides difficile on farms, in abattoirs and in retail foods in Ireland. Food Microbiol 98:103781

    Article  CAS  PubMed  Google Scholar 

  18. Rodriguez C, Bouchafa L, Soumillion K, Ngyuvula E, Taminiau B, Van Broeck J, Delmée M, Daube G (2019) Seasonality of Clostridium difficile in the natural environment. Transbound Emerg Dis 66(6):2440–2449

    Article  CAS  PubMed  Google Scholar 

  19. Simango C, Mwakurudza S (2008) Clostridium difficile in broiler chickens sold at market places in Zimbabwe and their antimicrobial susceptibility. Int J Food Microbiol 124:268–270

    Article  CAS  PubMed  Google Scholar 

  20. Al Saif N, Brazier JS (1996) The distribution of Clostridium difficile in the environment of South Wales. J Med Microbiol 45:133–137

    Article  CAS  PubMed  Google Scholar 

  21. Båverud V, Gustafsson A, Franklin A, Aspán A, Gunnarsson A (2010) Clostridium difficile: prevalence in horses and environment, and antimicrobial susceptibility. Equine Vet J 35:465–471

    Article  Google Scholar 

  22. Higazi TB, Al-Saghir M, Burkett M, Pusok R (2011) PCR detection of Clostridium difficile and its toxigenic strains in public places in Southeast Ohio. Int J Microbiol Res 2:105–111

    Google Scholar 

  23. Girardin H, Morris CE, Albagnac C, Dreux N, Glaux C, Nguyen-The C (2005) Behaviour of the pathogen surrogates Listeria innocua and Clostridium sporogenes during production of parsley in fields fertilized with contaminated amendments. FEMS Microbiol Ecol 54(2):287–295

    Article  CAS  PubMed  Google Scholar 

  24. Primavilla S, Farneti S, Petruzzelli A, Drigo I, Scuota S (2019) Contamination of hospital food with Clostridium difficile in Central Italy. Anaerobe 55:8–10

    Article  PubMed  Google Scholar 

  25. Lim SC, Foster NF, Elliott B, Riley TV (2018) High prevalence of Clostridium difficile on retail root vegetables, Western Australia. J Appl Microbiol 124:585–590

    Article  CAS  PubMed  Google Scholar 

  26. Le Maréchal C, Druilhe C, Repérant E, Boscher E, Rouxel S, Le Roux S, Poëzévara T, Ziebal C, Houdayer C, Nagard B, Barbut F, Pourcher AM, Denis M (2019) Evaluation of the occurrence of sporulating and nonsporulating pathogenic bacteria in manure and in digestate of five agricultural biogas plants. Microbiol Open 8:1–10

    Article  Google Scholar 

  27. Hampikyan H, Bingol EB, Muratoglu K, Akkaya E, Cetin O, Colak H (2018) The prevalence of Clostridium difficile in cattle and sheep carcasses and the antibiotic susceptibility of isolates. Meat Sci 139:120–124

    Article  CAS  PubMed  Google Scholar 

  28. Marcos P, Whyte P, Burgess C, Ekhlas D, Bolton D (2022) Detection and genomic characterisation of Clostridioides difficile from spinach fields. Pathogens 11(11):1310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670–679

    Article  CAS  PubMed  Google Scholar 

  30. Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011:2957–2963

    Article  Google Scholar 

  31. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10(1):57–59

    Article  CAS  PubMed  Google Scholar 

  32. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21(3):494–504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  36. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596

    Article  CAS  PubMed  Google Scholar 

  37. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Usui M, Kawakura M, Yoshizawa N, San LL, Nakajima C, Suzuki Y, Tamura Y (2017) Survival and prevalence of Clostridium difficile in manure compost derived from pigs. Anaerobe 43:15–20

    Article  PubMed  Google Scholar 

  39. Knight DR, Riley TV (2013) Prevalence of gastrointestinal Clostridium difficile carriage in Australian sheep and lambs. Appl Environ Microbiol 79(18):5689–5692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wetzel D, McBride SM (2020) The impact of pH on Clostridioides difficile sporulation and physiology. Appl Environ Microbiol 86(4):e02706-e2719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Fredua-Agyeman M, Stapleton P, Basit AW, Beezer AE, Gaisford S (2017) In vitro inhibition of Clostridium difficile by commercial probiotics: a microcalorimetric study. Int J Pharm 517(1–2):96–103

    Article  CAS  PubMed  Google Scholar 

  42. Wheeldon LJ, Worthington T, Hilton AC, Elliott TS, Lambert PA (2008) Physical and chemical factors influencing the germination of Clostridium difficile spores. J Appl Microbiol 105(6):2223–2230

    Article  CAS  PubMed  Google Scholar 

  43. University of Massachusetts Amherst (UMA) (2013) Soil basics part II: chemical properties of soil. https://ag.umass.edu/vegetable/fact-sheets/soil-basics-part-ii-chemical-properties-of-soil Accessed 05 Oct 2022

  44. Andersson S, Nilsson SI, Saetre P (2000) Leaching of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) in mor humus as affected by temperature and pH. Soil Biol Biochem 1(32):1–10

    Article  Google Scholar 

  45. Curtin D, Peterson ME, Anderson CR (2016) pH-dependence of organic matter solubility: base type effects on dissolved organic C, N, P, and S in soils with contrasting mineralogy. Geoderma 271:161–172

    Article  CAS  Google Scholar 

  46. Mathew RP, Feng Y, Githinji L, Ankumah R, Balkcom KS (2012) Impact of no-tillage and conventional tillage systems on soil microbial communities. Appl Environ Soil Sci 2021:548620

    Google Scholar 

  47. Neina D (2019) The role of soil pH in plant nutrition and soil remediation. Appl Environ Soil Sci 2019:1–10

    Article  Google Scholar 

  48. Smith CR, Blair PL, Boyd C, Cody B, Hazel A, Hedrick A, Kathuria H, Khurana P, Kramer B, Muterspaw K, Peck C, Sells E, Skinner J, Tegeler C, Wolfe Z (2016) Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem. Ecol Evol 6(22):8075–8084

    Article  PubMed  PubMed Central  Google Scholar 

  49. Nale JY, Redgwell TA, Millard A, Clokie MRJ (2018) Efficacy of an optimised bacteriophage cocktail to clear Clostridium difficile in a batch fermentation model. Antibiotics (Basel) 7(1):13

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors thank Linda Moloney Finn, Patricia Berry, Carmel O’Connor, Brendan Healy and Felipe Bachion de Santana for their work on the soil characterisation.

Funding

This project was funded by the Food Institutional Research Measure (FIRM) administered by the Department for Agriculture, Food and the Marine (DAFM) (Grant number 17F206). Pilar Marcos was supported by the Teagasc Walsh Scholarship Scheme (number 2018210).

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Authors and Affiliations

  1. Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland

    Pilar Marcos, Catherine Burgess & Declan Bolton

  2. School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland

    Pilar Marcos & Paul Whyte

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Contributions

PM was involved in the conceptualization, experimental design, investigation, formal analysis, writing the original draft as well as review & editing. PW and CB contributed to the methodology, supervision and writing (review & editing). DB was responsible for the conceptualization, funding acquisition, experimental design, methodology, project administration, supervision and writing including review &editing.

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Correspondence to Declan Bolton.

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Marcos, P., Whyte, P., Burgess, C. et al. A Small Study on Clostridioides difficile in Spinach Field Soil and the Chemical and Microbial Factors that may Influence Prevalence. Curr Microbiol 80, 236 (2023). https://doi.org/10.1007/s00284-023-03328-7

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